Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cccttcacttttgttaggatgaatttatgtgaaaaagtggttcaggttagagcctatataaaaaaaattaactgttgattgttctggaatgtctttttagGTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTTATGAAATGAAGTTGGTAGATTTGACTAACAAGCCAGAATG

Basic information

species Vitis vinifera
transcript Vv14s0006g00630.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0006g00630.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA18G04510.1 (Glycine max), 3'ss of exon 1
--------cccttcacttttgttaggatgaatttatgtgaaaaagtggttcaggttagagcctatataaaaaaaattaactgttgattgttctggaatgtctttttagGTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTTATGAAATGAAGTTGGTAGATTTGACTAACAAGCCAGAATG
              | | |  ||    |  |||||| |||         || | ||||  |||||     |  | |||     ||| | || || | |||||||||||| || || |  |||||| | |||||||| || |||||||||||||| ||||||||    |||||||| |||||||| ||||||||||||| 
gtttaagaaaacaaattatgatttttgttgatttatttgagctttaaactcggattagtacctatg----attagttagtg--tgactctt-tgaattgtctttttaGGCCCTTTTTGCCAAAGGGTGCTGCTGACACTGGAGGAAAAACATCTACCTTATGACCCCAAGTTGGTGGATTTGACCAACAAGCCAGAAT-

upper sequence: Vv14s0006g00630.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA11G33700.2 (Glycine max), 3'ss of exon 1
-cccttcacttttgttaggatgaatttatgtgaaaaagtggttcaggttagagcctata--taaaaaaaattaactgttgattgttctggaatgtctttttagGTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTTATGAAATGAAGTTGGTAGATTTGACTAACAAGCCAGAATG
       | | |  ||  | |  |||||| |||         ||||| |||  |   ||  ||  |  | |||  |  ||| | || || | |||||||| ||| || || |  |||||| |  ||||||| || |||||||||||||| ||||||||    |||||||| |||||||| ||||||||||||||
aaaacaaaatatgattttggttgatttatttgagctttaaactcagggtagtactagtacctatgattagttagtt--tgactctt-tgaattgtcttttcagGCCCTTTTTGCCAAAGGGTGTTGCTGACACTGGAGGAAAAACATCTACCTTATGACCCCAAGTTGGTGGATTTGACCAACAAGCCAGAATG
















