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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCTCACATCCATGTGCTGATCTGCGGTCAGGATATCTCTTGAATAGCAACATTGCTGGGCTTGAAAAGGCAGATGTTTTCCTTTTGGTTGGCACCCAGgtaattttctgacctctttattaaagtctaactttagtagtatatgactagcagggttgtgttatttaaataacactgatgatttgtggtgtcagattgc...

Basic information

species Vitis vinifera
transcript Vv14s0006g02020.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0006g02020.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os03g50540.1 (Oryza sativa), 5'ss of exon 4
TGGCTCACATCCATGTGCTGATCTGCGGTCAGGATATCTCTTGAATAGCAACATTGCTGGGCTTGAAAAGGCAGATGTTTTCCTTTTGGTTGGCACCCAGgtaattttctgacct--ctttattaaagtctaactttagtagt--atatgactagcagggttgtgttatttaaataacactgatgatttgtggtgtcagattgc
|||  ||  |||   ||| ||||| || ||    || ||  ||||||  | ||||||||||||||| || || ||||| |||||||||||||| || |||||||  |  ||||    | |||     | |||   ||    |   || |  || | |   ||   || |  ||  ||  |||   | |||   || |  |    
TGGTCCAAGTCCTCCTGCGGATCTACGTTCTAACTACCTAATGAATACTAGCATTGCTGGGCTTGAGAAAGCTGATGTCTTCCTTTTGGTTGGTACACAGgtaaaatcttgactataccttacctgtggctattatttactgccaatttttcttgaattcttcacttctccaagaaatgctgtgtaattgcattgcctca----

upper sequence: Vv14s0006g02020.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G126038_T01 (Zea mays), 5'ss of exon 4
TGGCTCACATCCATGTGCTGATCTGCGGTCAGGATATCTCTTGAATAGCAACATTGCTGGGCTTGAAAAGGCAGATGTTTTCCTTTTGGTTGGCACCCAGgtaattttctgacctctttattaaagtctaactttagtag-tatatg-actagcagggttgtgttatt-taaataacactgatgatttgtggtgtcagattgc
|||  |  ||||    || || ||||| ||    || ||  |||||| || ||||||||||||||||||||| ||||| ||||||||||||||||| ||||||| || ||   |  |   |       |    || || | ||  || | |  | |   | |   ||| || ||||     ||   ||||| ||   |     
TGGTCCCAATCCTCCAGCAGACCTGCGATCTAACTACCTAATGAATACCAGCATTGCTGGGCTTGAAAAGGCTGATGTGTTCCTTTTGGTTGGCACTCAGgtaaattactcctcaatgcctagtgccattttcttggttgctacttgcattctctgaaatataccattatatataatcactatatcttgtgctggtggca---

upper sequence: Vv14s0006g02020.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G145854_T01 (Zea mays), 5'ss of exon 4
TGGCTCACATCCATGTGCTGATCTGCGGTCAGGATATCTCTTGAATAGCAACATTGCTGGGCTTGAAAAGGCAGATGTTTTCCTTTTGGTTGGCACCCAGgtaat-----tttctgacctctttattaaagtctaactttagtagtatatgactagcagggttgtgttat-ttaaataa-cactgatgatttgtggtgtcagattgc
|||  |  ||||    || |||||||| ||    || ||  ||||||  | ||||||||||||||||||||| ||||| ||||||||||||||||| |||||||      | ||||  |    |   |   |||  |||   |  |  || |   | |   |    |||| ||  |||| |||||     ||||| |||  |     
TGGTCCTAATCCTCCAGCAGATCTGCGATCTAACTACCTAATGAATACGAGCATTGCTGGGCTTGAAAAGGCTGATGTCTTCCTTTTGGTTGGCACTCAGgtaaaattcatctctgtgcctagtgccactttctttcttgcttcttgcattatctg-aatataccattatattgtataatcactgg-atcttgtgctgttgg-----

upper sequence: Vv14s0006g02020.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA11G33480.1 (Glycine max), 5'ss of exon 4
TGGCTCACATCCATGTGCTGATCTGCGGTCAGGATATCTCTTGAATAGCAACATTGCTGGGCTTGAAAAGGCAGATGTTTTCCTTTTGGTTGGCACCCAGgtaattttctgacctctttattaaagtctaactttagtagtatatgactagcagggttgt-gttatttaaataacactgatgatttgtggtgtcagattgc---
|||   | || |   ||||||| |  | ||||||||| |  ||||||  | ||||||||| |||||||| || ||||  ||||| ||||||||||||||||||  | ||| | |||| || |  | | |||   || || |  |||  |   |  |||   | |  | |||| |  |   || |        | |  ||     
TGGTGTAAATACTAATGCTGATTTCAGATCAGGATATATTATGAATACTAGCATTGCTGGTCTTGAAAAAGCGGATGCGTTCCTGTTGGTTGGCACCCAGgtatatctcttatctctctaatgtattttaa---taata-tgcatgttttttaatgttacagatggtcaaatgattcctgtgttagactaaataatttttttaa

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|110698529|gb|EE076131.1|EE076131
EST:     ACATTGCTGGGCTTGAAAAGGCAGATATTTTCCTTTTGGTTGGCACCTAG                         CCAAGGGTGGAAGCTCCCATGGTAAATGCCCGAATCCGGAAAACAGTACAA
genomic: ACATTGCTGGGCTTGAAAAGGCAGATGTTTTCCTTTTGGTTGGCACCCAGgtaattttct ... caattggcagCCAAGGGTGGAAGCTCCCATGGTAAATGCCCGAATCCGGAAAACAGTACAA
EST: gi|110719363|gb|EE097252.1|EE097252
EST:     ACATTGCTGGGCTTGAAAAGGCAGATATTTTCCTTTTGGTTGGCACCCAG                         CCAAGGGTGGAAGCTCCCATGGTAAATGCCCGAATCCGGAAAACAGTACAA
genomic: ACATTGCTGGGCTTGAAAAGGCAGATGTTTTCCTTTTGGTTGGCACCCAGgtaattttct ... caattggcagCCAAGGGTGGAAGCTCCCATGGTAAATGCCCGAATCCGGAAAACAGTACAA
EST: gi|110693407|gb|EE069609.1|EE069609
EST:     ACATTGCTGGGCTTGAAAAGGCAGATGTTTTCCTTTTGGTTGGCACCCAG                         CCAAGGGTGGAAGCTCCCATGGTAAATGCCCGAATCCGGAAAACAGTACAA
genomic: ACATTGCTGGGCTTGAAAAGGCAGATGTTTTCCTTTTGGTTGGCACCCAGgtaattttct ... caattggcagCCAAGGGTGGAAGCTCCCATGGTAAATGCCCGAATCCGGAAAACAGTACAA
EST: gi|71861483|gb|DT010538.1|DT010538
EST:     ACATTGCTGGGCTTGAAAAGGCAGATGTTTTCCTTTTGGTTGGCACCCAG                         CCAAGGGTGGAAGCTCCCATGGTAAATGCCCGAATCCGGAAAACAGTACAA
genomic: ACATTGCTGGGCTTGAAAAGGCAGATGTTTTCCTTTTGGTTGGCACCCAGgtaattttct ... caattggcagCCAAGGGTGGAAGCTCCCATGGTAAATGCCCGAATCCGGAAAACAGTACAA
EST: gi|110690735|gb|EE068153.1|EE068153
EST:     ACATTGCTGGGCTTGAAAAGGCAGATGTTTTCCTTTTGGTTGGCACCCAG                         CCAAGGGTGGAAGCTCCCATGGTAAATGCCCGAATCCGGAAAACAGTACAA
genomic: ACATTGCTGGGCTTGAAAAGGCAGATGTTTTCCTTTTGGTTGGCACCCAGgtaattttct ... caattggcagCCAAGGGTGGAAGCTCCCATGGTAAATGCCCGAATCCGGAAAACAGTACAA
EST: gi|71861944|gb|DT010999.1|DT010999
EST:     ACATTGCTGGGCTTGAAAAGGCAGATGTTTTCCTTTTGGTTGGCACCCAG                         CCAAGGGTGGAAGCTCCCATGGTAAATGCCCGAATCCGGAAAACAGTACAA
genomic: ACATTGCTGGGCTTGAAAAGGCAGATGTTTTCCTTTTGGTTGGCACCCAGgtaattttct ... caattggcagCCAAGGGTGGAAGCTCCCATGGTAAATGCCCGAATCCGGAAAACAGTACAA
EST: gi|71863103|gb|DT012158.1|DT012158
EST:     ACATTGCTGGGCTTGAAAAGGCAGATGTTTTCCTTTTGGTTGGCACCCAG                         CCAAGGGTGGAAGCTCCCATGGTAAATGCCCGAATCCGGAAAACAGTACAA
genomic: ACATTGCTGGGCTTGAAAAGGCAGATGTTTTCCTTTTGGTTGGCACCCAGgtaattttct ... caattggcagCCAAGGGTGGAAGCTCCCATGGTAAATGCCCGAATCCGGAAAACAGTACAA
EST: gi|110698347|gb|EE075766.1|EE075766
EST:     ACATTGCTGGGCTTGAAAAGGCAGATATTTTCCTTTTGGTTGGCACCCAG                         CCAAGGGTGGAAGCTCCCATGGTAAATGCCCGAATCCGGAAAACAGTACAA
genomic: ACATTGCTGGGCTTGAAAAGGCAGATGTTTTCCTTTTGGTTGGCACCCAGgtaattttct ... caattggcagCCAAGGGTGGAAGCTCCCATGGTAAATGCCCGAATCCGGAAAACAGTACAA
EST: gi|110699198|gb|EE075987.1|EE075987
EST:     ACATTGCTGGGCTTGAAAAGGCAGATATTTTCCTTTTGGTTGGCACCCAG                         CCAAGGGTGGAAGCTCCCATGGTAAATGCCCGAATCCGGAAAACAGTACAA
genomic: ACATTGCTGGGCTTGAAAAGGCAGATGTTTTCCTTTTGGTTGGCACCCAGgtaattttct ... caattggcagCCAAGGGTGGAAGCTCCCATGGTAAATGCCCGAATCCGGAAAACAGTACAA

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGCTCACATCCATGTGCTGATCTGCGGTCAGGATATCTCTTGAATAGCAACATTGCTGGGCTTGAAAAGGCAGATGTTTTCCTTTTGGTTGGCACCCAGgtaattttctgacctctttattaaagtctaactttagtagtatatgactagcagggttgtgttatttaaataacactgatgatttgtggtgtcagattgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taaataa