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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggagtataatttctttaggtgcaattgtttttctttgtggttctatgcactggttgatttcataagccttgttggtatgtgtttgagcagATTGAGAAACACGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAAGCAGGCAGATGGAAGCAATCAATTGCATTGTCGAAGAAAGACA

Basic information

species Vitis vinifera
transcript Vv13s0067g01290.t01
intron # 26
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 26
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 26
gtggagta--taatttctttaggtgca-attgtttttctttgtggttctatgcactggttgatttcataagccttgttggtatgtgtttgagcagATTGAGAAACACGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAAGCAGGCAGATGGAAGCAATCAATTGCATTGTCGAAGAAAGACA
||  ||    ||  |  ||    |||  |||| | || ||| |  || | |       |||| |   |||   | | ||| |||   |||| ||| ||||||| || ||  | |||||||||||  |  | ||||| || ||||||||||| || ||||||||||||||||| |||||  |||||||||||||||
gtaaagcgattagatgattgtactgcttattgatgttatttttccttttttttttattttgaataactaa---tggctggaatgc-cttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 26
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 26
gtggagt-ataatttcttta-ggtgca-attgtttttctttgtggttctatgcactggttgatttcataagccttgttggtatgtgtttgagcagATTGAGAAACACGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAAGCAGGCAGATGGAAGCAATCAATTGCATTGTCGAAGAAAGACA
||  ||  || || |  ||    |||  |||| | || ||| |  || | |    |  ||    | |  |   | | ||| |||   |||| ||| ||||||| || ||  | |||||||||||  |  | ||||| || ||||||||||| || ||||||||||||||||| |||||  |||||||||||||||
gtaaagcgattatatgattgtactgcttattgatgttatttttccttttttattttattttgaataactaa--tggctggaatgc-cttgatcagCTTGAGAAGCATGAATTGCTTGAGATGAGGAGGATCGCTGCCTACATTTACAAGAAGGCTGGCAGATGGAAGCAATCTATTGCCCTGTCGAAGAAAGACA

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 26
lower sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 3
-----------------------gtggag--tataatttctttaggtgcaattgtttttctttgtg-gttctatgcactggttgatttcataagccttgttggtatgtgtttgagcagATTGAGAAACACGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAAGCAGGCAGATGGAAGCAATCAATTGCATTGTCGAAGAAAGACA
                       |  | |  |||   | ||   | ||   |  |  | |  ||    || |     ||  || |||| |||| |  |||   | | ||   |||||| ||||||| || ||  | || ||||||||  |  ||||||| || ||||||||||| || ||||| ||||||||||| |||||  | || |||||||| |
gtacaaaatagccagataatcttgcagtgcctattgctgctgctgttgttgtaatcgtgcgatgcatattgttactgctttttaatttaataacctgtgtccatttctg---gagcagCTTGAGAAGCATGAATTGCTGGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 26
lower sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 3
------------gtggagtataatttctttaggtgcaattgtttttctttg-tggttctatgcactggtt--gatttcataagccttgttggtatgtgtttgagcagATTGAGAAACACGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAAGCAGGCAGATGGAAGCAATCAATTGCATTGTCGAAGAAAGACA
              |  |   | |  || | | ||   ||||  |  | || || || |    |||| ||   |||| || | |  ||||  | |    |||||||| | ||||| || ||  | |||||||||||  |  ||||||| || ||||||||||| || ||||| ||||||||||| |||||  | || |||||||| |
gtacaaaacagccagatgcgcagtgcctattgttgttgttgtaatggtgtgatgcttattgttactgttttcaatttaattacctgtgttcattt---cttgagcagCTGGAGAAGCATGAATTGCTTGAGATGAGGAGGATTGCTGCCTACATTTACAAGAAGGCTGGCAGGTGGAAGCAATCCATTGCTCTATCAAAGAAAGATA