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|110719968|gb|EE095537.1|EE095537
EST:     CGAAGTCTGCGTCAAGGCTTCCGTCATAATCCCCAACAAGCTCGGTGACT                         GTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTT
genomic: CGAAGTCTGCGTCAAGGCTTCCGTCATAATCCCCAACAAGCTCGGTGACTgtaaggcttc ... gtctttttagGTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTT
EST: gi|349817724|gb|FQ407713.1|FQ407713
EST:     CGAAGTCTGCGTCAAGGCTTCCGTCATAATCCCCAACAAGCTCGGTGACT                         GTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTT
genomic: CGAAGTCTGCGTCAAGGCTTCCGTCATAATCCCCAACAAGCTCGGTGACTgtaaggcttc ... gtctttttagGTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTT
EST: gi|33402764|gb|CF208391.1|CF208391
EST:     CGAAGTCTGCGTCAAGGCTTCCGTCATAATCCCCAACAAGCTCGGTGACT                         GTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTT
genomic: CGAAGTCTGCGTCAAGGCTTCCGTCATAATCCCCAACAAGCTCGGTGACTgtaaggcttc ... gtctttttagGTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTT
EST: gi|26265541|gb|CA816604.1|CA816604
EST:     CGAAGTCTGCGTCAAGGCTTCCGTCATAATCCCCAACAAGCTCGGTGACT                         GTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTT
genomic: CGAAGTCTGCGTCAAGGCTTCCGTCATAATCCCCAACAAGCTCGGTGACTgtaaggcttc ... gtctttttagGTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTT
EST: gi|351024071|gb|FQ423494.1|FQ423494
EST:     CGAAGTCTGCGTCAAGGCTTCCGTCATAATCCCCAACAAGCTCGGTGACT                         GTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTT
genomic: CGAAGTCTGCGTCAAGGCTTCCGTCATAATCCCCAACAAGCTCGGTGACTgtaaggcttc ... gtctttttagGTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTT
EST: gi|33404427|gb|CF210054.1|CF210054
EST:     CGAAGTCTGCGTCAAGGCTTCCGTCATAATCCCCAACAAGCTCGGTGACT                         GTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTT
genomic: CGAAGTCTGCGTCAAGGCTTCCGTCATAATCCCCAACAAGCTCGGTGACTgtaaggcttc ... gtctttttagGTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTT
EST: gi|349826855|gb|FQ418946.1|FQ418946
EST:     CGAAGTCTGCGTCAAGGCTTCCGTCATAATCCCCAACAAGCTCGGTGACT                         GTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTT
genomic: CGAAGTCTGCGTCAAGGCTTCCGTCATAATCCCCAACAAGCTCGGTGACTgtaaggcttc ... gtctttttagGTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTT
EST: gi|110691855|gb|EE070437.1|EE070437
EST:     CGAAGTCTGCGTCAAGGCTTCCGTCATAATCCCCAACAAGCTCGGTGACT                         GTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTT
genomic: CGAAGTCTGCGTCAAGGCTTCCGTCATAATCCCCAACAAGCTCGGTGACTgtaaggcttc ... gtctttttagGTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTT
EST: gi|351046545|gb|FQ453161.1|FQ453161
EST:     CGAAGTCTGCGTCAAGGCTTCCGTCATAATCCCCAACAAGCCCGGTGACT                         GTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTT
genomic: CGAAGTCTGCGTCAAGGCTTCCGTCATAATCCCCAACAAGCTCGGTGACTgtaaggcttc ... gtctttttagGTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTT
EST: gi|294966595|gb|GW837730.1|GW837730
EST:     CGAAGTCTGCGTCAAGGCTTCCGTCATAATCCCCAACAAGCTCGGTGACT                         GTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTT
genomic: CGAAGTCTGCGTCAAGGCTTCCGTCATAATCCCCAACAAGCTCGGTGACTgtaaggcttc ... gtctttttagGTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTT
EST: gi|77577773|gb|DV217632.1|DV217632
EST:     CGAAGTCTGCGTCAAGGCTTCCGTCATAATCCCCAACAAGCTCGGTGACT                         GTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTT
genomic: CGAAGTCTGCGTCAAGGCTTCCGTCATAATCCCCAACAAGCTCGGTGACTgtaaggcttc ... gtctttttagGTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTT
EST: gi|26261684|gb|CA812747.1|CA812747
EST:     CGAAGTCTGCGTCAAGGCTTCCGCCATAATCCCCAACAAGCTCGGTGACT                         GTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTT
genomic: CGAAGTCTGCGTCAAGGCTTCCGTCATAATCCCCAACAAGCTCGGTGACTgtaaggcttc ... gtctttttagGTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTT
EST: gi|26262274|gb|CA813337.1|CA813337
EST:     CGAAGTCTGCGTCAAGGCTTCCGTCATAATCCCCAACAAGCTCGGTGACT                         GTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTT
genomic: CGAAGTCTGCGTCAAGGCTTCCGTCATAATCCCCAACAAGCTCGGTGACTgtaaggcttc ... gtctttttagGTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTT
EST: gi|37190755|gb|CF610104.1|CF610104
EST:     CGAAGTCTGCGTCAAGGCTTCCGTCATAATCCCCAACAAGCTCGGTGACT                         GTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAA-CATCTCCCTT
genomic: CGAAGTCTGCGTCAAGGCTTCCGTCATAATCCCCAACAAGCTCGGTGACTgtaaggcttc ... gtctttttagGTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTT
EST: gi|26263937|gb|CA815000.1|CA815000
EST:     CGAAGTCTGCGTCAAGGCTTCCGTCATAATCCCCAACAAGCTCGGTGACT                         GTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTT
genomic: CGAAGTCTGCGTCAAGGCTTCCGTCATAATCCCCAACAAGCTCGGTGACTgtaaggcttc ... gtctttttagGTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTT
EST: gi|349809187|gb|FQ398960.1|FQ398960
EST:     CGAAGTCTGCGTCAAGGCTTCCGTCATAATCCCCAACAAGCTCGGTGACT                         GTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTT
genomic: CGAAGTCTGCGTCAAGGCTTCCGTCATAATCCCCAACAAGCTCGGTGACTgtaaggcttc ... gtctttttagGTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTT
EST: gi|349827950|gb|FQ422818.1|FQ422818
EST:     CGAAGTCTGCGTCAAGGCTTCCGCCATAATCCCCAACAAGCTCGGTGACT                         GTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTT
genomic: CGAAGTCTGCGTCAAGGCTTCCGTCATAATCCCCAACAAGCTCGGTGACTgtaaggcttc ... gtctttttagGTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTT
EST: gi|349814904|gb|FQ410127.1|FQ410127
EST:     CGAAGTCTGCGTCAAGGCTTCCGTCATAATCCCCAACAAGCTCGGTGACT                         GTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTT
genomic: CGAAGTCTGCGTCAAGGCTTCCGTCATAATCCCCAACAAGCTCGGTGACTgtaaggcttc ... gtctttttagGTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttagagcctatataaaaaaaattaactgttgattgttctggaatgtctttttagGTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTTATGAAATGAAGTTGGTAGATTTGACTAACAAGCCAGAATG
                                            tgtcttttt  CT-rich tract
         tatataaaaaaaatta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cccttcacttttgttaggatgaatttatgtgaaaaagtggttcaggttagagcctatataaaaaaaattaactgttgattgttctggaatgtctttttagGTCCCTTCTCACAAAGGATTCTGCTGACTCTCGAGGAAAAACATCTCCCTTATGAAATGAAGTTGGTAGATTTGACTAACAAGCCAGAATG

cccttca
- - - - - - - - - - - - - - -tgaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgttga