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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGATGAGCCTCAGATCGAGCACTTGCTGCAGACAGCTGAGGCCATCCGAAAAGACTATCCTAACGAGGATTGGATGCACCTCACTGCTCTTATCCATGgtaaattctctgcttcatctccttaaatcctatgaatagtattaggtagaggccagaggacctgtgtaaggaacactcccaacctcattgatattgtacg...

Basic information

species Vitis vinifera
transcript Vv09s0002g02940.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g02940.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G126900_T01 (Zea mays), 5'ss of exon 2
TTGGATGAGCCTCAGATCGAGCACTTGCTGCAGACAGCTGAGGCCATCCGAAAAGACTATCCTAACGAGGATTGGATGCACCTCACTGCTCTTATCCATGgtaaattctctgct--tcatctccttaaatcctatgaatagtattaggtagaggccagaggacctgtgtaaggaacactcccaacctcattgatattgtacg
 ||||   ||| |||||||||||| |||||||||| || ||||||||||| || ||||| ||  ||||||| ||| | |||||||| |  || ||||| ||||    ||   ||  |    | |||   | ||    ||   | |  || |  ||||     |     |      ||||  ||   |||             
CTGGACATGCCCCAGATCGAGCACCTGCTGCAGACCGCCGAGGCCATCCGCAAGGACTACCCCGACGAGGACTGGCTCCACCTCACCGGACTCATCCACGgtatggcctgcactgcttgcttgcttgcttactgccgatgcaact--gtcgtcgccacgcttctctaatctaactcactgtcattttcag------------

upper sequence: Vv09s0002g02940.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA07G01660.1 (Glycine max), 5'ss of exon 4
TTGGATGAGCCTCAGATCGAGCACTTGCTGCAGACAGCTGAGGCCATCCGAAAAGACTATCCTAACGAGGATTGGATGCACCTCACTGCTCTTATCCATGgtaaattctctgcttcatctccttaaat-----cctatgaatagtattaggtagaggccagagg-acctgtgtaaggaacactcccaacctcat-tgatattgtacg-------------------------------------------------------------------------------------
|||||||| ||||| || ||||||||||| ||||||||||| || ||  | |  ||||| ||  | || |||||| ||||| | ||||  |||||||||||||  ||||    |  |  ||  ||| |     | ||     | |  ||  |       | ||  | ||   |||   |  ||       | || |  | || |                                                                                        
TTGGATGAACCTCAAATTGAGCACTTGCTCCAGACAGCTGAAGCTATAAGGAGGGACTACCCAGATGAAGATTGGTTGCACTTAACTGGCCTTATCCATGgtactttctacattctaaatctctaattatccccttacatgcattgctactttatacttaaagatatctacttaaaagatcctttggctatgatatagttttttttatttttggtttcatatggactattggaaatgaaagataggaaattactagaaaaactccacttcttataccacaagcatttaccag

upper sequence: Vv09s0002g02940.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA07G01660.5 (Glycine max), 5'ss of exon 2
TTGGATGAGCCTCAGATCGAGCACTTGCTGCAGACAGCTGAGGCCATCCGAAAAGACTATCCTAACGAGGATTGGATGCACCTCACTGCTCTTATCCATGgtaaattctctgcttcatctccttaa--atcctatgaatagtatta--ggtagaggccagaggacctgtgtaaggaacactcccaacctcattgatattgtacg
|||||||| ||||| || ||||||||||| ||||||||||| || ||  | |  ||||| ||  | || |||||| ||||| | ||||  |||||||||||||  ||||    |  |  ||  |||  ||||  | |   | |||     |  |  |   | ||  | |      || |  |     ||   |||||| ||   
TTGGATGAACCTCAAATTGAGCACTTGCTCCAGACAGCTGAAGCTATAAGGAGGGACTACCCAGATGAAGATTGGTTGCACTTAACTGGCCTTATCCATGgtactttctacattctaaatctctaattatccccttacatgcattgctactttatacttaaagatatctacttaaaagatcctttggcta--tgatatagtt--

upper sequence: Vv09s0002g02940.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT1G14520.1 (Arabidopsis thaliana), 5'ss of exon 4
TTGGATGAGCCTCAGATCGAGCACTTGCTGCAGACAGCTGAGGCCATCCGAAAAGACTATCCTAACGAGGATTGGATGCACCTCACTGCTCTTATCCATGgtaaattct-ctgcttcatctccttaaatcctatgaatagtattaggtagaggccagaggacct-gtgtaaggaacactcccaacctcattgatattgtacg
||||| || ||||||||||||||  |||| ||||||||||| |||||| ||||||| || ||| | || || ||| | || || || | ||||||||| |||||||| | || | | ||    ||  |||   | || | |||    ||  ||    | ||  | ||||  ||          |                  
TTGGACGAACCTCAGATCGAGCATCTGCTTCAGACAGCTGAAGCCATCAGAAAAGATTACCCTGATGAAGACTGGCTCCATCTGACCGGTCTTATCCACGgtaaattatactccctgattcggtttgatcacgttaa-aatatcgtttaccggtttaatgattttgtgtttggtgtgtatgtgaatcag-------------