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 26
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 25
gtggagtataat--ttctttaggtgcaattgtttttctttgtggttctatgca-ctggttgatttcataagccttgttggtatgtgtttgagcagATTGAGAAACACGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAAGCAGGCAGATGGAAGCAATCAATTGCATTGTCGAAGAAAGACA
|| |  |  | |  ||||| | ||   | | ||||||  | |  || || | | | | | ||||         || ||  ||| ||     ||||||||| || || |||||||||||||||||||||||||||||||||||||||||||| ||||| ||||||||||| || ||||| ||||| ||||| || |
gttggctgcattcattcttcatgt-tgactatttttcagt-taattataggaaaccgatagatta--------ttattattatctgga-atgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAGGCAGGTAGATGGAAGCAGTCCATTGCCTTGTCAAAGAAGGATA

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 26
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 26
gtggagtataatttctttaggtgcaattgtttttctttgtggttctatgcactggttgatttcataagccttgttggtatgtgtttga-gcagATTGAGAAACACGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAAGCAGGCAGATGGAAGCAATCAATTGCATTGTCGAAGAAAGACA
|||  | |   |    |||  || || | ||||| |     ||| ||      |    || |||  |   ||  |  ||  ||| ||| ||||||||| || || |||||||||||||||||||||||||||||||||||||||||||| ||||| || |||||||| || ||||| ||||| ||||| || |
gtgtggaaatttgctcttaattggaactattttttt-----gttttagttgtgga--aatctca-gattattactattac-tgtatgatgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAGGCAGGTAGGTGGAAGCAGTCTATTGCTTTGTCAAAGAAGGATA

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 26
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 26
gtggagtataatttctttaggtgcaattgtttttctttgtggttctatgcactggttgatttcataagccttgttggtatgtgtttgagcagATTGAGAAACACGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAAGCAGGCAGATGGAAGCAATCAATTGCATTGTCGAAGAAAGACA
|||  | |   |    |||  || || | |||||     |||||  | ||  |||   || |||  |   |||||  ||  ||| |  ||||||||| || || |||||||||||||||||||||||||||||||||||||||||||| ||||| || |||||||| || ||||| ||||| ||||| || |
gtgtggaaatttgctcttaattggaactattttt-----tggtttca-gctgtgga-aatctca-gattattgttattac-tgtatacgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAGGCAGGTAGGTGGAAGCAGTCTATTGCTTTGTCAAAGAAGGATA

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 26
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 25
gtggagtataatttctttaggtgcaattgtttttctttgtggttctatgcactggttgatttcataagccttgttggt-atg--tgtttga---gcagATTGAGAAACACGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAAGCAGGCAGATGGAAGCAATCAATTGCATTGTCGAAGAAAGACA
                |||| |||| || || ||| |  ||  | | |   | | |  |||  |  |  |  || | | ||   | ||||    ||||||||| || || ||||||||||||||||||||||| |||||||||||||||||||| ||||| |||||||| || || ||||| ||||| |||||||| |
---------------gttagctgcatttattcttcatgttgactattttt-cagttcaattataggaaaccagtggattattattatttggaatgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTCGCTGCTTATATTTACAAGAAGGCAGGTAGATGGAAACAGTCCATTGCCTTGTCAAAGAAAGATA

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 26
lower sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 26
gtggagtataatttctttaggtgcaattgtttttctttgtggttctatgcactggttgatttcataagccttgttggtatgtgtttgagcagATTGAGAAACACGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAAGCAGGCAGATGGAAGCAATCAATTGCATTGTCGAAGAAAGACA
|||  | |   |    |||  || || | |||||     |||||  | ||  |||   || |||  |   |||||  ||  ||| |  ||||||||| || || ||||||||||||||||||||||||||||||||||||||||||||                                            
gtgtggaaatttgctcttaattggaactattttt-----tggtttca-gctgtgga-aatctca-gattattgttattac-tgtatacgcagATTGAAAAGCATGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAG-------------------------------------------

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 26
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 26
gtggagtataatttctttagg--tgcaattgtttttctttgtggttctatgcactggttgatttcata--------agccttgttggtatgtgtttgagcagATTGAGAAACACGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAAGCAGGCAGATGGAAGCAATCAATTGCATTGTCGAAGAAAGACA
||  |||  || |    ||    |  |||  ||| ||| | |     |    |  |  ||   | | |        |  |||  ||  |   ||  || ||||| ||||||||||| ||| |||| ||||||||||| ||||||||||| ||||||||||| |||||||||||||||||||||||||| || ||||||||||
gtaaagttcaaatatactacccctttaatattttctctctttaaaaatggaaaaagaatggccttagagatgatataatcttcctgtgaatggtgcgaacagATCGAGAAACACGAACTTGTTGAAATGAGACGTGTGGCTGCTTATATCTACAAGAAAGCGGGCAGATGGAAGCAATCAATTGCATTATCAAAGAAAGACA

upper sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 26
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 26
gtg-gagtataatttctttaggtgcaattgtttttctttgtggttctatgcactggttgatttcataagccttgttggtatgtgtttgagcagATTGAGAAACACGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAAGCAGGCAGATGGAAGCAATCAATTGCATTGTCGAAGAAAGACA
||  |||| ||| |   |     |        ||| | | |     ||   |||  || ||         | |  ||| |||      |  |||||||||||||||||||| |||| ||||||||||| ||||||||||| || |||||||| || |||||||||||||| ||||| ||||| |||||||| |
gtaagagtttaaatctatctatcgagtacacatttatatttccccttaaatactaatttat---------cgttatgggatggtgcgaaatagATTGAGAAACACGAGCTTGTTGAAATGAGACGTGTGGCTGCTTATATCTATAAGAAAGCTGGTAGATGGAAGCAATCGATTGCTTTGTCAAAGAAAGATA

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|71858842|gb|DT007897.1|DT007897
EST:     AATCAATTGATATGCATGATAACTTTGATCAGATTGGCCTTGCACAGAAG                         ATTGAGAAACACGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTAC
genomic: AATCAATTGATATGCATGATAACTTTGATCAGATTGGCCTTGCACAGAAGgtggagtata ... gtttgagcagATTGAGAAACACGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTAC
EST: gi|71857909|gb|DT006964.1|DT006964
EST:     AATCAATTGATATGCATGATAACTTTGATCAGATTGGCCTTGCACAGAAG                         ATTGAGAAACACGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTAC
genomic: AATCAATTGATATGCATGATAACTTTGATCAGATTGGCCTTGCACAGAAGgtggagtata ... gtttgagcagATTGAGAAACACGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTAC
EST: gi|71888995|gb|DT038050.1|DT038050
EST:     AATCAATTGATATGCATGATAACTTTGATCAGATTGGCCTTGCACAGAAG                         ATTGAGAAACACGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTAC
genomic: AATCAATTGATATGCATGATAACTTTGATCAGATTGGCCTTGCACAGAAGgtggagtata ... gtttgagcagATTGAGAAACACGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTAC
EST: gi|33402568|gb|CF208195.1|CF208195
EST:     AATCAATTGATATGCATGATAACTTTGATCAGATTGGCCTTGCACAGAAG                         ATTGAGAAACACGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTAC
genomic: AATCAATTGATATGCATGATAACTTTGATCAGATTGGCCTTGCACAGAAGgtggagtata ... gtttgagcagATTGAGAAACACGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTAC
EST: gi|30132054|gb|CB917393.1|CB917393
EST:     AATCAATTGATATGCATGATAACTTTGATCAGATTGGCCTTGCACAGAAG                         ATTGAGAAACACGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATA
genomic: AATCAATTGATATGCATGATAACTTTGATCAGATTGGCCTTGCACAGAAGgtggagtata ... gtttgagcagATTGAGAAACACGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATA
EST: gi|30132996|gb|CB918335.1|CB918335
EST:     AATCAATTGATATGCATGATAACTTTGATCAGATTGGCCTTGCACAGAAG                         ATTGAGAAACACGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTAC
genomic: AATCAATTGATATGCATGATAACTTTGATCAGATTGGCCTTGCACAGAAGgtggagtata ... gtttgagcagATTGAGAAACACGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtggttctatgcactggttgatttcataagccttgttggtatgtgtttgagcagATTGAGAAACACGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAAGCAGGCAGATGGAAGCAATCAATTGCATTGTCGAAGAAAGACA
                ggttgat  putative branch site (score: 5)
                     atttcataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggagtataatttctttaggtgcaattgtttttctttgtggttctatgcactggttgatttcataagccttgttggtatgtgtttgagcagATTGAGAAACACGAGCTTCTTGAGATGAGACGTGTTGCTGCTTATATTTACAAGAAAGCAGGCAGATGGAAGCAATCAATTGCATTGTCGAAGAAAGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA