医学信息学实验报告

医学生物信息学实验报告


RCAS1(receptorbinding cancer antigen expressed on SiSo cells)是由Nakashima等于1999年发现的一种肿瘤相关抗原，在多种肿瘤组织都有表达，可被2211单克隆抗体识别，可能参与肿瘤的免疫逃避机制，与肿瘤的发生发展及预后有关。2211抗体是用人子宫腺癌细胞系SiSo细胞免疫的小鼠骨髓瘤细胞和脾细胞通过细胞融合方法获得的。本次信息学作业以次肿瘤相关性抗原为实习对象。

第一部分

查询RCAS1基因的相关信息
登陆NCBI主页
seach栏中选Nucleotide
for栏中键入RCAS1
（回车）
查询相关信息23条，
选取AY515724
点击进入顺序全貌
阅读信息：RCAS1属mRNA802个碱基，为完全cds表达，为一个开放的阅读柜。cds表达194..>802之间的碱基。


1: AY515724. Reports Homo sapiens rece...[gi:40965475] Links

FeaturesSequenceLOCUS AY515724 802 bp mRNA linear PRI 21-JAN-2004
DEFINITION Homo sapiens receptor-binding cancer antigen expressed on SiSo
cells (RCAS1) mRNA, partial cds.
ACCESSION AY515724
VERSION AY515724.1 GI:40965475
KEYWORDS .
SOURCE Homo sapiens (human)
ORGANISM Homo sapiens
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
REFERENCE 1 (bases 1 to 802)
AUTHORS Leelawat,K., Watanabe,T., Nakajima,M., Tujinda,S.,
Suthipintawong,C. and Leardkamolkarn,V.
TITLE Upregulation of tumour associated antigen RCAS1 is implicated in
high stages of colorectal cancer
JOURNAL J. Clin. Pathol. 56 (10), 764-768 (2003)
PUBMED 14514780
REFERENCE 2 (bases 1 to 802)
AUTHORS Leelawat,K., Engprasert,S. and Leardkamolkarn,V.
TITLE Direct Submission
JOURNAL Submitted (02-JAN-2004) Surgery, Rajavithi Hospital, Rajavithi Rd.,
Rajathevi, Bangkok 10400, Thailand
FEATURES Location/Qualifiers
source 1..802
/organism="Homo sapiens"
/mol_type="mRNA"
/db_xref="taxon:9606"
/tissue_type="colon carcinoma"
gene 1..>802
/gene="RCAS1"
CDS 194..>802
/gene="RCAS1"
/codon_start=1
/product="receptor-binding cancer antigen expressed on
SiSo cells"
/protein_id="AAR97974.1"
/db_xref="GI:40965476"
/translation="MAITQFRLFKFCTCLATVFSFLKRLICRSGRGRKLSGDQITLPT
TVDYSSVPKQTDVEEWTSWDEDAPTSVKIEGGNGNVATQQNSLEQLEPDYFKDMTPTI
RKTQKIVIKKREPLNFGIPDGSTGFSSRLAATQDLPFIHQSSELGDLDTWQENTNAWE

EEEDAAWQAEEVLRQQKLADREKRAAEQQRKKMEKEAQRLMKK"
ORIGIN
1 accttactgc cctccgtcta caggccttgt acctctccag gccgattttt ccacaattta
61 aatcccagtt cacctggtat ccagctccag caacttagag cgtttcacgt cacgccgggc
121 gccaggcgtc ggcttgtata acctgaaaac gctcctgttt ttctcatctg tgcagtgggt
181 tttgattccc accatggcca tcacccagtt tcggttattt aaattttgta cctgcctagc
241 aacagtattc tcattcctaa agagattaat atgcagatct ggcagaggac ggaaattaag
301 tggagaccaa ataactttgc caactacagt tgattattca tcagttccta agcagacaga
361 tgttgaagag tggacttcct gggatgaaga tgcacccacc agtgtaaaga tcgaaggagg
421 gaatgggaat gtggcaacac aacaaaattc tttggaacaa ctggaacctg actattttaa
481 ggacatgaca ccaactatta ggaaaactca gaaaattgtt attaagaaga gagaaccatt
541 gaattttggc atcccagatg ggagcacagg tttctctagt agattagcag ctacacaaga
601 tctgcctttt attcatcagt cttctgaatt aggtgactta gatacctggc aggaaaatac
661 caatgcatgg gaagaagaag aagatgcagc ctggcaagca gaagaagttc tgagacagca
721 gaaactagca gacagagaaa agagagcagc cgaacaacaa aggaagaaaa tggaaaagga
781 agcacaacgg ctaatgaaga ag

第二部分 设计引物。PCR扩张（cds区）
进入网站/
查询RCAS1 AY515724 的CDS序列
复制序列，键入primer方框内
选择引物大小 Min15 Max25
选择引物Tm Min40 Max60
选择引物GC% Min40 Max60
点击 Pick primers
得到结果
选择第一条，为可用扩增的CDS序列。
Using mispriming library rodent_ref.txt
Using 1-based sequence positions
OLIGO start len tm gc% any 3' rep seq
LEFT PRIMER 154 25 59.65 44.00 4.00 1.00 11.00 ctaagcagacagatgttgaagagtg
RIGHT PRIMER 402 29 59.60 41.38 7.00 1.00 10.00 gtgtagctgctaatctactagagaaacct
SEQUENCE SIZE: 608
INCLUDED REGION SIZE: 608

PRODUCT SIZE: 249, PAIR ANY COMPL: 5.00, PAIR 3' COMPL: 1.00

1 tggccatcacccagtttcggttatttaaattttgtacctgcctagcaacagtattctcat


61 tcctaaagagattaatatgcagatctggcagaggacggaaattaagtggagaccaaataa


121 ctttgccaactacagttgattattcatcagttcctaagcagacagatgttgaagagtgga
>>>>>>>>>>>>>>>>>>>>>>>>>

181 cttcctgggatgaagatgcacccaccagtgtaaagatcgaaggagggaatgggaatgtgg


241 caacacaacaaaattctttggaacaactggaacctgactattttaaggacatgacaccaa


301 ctattaggaaaactcagaaaattgttattaagaagagagaaccattgaattttggcatcc


361 cagatgggagcacaggtttctctagtagattagcagctacacaagatctgccttttattc
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

421 atcagtcttctgaattaggtgacttagatacctggcaggaaaataccaatgcatgggaag


481 aa

gaagaagatgcagcctggcaagcagaagaagttctgagacagcagaaactagcagaca


541 gagaaaagagagcagccgaacaacaaaggaagaaaatggaaaaggaagcacaacggctaa


601 tgaagaag


KEYS (in order of precedence):
>>>>>> left primer
<<<<<< right primer

ADDITIONAL OLIGOS
start len tm gc% any 3' rep seq

1 LEFT PRIMER 154 25 59.65 44.00 4.00 1.00 11.00 ctaagcagacagatgttgaagagtg
RIGHT PRIMER 400 29 59.60 41.38 7.00 2.00 11.00 gtagctgctaatctactagagaaacctgt
PRODUCT SIZE: 247, PAIR ANY COMPL: 5.00, PAIR 3' COMPL: 2.00

2 LEFT PRIMER 151 24 59.95 41.67 4.00 1.00 10.00 ttcctaagcagacagatgttgaag
RIGHT PRIMER 400 29 59.60 41.38 7.00 2.00 11.00 gtagctgctaatctactagagaaacctgt
PRODUCT SIZE: 250, PAIR ANY COMPL: 5.00, PAIR 3' COMPL: 3.00

3 LEFT PRIMER 153 24 59.60 45.83 4.00 2.00 10.00 cctaagcagacagatgttgaagag
RIGHT PRIMER 402 29 59.60 41.38 7.00 1.00 10.00 gtgtagctgctaatctactagagaaacct
PRODUCT SIZE: 250, PAIR ANY COMPL: 5.00, PAIR 3' COMPL: 2.00

4 LEFT PRIMER 153 24 59.60 45.83 4.00 2.00 10.00 cctaagcagacagatgttgaagag
RIGHT PRIMER 400 29 59.60 41.38 7.00 2.00 11.00 gtagctgctaatctactagagaaacctgt
PRODUCT SIZE: 248, PAIR ANY COMPL: 5.00, PAIR 3' COMPL: 3.00

Statistics
con too in in no tm tm high high high high
sid many tar excl bad GC too too any 3' lib poly end
ered Ns get reg GC% clamp low high compl compl sim X stab ok
Left 7299 0 0 0 3732 0 135 1884 0 12 0 0 59 1477
Right 7265 0 0 0 3152 0 161 2215 0 2 0 0 62 1673
Pair Stats:
considered 271, unacceptable product size 263, ok 8
primer3 release 1.1.0


(primer3_results.cgi 0.4.0 modified for WI)

第三部分 利用BLASTN定RCAS1 基因相关位置
进入BCBI主页 ，点击BLAST建
点击nucleotide blast（全基因组对比）
进入对比页
键入AY515724 点击BLAST
进入结果页面，阅读结果


gb|AY515724| (802 letters)
Results for:
gb|AY515724.1 Homo sapiens receptor-binding cancer antigen expressed on SiSo cells (RCAS1) mRNA, partial cds(802bp) What's this?
Your BLAST job specified more than one input sequence. This box lets you choose which input sequence to show BLAST results for.

Query ID gi|40965475|gb|AY515724.1|
Description Homo sapiens receptor-binding cancer antigen expressed on SiSo cells (RCAS1) mRNA, partial cds
Molecule type nucleic acid
Query Length 802 Database Name dbindex/9606/allcontig_and_rna
Description Human build 36.3 RNA, reference, and HuRef assemblies See details
Program BLASTN 2.2.19+ Citation

Database Descri

ption Posted Date

Reference
Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), "A greedy algorithm for aligning DNA sequences", J Comput Biol 2000; 7(1-2):203-14.
Reference - database indexing
Aleksandr Morgulis, George Coulouris, Yan Raytselis, Thomas L. Madden, Richa Agarwala, Alejandro A. Sch?ffer (2008), "Database Indexing for Production MegaBLAST Searches", Bioinformatics 24:1757-1764.
Other reports: Search Summary [Taxonomy reports] [Distance tree of results] [Human genome view]
Search Parameters
Program blastn
Word size 28
Expect value 10
Hitlist size 100
Match/Mismatch scores 1,-2
Gapcosts 0,0
Filter string F
Genetic Code 1
Database
Posted date Dec 2, 2008 11:49 AM
Number of letters 58,011,736
Number of sequences 49,942
Entrez query none
Karlin-Altschul statistics
Params Ungapped Gapped
Lambda 1.33271 1.28
K 0.620991 0.46
H 1.12409 0.85
Results Statistics
Length adjustment 31
Effective length of query 771
Effective length of database 5816463534
Effective search space 4484493384714
Effective search space used 4484493384714
Graphic Summary
Distribution of 14 Blast Hits on the Query Sequence [?]
An overview of the database sequences aligned to the query sequence is shown. The score of each alignment is indicated by one of five different colors, which divides the range of scores into five groups. Multiple alignments on the same database sequence are connected by a striped line. Mousing over a hit sequence causes the definition and score to be shown in the window at the top, clicking on a hit sequence takes the user to the associated alignments. New: This graphic is an overview of database sequences aligned to the query sequence. Alignments are color-coded by score, within one of five score ranges. Multiple alignments on the same database sequence are connected by a dashed line. Mousing over an alignment shows the alignment definition and score in the box at the top. Clicking an alignment displays the alignment detail.
--------------------------------------------------------------------------------
Descriptions
Legend for links to other resources: UniGene GEO Gene Structure Map Viewer
Sequences producing significant alignments:
(Click headers to sort columns)
Accession Description Max score Total score Query coverage E value Max ident Links Transcripts NM_004215.3 Homo sapiens estrogen receptor binding site associated, antigen, 9 (EBAG9), transcript variant 1, mRNA 1476 1476 100% 0.0 99% NM_198120.1 Homo sapiens estrogen receptor binding site associated, antigen, 9 (EBAG9), transcript variant 2, mRNA 1155 1155 77% 0.0 100% Genomic sequences [show first] NW_001839136.1 Homo sapiens chromosome 8 genomic contig, alternate assembly (based on HuRef SCAF_1103279188253) 333 1341 89% 2e-88 100% NT_008046.15 Homo sapiens chromosome 8 genomic contig, reference assembly 327 1336 89% 8e-87 100%

Alignments Select All Get selected sequences Distance tr

ee of results



>ref|NM_004215.3| Homo sapiens estrogen receptor binding site associated, antigen,
9 (EBAG9), transcript variant 1, mRNA
Length=1655

GENE ID: 9166 EBAG9 | estrogen receptor binding site associated, antigen, 9
[Homo sapiens] (Over 10 PubMed links)


Score = 1476 bits (799), Expect = 0.0
Identities = 801/802 (99%), Gaps = 0/802 (0%)
Strand=Plus/Plus

Query 1 ACCTTACTGCCCTCCGTCTACAGGCCTTGTACCTCTCCAGGCCGATTTTTCCACAATTTA 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 204 ACCTTACTGCCCTCCGTCTACAGGCCTTGTACCTCTCCAGGCCGATTTTTCCACAATTTA 263

Query 61 AATCCCAGTTCACCTGGTATCCAGCTCCAGCAACTTAGAGCGTTTCACGTCACGCCGGGC 120
|||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 264 AATCTCAGTTCACCTGGTATCCAGCTCCAGCAACTTAGAGCGTTTCACGTCACGCCGGGC 323

Query 121 GCCAGGCGTCGGCTTGTATAACCTGAAAACGCTCCTGTTTTTCTCATCTGTGCAGTGGGT 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 324 GCCAGGCGTCGGCTTGTATAACCTGAAAACGCTCCTGTTTTTCTCATCTGTGCAGTGGGT 383

Query 181 TTTGATTCCCACCATGGCCATCACCCAGTTTCGGTTATTTAAATTTTGTACCTGCCTAGC 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 384 TTTGATTCCCACCATGGCCATCACCCAGTTTCGGTTATTTAAATTTTGTACCTGCCTAGC 443

Query 241 AACAGTATTCTCATTCCTAAAGAGATTAATATGCAGATCTGGCAGAGGACGGAAATTAAG 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 444 AACAGTATTCTCATTCCTAAAGAGATTAATATGCAGATCTGGCAGAGGACGGAAATTAAG 503

Query 301 TGGAGACCAAATAACTTTGCCAACTACAGTTGATTATTCATCAGTTCCTAAGCAGACAGA 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 504 TGGAGACCAAATAACTTTGCCAACTACAGTTGATTATTCATCAGTTCCTAAGCAGACAGA 563

Query 361 TGTTGAAGAGTGGACTTCCTGGGATGAAGATGCACCCACCAGTGTAAAGATCGAAGGAGG 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 564 TGTTGAAGAGTGGACTTCCTGGGATGAAGATGCACCCACCAGTGTAAAGATCGAAGGAGG 623

Query 421 GAATGGGAATGTGGCAACACAACAAAATTCTTTGGAACAACTGGAACCTGACTATTTTAA 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 624 GAATGGGAATGTGGCAACACAACAAAATTCTTTGGAACAACTGGAACCTGACTATTTTAA 683

Query 481 GGACATGACACCAACTATTAGGAAAACTCAGAAAATTGTTATTAAGAAGAGAGAACCATT 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 684 GGACATGACACCAACTATTAGGAAAACTCAGAAAATTGTTATTAAGAAGAGAGAACCATT 743

Query 541 GAATTTTGGCATCCCAGATGGGAGCACAGGTTTCTCTAGTAGATTAGCAGCTACACAAGA 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 744 GAATTTTGGCATCCCAGATGGGAGCACAGGTTTCTCTAGTAGATTAGCAGCTACACAAGA 803

Query 601 TCTGCCTTTTATTCATCAGTCTTCTGAATTAGGTGACTTAGATACCTGGCAGGAAAATAC 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 804 TCTGCCTTTTATTCATCAGTCTTCTGAATTAGGTGACTTAGATACCTGGCAGGAAAATAC 86

3

Query 661 CAATGCATGGGAAGAAGAAGAAGATGCAGCCTGGCAAGCAGAAGAAGTTCTGAGACAGCA 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 864 CAATGCATGGGAAGAAGAAGAAGATGCAGCCTGGCAAGCAGAAGAAGTTCTGAGACAGCA 923

Query 721 GAAACTAGCAGACAGAGAAAAGAGAGCAGCCGAACAACAAAGGAAGAAAATGGAAAAGGA 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 924 GAAACTAGCAGACAGAGAAAAGAGAGCAGCCGAACAACAAAGGAAGAAAATGGAAAAGGA 983

Query 781 AGCACAACGGCTAATGAAGAAG 802
||||||||||||||||||||||
Sbjct 984 AGCACAACGGCTAATGAAGAAG 1005


>ref|NM_198120.1| Homo sapiens estrogen receptor binding site associated, antigen,
9 (EBAG9), transcript variant 2, mRNA
Length=1494

GENE ID: 9166 EBAG9 | estrogen receptor binding site associated, antigen, 9
[Homo sapiens] (Over 10 PubMed links)


Score = 1155 bits (625), Expect = 0.0
Identities = 625/625 (100%), Gaps = 0/625 (0%)
Strand=Plus/Plus

Query 178 GGTTTTGATTCCCACCATGGCCATCACCCAGTTTCGGTTATTTAAATTTTGTACCTGCCT 237
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 220 GGTTTTGATTCCCACCATGGCCATCACCCAGTTTCGGTTATTTAAATTTTGTACCTGCCT 279

Query 238 AGCAACAGTATTCTCATTCCTAAAGAGATTAATATGCAGATCTGGCAGAGGACGGAAATT 297
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 280 AGCAACAGTATTCTCATTCCTAAAGAGATTAATATGCAGATCTGGCAGAGGACGGAAATT 339

Query 298 AAGTGGAGACCAAATAACTTTGCCAACTACAGTTGATTATTCATCAGTTCCTAAGCAGAC 357
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 340 AAGTGGAGACCAAATAACTTTGCCAACTACAGTTGATTATTCATCAGTTCCTAAGCAGAC 399

Query 358 AGATGTTGAAGAGTGGACTTCCTGGGATGAAGATGCACCCACCAGTGTAAAGATCGAAGG 417
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 400 AGATGTTGAAGAGTGGACTTCCTGGGATGAAGATGCACCCACCAGTGTAAAGATCGAAGG 459

Query 418 AGGGAATGGGAATGTGGCAACACAACAAAATTCTTTGGAACAACTGGAACCTGACTATTT 477
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 460 AGGGAATGGGAATGTGGCAACACAACAAAATTCTTTGGAACAACTGGAACCTGACTATTT 519

Query 478 TAAGGACATGACACCAACTATTAGGAAAACTCAGAAAATTGTTATTAAGAAGAGAGAACC 537
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 520 TAAGGACATGACACCAACTATTAGGAAAACTCAGAAAATTGTTATTAAGAAGAGAGAACC 579

Query 538 ATTGAATTTTGGCATCCCAGATGGGAGCACAGGTTTCTCTAGTAGATTAGCAGCTACACA 597
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 580 ATTGAATTTTGGCATCCCAGATGGGAGCACAGGTTTCTCTAGTAGATTAGCAGCTACACA 639

Query 598 AGATCTGCCTTTTATTCATCAGTCTTCTGAATTAGGTGACTTAGATACCTGGCAGGAAAA 657
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 640 AGATCTGCCTTTTATTCATCAGTCTTCTGAATTAGGTGACTTAGATACCTGGCAGGAAAA 699

Query 658 TACCAATGCATGGGAAGAAGAAGAAGATGCAGCCTGGCAAGCAGAAGAAGTTCTGAGACA 717
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

Sbjct 700 TACCAATGCATGGGAAGAAGAAGAAGATGCAGCCTGGCAAGCAGAAGAAGTTCTGAGACA 759

Query 718 GCAGAAACTAGCAGACAGAGAAAAGAGAGCAGCCGAACAACAAAGGAAGAAAATGGAAAA 777
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 760 GCAGAAACTAGCAGACAGAGAAAAGAGAGCAGCCGAACAACAAAGGAAGAAAATGGAAAA 819

Query 778 GGAAGCACAACGGCTAATGAAGAAG 802
|||||||||||||||||||||||||
Sbjct 820 GGAAGCACAACGGCTAATGAAGAAG 844


>ref|NW_001839136.1|Hs8_WGA529_36 Homo sapiens chromosome 8 genomic contig, alternate assembly
(based on HuRef SCAF_1103279188253)
Length=44702525

Sort alignments for this subject sequence by:
E value Score Percent identity
Query start position Subject start position

Features flanking this part of subject sequence:
10201 bp at 5' side: fibrocystin L
10357 bp at 3' side: estrogen receptor binding site associated antigen 9


Score = 333 bits (180), Expect = 2e-88
Identities = 185/187 (98%), Gaps = 1/187 (0%)
Strand=Plus/Plus

Query 1 ACCTTACTGCCCTCCGTCTACAGGCCTTGTACCTCTCCAGGCCGATTTTTCCACAATTTA 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 23816021 ACCTTACTGCCCTCCGTCTACAGGCCTTGTACCTCTCCAGGCCGATTTTTCCACAATTTA 23816080

Query 61 AATCCCAGTTCACCTGGTATCCAGCTCCAGCAACTTAGAGCGTTTCACGTCACGCCGGGC 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 23816081 AATCCCAGTTCACCTGGTATCCAGCTCCAGCAACTTAGAGCGTTTCACGTCACGCCGGGC 23816140

Query 121 GCCAGGCGTCGGCTTGTATAACCTGAAAACGCTCCTGTTTTTCTCATCTGTGCAGTGGGT 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 23816141 GCCAGGCGTCGGCTTGTATAACCTGAAAACGCTCCTGTTTTTCTCATCTGTGCAGTGGGT 23816200

Query 181 TTTGATT 187
| ||||
Sbjct 23816201 AT-GATT 23816206


Features in this part of subject sequence:
estrogen receptor binding site associated antigen 9
estrogen receptor binding site associated antigen 9


Score = 300 bits (162), Expect = 2e-78
Identities = 167/169 (98%), Gaps = 1/169 (0%)
Strand=Plus/Plus

Query 354 AGACAGATGTTGAAGAGTGGACTTCCTGGGATGAAGATGCACCCACCAGTGTAAAGATCG 413
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 23830463 AGACAGATGTTGAAGAGTGGACTTCCTGGGATGAAGATGCACCCACCAGTGTAAAGATCG 23830522

Query 414 AAGGAGGGAATGGGAATGTGGCAACACAACAAAATTCTTTGGAACAACTGGAACCTGACT 473
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 23830523 AAGGAGGGAATGGGAATGTGGCAACACAACAAAATTCTTTGGAACAACTGGAACCTGACT 23830582

Query 474 ATTTTAAGGACATGACACCAACTATTAGGAAAACTCAGAAAAT-TGTTA 521
||||||||||||||||||||||||||||||||||||||||| | |||||
Sbjct 23830583 ATTTTAAGGACATG

ACACCAACTATTAGGAAAACTCAGAAAGTATGTTA 23830631


Features in this part of subject sequence:
estrogen receptor binding site associated antigen 9
estrogen receptor binding site associated antigen 9


Score = 200 bits (108), Expect = 2e-48
Identities = 108/108 (100%), Gaps = 0/108 (0%)
Strand=Plus/Plus

Query 515 ATTGTTATTAAGAAGAGAGAACCATTGAATTTTGGCATCCCAGATGGGAGCACAGGTTTC 574
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 23832671 ATTGTTATTAAGAAGAGAGAACCATTGAATTTTGGCATCCCAGATGGGAGCACAGGTTTC 23832730

Query 575 TCTAGTAGATTAGCAGCTACACAAGATCTGCCTTTTATTCATCAGTCT 622
||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 23832731 TCTAGTAGATTAGCAGCTACACAAGATCTGCCTTTTATTCATCAGTCT 23832778


Features in this part of subject sequence:
estrogen receptor binding site associated antigen 9
estrogen receptor binding site associated antigen 9


Score = 183 bits (99), Expect = 2e-43
Identities = 99/99 (100%), Gaps = 0/99 (0%)
Strand=Plus/Plus

Query 178 GGTTTTGATTCCCACCATGGCCATCACCCAGTTTCGGTTATTTAAATTTTGTACCTGCCT 237
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 23826547 GGTTTTGATTCCCACCATGGCCATCACCCAGTTTCGGTTATTTAAATTTTGTACCTGCCT 23826606

Query 238 AGCAACAGTATTCTCATTCCTAAAGAGATTAATATGCAG 276
|||||||||||||||||||||||||||||||||||||||
Sbjct 23826607 AGCAACAGTATTCTCATTCCTAAAGAGATTAATATGCAG 23826645


Features in this part of subject sequence:
estrogen receptor binding site associated antigen 9
estrogen receptor binding site associated antigen 9


Score = 171 bits (92), Expect = 1e-39
Identities = 92/92 (100%), Gaps = 0/92 (0%)
Strand=Plus/Plus

Query 623 TCTGAATTAGGTGACTTAGATACCTGGCAGGAAAATACCAATGCATGGGAAGAAGAAGAA 682
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 23836573 TCTGAATTAGGTGACTTAGATACCTGGCAGGAAAATACCAATGCATGGGAAGAAGAAGAA 23836632

Query 683 GATGCAGCCTGGCAAGCAGAAGAAGTTCTGAG 714
||||||||||||||||||||||||||||||||
Sbjct 23836633 GATGCAGCCTGGCAAGCAGAAGAAGTTCTGAG 23836664


Features in this part of subject sequence:
estrogen receptor binding site associated antigen 9
estrogen receptor binding site associated antigen 9


Score = 152 bits (82), Expect = 5e-34
Identities = 82/82 (100%), Gaps = 0/82 (0%)
Strand=Plus/Plus

Query 274 CAGATCTGGCAGAGGACGGAAATTAAGTGGAGACCAAATAACTTTGCCAACTACAGTTGA 333
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 23829598 CAGATCTGGCAGAGGACGGAAATTAAGTGGAGACCAAATAACTTTGCCAACTACAGTTGA 23829657

Query 334 TTATTCATCAGTTCCTAAGCAG 355
||||||||||||||||||||||
Sbjct 23829658 TTATTCATCAGTTCCTAAGCAG 23829679


>ref|NT_008046.15|Hs8_8203 Homo sapiens chromosome 8 genomic contig, reference assembly
Length=57155273

Sort alignments for this subject sequence by:
E value Score Percent identity
Query start position Subject start position

Features flanking this part of subject sequence:
10194 bp at 5' side: fibrocystin L
10356 bp at 3' side: estrogen receptor binding site associated antigen 9


Score = 327 bits (177), Expect = 8e-87
Identities = 184/187 (98%), Gaps = 1/187 (0%)
Strand=Plus/Plus

Query 1 ACCTTACTGCCCTCCGTCTACAGGCCTTGTACCTCTCCAGGCCGATTTTTCCACAATTTA 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 23770686 ACCTTACTGCCCTCCGTCTACAGGCCTTGTACCTCTCCAGGCCGATTTTTCCACAATTTA 23770745

Query 61 AATCCCAGTTCACCTGGTATCCAGCTCCAGCAACTTAGAGCGTTTCACGTCACGCCGGGC 120
|||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 23770746 AATCTCAGTTCACCTGGTATCCAGCTCCAGCAACTTAGAGCGTTTCACGTCACGCCGGGC 23770805

Query 121 GCCAGGCGTCGGCTTGTATAACCTGAAAACGCTCCTGTTTTTCTCATCTGTGCAGTGGGT 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 23770806 GCCAGGCGTCGGCTTGTATAACCTGAAAACGCTCCTGTTTTTCTCATCTGTGCAGTGGGT 23770865

Query 181 TTTGATT 187
| ||||
Sbjct 23770866 AT-GATT 23770871


Features in this part of subject sequence:
estrogen receptor binding site associated antigen 9
estrogen receptor binding site associated antigen 9


Score = 300 bits (162), Expect = 2e-78
Identities = 167/169 (98%), Gaps = 1/169 (0%)
Strand=Plus/Plus

Query 354 AGACAGATGTTGAAGAGTGGACTTCCTGGGATGAAGATGCACCCACCAGTGTAAAGATCG 413
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 23785129 AGACAGATGTTGAAGAGTGGACTTCCTGGGATGAAGATGCACCCACCAGTGTAAAGATCG 23785188

Query 414 AAGGAGGGAATGGGAATGTGGCAACACAACAAAATTCTTTGGAACAACTGGAACCTGACT 473
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 23785189 AAGGAGGGAATGGGAATGTGGCAACACAACAAAATTCTTTGGAACAACTGGAACCTGACT 23785248

Query 474 ATTTTAAGGACATGACACCAACTATTAGGAAAACTCAGAAAAT-TGTTA 521
||||||||||||||||||||||||||||||||||||||||| | |||||
Sbjct 23785249 ATTTTAAGGACATGACACCAACTATTAGGAAAACTCAGAAAGTATGTTA 23785297


Features in this part of subject sequence:
estrogen receptor binding site associated antigen 9
estrogen receptor binding site associated antigen 9


Score = 200 bits (108), Expect = 2e-48
Identities = 108/108 (100%), Gaps = 0/108 (0%)
Strand=Plus/Plus

Query 515 ATTGTTATTAAGAAGAGAGAACCATTGAATTTTGGCATCCCAGATGGGAGCACAGGTTTC 574
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 23787337 ATTGTTATTAAGAAGAGAGAACCATTGAATTTTGGCATCCCAGATGGGAGCACAGGTTTC 23787396

Query 575 TCTAGTAGATTAGCAGCTA

CACAAGATCTGCCTTTTATTCATCAGTCT 622
||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 23787397 TCTAGTAGATTAGCAGCTACACAAGATCTGCCTTTTATTCATCAGTCT 23787444


Features in this part of subject sequence:
estrogen receptor binding site associated antigen 9
estrogen receptor binding site associated antigen 9


Score = 183 bits (99), Expect = 2e-43
Identities = 99/99 (100%), Gaps = 0/99 (0%)
Strand=Plus/Plus

Query 178 GGTTTTGATTCCCACCATGGCCATCACCCAGTTTCGGTTATTTAAATTTTGTACCTGCCT 237
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 23781211 GGTTTTGATTCCCACCATGGCCATCACCCAGTTTCGGTTATTTAAATTTTGTACCTGCCT 23781270

Query 238 AGCAACAGTATTCTCATTCCTAAAGAGATTAATATGCAG 276
|||||||||||||||||||||||||||||||||||||||
Sbjct 23781271 AGCAACAGTATTCTCATTCCTAAAGAGATTAATATGCAG 23781309


Features in this part of subject sequence:
estrogen receptor binding site associated antigen 9
estrogen receptor binding site associated antigen 9


Score = 171 bits (92), Expect = 1e-39
Identities = 92/92 (100%), Gaps = 0/92 (0%)
Strand=Plus/Plus

Query 623 TCTGAATTAGGTGACTTAGATACCTGGCAGGAAAATACCAATGCATGGGAAGAAGAAGAA 682
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 23791240 TCTGAATTAGGTGACTTAGATACCTGGCAGGAAAATACCAATGCATGGGAAGAAGAAGAA 23791299

Query 683 GATGCAGCCTGGCAAGCAGAAGAAGTTCTGAG 714
||||||||||||||||||||||||||||||||
Sbjct 23791300 GATGCAGCCTGGCAAGCAGAAGAAGTTCTGAG 23791331


Features in this part of subject sequence:
estrogen receptor binding site associated antigen 9
estrogen receptor binding site associated antigen 9


Score = 152 bits (82), Expect = 5e-34
Identities = 82/82 (100%), Gaps = 0/82 (0%)
Strand=Plus/Plus

Query 274 CAGATCTGGCAGAGGACGGAAATTAAGTGGAGACCAAATAACTTTGCCAACTACAGTTGA 333
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 23784264 CAGATCTGGCAGAGGACGGAAATTAAGTGGAGACCAAATAACTTTGCCAACTACAGTTGA 23784323

Query 334 TTATTCATCAGTTCCTAAGCAG 355
||||||||||||||||||||||
Sbjct 23784324 TTATTCATCAGTTCCTAAGCAG 23784345

第四部分 分析RCAS1蛋白序列
进入网站 /uniprot/O00559
输入RCAS1，
go
进入结果页面，读取结果：
总原子数：4632
脂肪性：98。88
GRAVY -0.340
10 20 30 40 50 60
MAITQFRLFK FCTCLATVFS FLKRLICRSG RGRKLSGDQI TLPTTVDYSS VPKQTDVEEW

70 80 90 100 110 120
TSWDEDAPTS VKIEGGNGNV ATQQNSLEQL EPDYFKDMTP TIRKTQKIVI KKREPLNFGI

130 140 150 160 170 180
PDGSTGFSSR LAATQDLPFI HQSSELGDLD TWQENTNAWE EEEDAAWQAE EVLRQQKLAD

190 200 210
REKRAAEQQR KKMEKEAQRL MKKEQNKIGV
KLS O00559-1 [UniParc].
Last modified July 1, 199

7. Version 1.
Checksum: B115E741E23891C5
Show ?
FASTA 213 24,377
分子
4632 98.88 -0.340


第五部分 RCAS1的二级结构
进入/software/TMPRED_form.html
在QUERY Seuence中键入 RCAS1蛋白质序列
点击RUNTMPED
进入结果界面
结果：从内向外跨膜1个区域（73-92位）
从外向内跨膜1个区域（73-86位）


第六部分 预测RCAS1信号肽的位置
进入http：//www.cbs.dtu.dk/services/signalp
在submssion中键入RCAS1氨基酸序列
点击submit
结果：signalp-NN result NO
signalp-HNM result NO
不存在信号肽