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|30302571|gb|CB979365.1|CB979365
EST:     AAAAGACTATCCTAACGAGGATTGGATGCACCTCACTGCCCTTATCCATG                         ATCTGGGAAAGGTCCTCCTCCTTCCTTCCTTTGGAGAACTGCCTCAGCGGG
genomic: AAAAGACTATCCTAACGAGGATTGGATGCACCTCACTGCTCTTATCCATGgtaaattctc ... tggactacagATCTGGGAAAGGTCCTCCTCCTTCCTTCCTTTGGAGAACTGCCTCAGTGGG
EST: gi|110357458|gb|EC921014.1|EC921014
EST:     AAAAGACTATCCTAACGAGGATTGGATGCACCTCACTGCCCTTATCCATG                         ATCTGGGAAAGGTCCTCCTCCTTCCTTCCTTTGGAGAACTGCCTCAGTGGG
genomic: AAAAGACTATCCTAACGAGGATTGGATGCACCTCACTGCTCTTATCCATGgtaaattctc ... tggactacagATCTGGGAAAGGTCCTCCTCCTTCCTTCCTTTGGAGAACTGCCTCAGTGGG
EST: gi|110357825|gb|EC921593.1|EC921593
EST:     AAAAGACTATCCTAACGAGGATTGGATGCACCTCACTGCCCTTATCCATG                         ATCTGGGAAAGGTCCTCCTCCTTCCTTCCTTTGGAGAACTGCCTCAGTGGG
genomic: AAAAGACTATCCTAACGAGGATTGGATGCACCTCACTGCTCTTATCCATGgtaaattctc ... tggactacagATCTGGGAAAGGTCCTCCTCCTTCCTTCCTTTGGAGAACTGCCTCAGTGGG
EST: gi|30302644|gb|CB979438.1|CB979438
EST:     AAAAGACTATCCTAACGAGGATTGGATGCACCTCACTGCCCTTATCCATG                         ATCTGGGAAAGGTCCTCCTCCTTCCTTCCTTTGGAGAACTGCCTCAGCGGG
genomic: AAAAGACTATCCTAACGAGGATTGGATGCACCTCACTGCTCTTATCCATGgtaaattctc ... tggactacagATCTGGGAAAGGTCCTCCTCCTTCCTTCCTTTGGAGAACTGCCTCAGTGGG
EST: gi|71856659|gb|DT005714.1|DT005714
EST:     AAAAGACTATCCTAACGAGGATTGGATGCACCTCACTGCCCTTATCCATG                         ATCTGGGAAAGGTCCTCCTCCTTCCTTCCTTCGGAGAACTGCCTCAGTGGG
genomic: AAAAGACTATCCTAACGAGGATTGGATGCACCTCACTGCTCTTATCCATGgtaaattctc ... tggactacagATCTGGGAAAGGTCCTCCTCCTTCCTTCCTTTGGAGAACTGCCTCAGTGGG
EST: gi|30302699|gb|CB979493.1|CB979493
EST:     AAAAGACTATCCCAACGAGGATTGGATGCACCTCACTGCCCTTATCCATG                         ATCTGGGAAAGGTCCTCCTCCTTCCTTCCTTTGGAGAACTGCCTCAGTGGG
genomic: AAAAGACTATCCTAACGAGGATTGGATGCACCTCACTGCTCTTATCCATGgtaaattctc ... tggactacagATCTGGGAAAGGTCCTCCTCCTTCCTTCCTTTGGAGAACTGCCTCAGTGGG
EST: gi|110358718|gb|EC923143.1|EC923143
EST:     AAAAGACTATCCTAACGAGGATTGGATGCACCTCACTGCCCTTATCCATG                         ATCTGGGAAAGGTCCTCCTCCTTCCTTCCTTTGGAGAACTGCCTCAGTGGG
genomic: AAAAGACTATCCTAACGAGGATTGGATGCACCTCACTGCTCTTATCCATGgtaaattctc ... tggactacagATCTGGGAAAGGTCCTCCTCCTTCCTTCCTTTGGAGAACTGCCTCAGTGGG
EST: gi|110720644|gb|EE096747.1|EE096747
EST:     AAAAGACTATCCTAACGAGGATTGGATGCACCTCACTGCTCTTATCCATG                         ATCTGGGAAAGGTCCTCCTCCTTCCTTCCTTTGGAGAACTGCCTCAGTGGG
genomic: AAAAGACTATCCTAACGAGGATTGGATGCACCTCACTGCTCTTATCCATGgtaaattctc ... tggactacagATCTGGGAAAGGTCCTCCTCCTTCCTTCCTTTGGAGAACTGCCTCAGTGGG
EST: gi|30302025|gb|CB978819.1|CB978819
EST:     AAAAGACTATCCTAACGAGGATTGGATGCACCTCACTGCCCTTATCCATG                         ATCTGGGAAAGGTCCTCCTCCTTCCTTCCTTTGGAGAACTGCCTCAGTGGG
genomic: AAAAGACTATCCTAACGAGGATTGGATGCACCTCACTGCTCTTATCCATGgtaaattctc ... tggactacagATCTGGGAAAGGTCCTCCTCCTTCCTTCCTTTGGAGAACTGCCTCAGTGGG
EST: gi|110357023|gb|EC920273.1|EC920273
EST:     AAAAGACTATCCTAACGAGGATTGGATGCACCTCACTGCCCTTATCCATG                         ATCTGGGAAAGGTCCTCCTCCTTCCTTCCTTTGGAGAACTGCCTCAGTGGG
genomic: AAAAGACTATCCTAACGAGGATTGGATGCACCTCACTGCTCTTATCCATGgtaaattctc ... tggactacagATCTGGGAAAGGTCCTCCTCCTTCCTTCCTTTGGAGAACTGCCTCAGTGGG
EST: gi|71859557|gb|DT008612.1|DT008612
EST:     AAAAGACTATCCTAACGAGGATTGGATGCACCTCACTGCCCTTATCCATG                         ATCTGGGAAAGGTCCTCCTCCTTCCTTCCTT
genomic: AAAAGACTATCCTAACGAGGATTGGATGCACCTCACTGCTCTTATCCATGgtaaattctc ... tggactacagATCTGGGAAAGGTCCTCCTCCTTCCTTCCTT
EST: gi|110358259|gb|EC922343.1|EC922343
EST:     AAAAGACTATCCTAACGAGGATTGGATGCACCTCACTGCCCTTATCCATG                         ATCTGGGAAAGGTCCTCCTCCTTCCTTCCTTTGGAGAACTGCCTCAGTGGG
genomic: AAAAGACTATCCTAACGAGGATTGGATGCACCTCACTGCTCTTATCCATGgtaaattctc ... tggactacagATCTGGGAAAGGTCCTCCTCCTTCCTTCCTTTGGAGAACTGCCTCAGTGGG
EST: gi|110726999|gb|EE103284.1|EE103284
EST:     AAAAGACTATCCTAACGAGGATTGGATGCACCTCACTGCTCTTATCCATG                         ATCTGGGAAAGGTCCTCCTCCTTCCTTCCTTTGGAGAACTGCCTCAGTGGG
genomic: AAAAGACTATCCTAACGAGGATTGGATGCACCTCACTGCTCTTATCCATGgtaaattctc ... tggactacagATCTGGGAAAGGTCCTCCTCCTTCCTTCCTTTGGAGAACTGCCTCAGTGGG
EST: gi|30302765|gb|CB979559.1|CB979559
EST:     AAAAGACTATCCCAACGAGGATTGGATGCACCTCACTGCCCTTATCCATG                         ATCTGGGAAAGGTCCTCCTCCTTCCTTCCTTTGGAGAACTGCCTCAGTGGG
genomic: AAAAGACTATCCTAACGAGGATTGGATGCACCTCACTGCTCTTATCCATGgtaaattctc ... tggactacagATCTGGGAAAGGTCCTCCTCCTTCCTTCCTTTGGAGAACTGCCTCAGTGGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGGATGAGCCTCAGATCGAGCACTTGCTGCAGACAGCTGAGGCCATCCGAAAAGACTATCCTAACGAGGATTGGATGCACCTCACTGCTCTTATCCATGgtaaattctctgcttcatctccttaaatcctatgaatagtattaggtagaggccagaggacctgtgtaaggaacactcccaacctcattgatattgtacg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggaaca