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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtactattttatgcctagttccataatgcaattgtggagactctaatttgttagtaaagtttgttctttttctgacaagttcttctattgttttacagGAAACTCAAGAAGCTGAGATTAAGATGCTTAGGAAGAGTTTGACCTTTAAAGCAACGCCCATGCCAAGCTTCTATCAGGAACCCCCACCTCCTAAAGTGG

Basic information

species Vitis vinifera
transcript Vv04s0008g05480.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g05480.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os02g10690.1 (Oryza sativa), 3'ss of exon 6
gttgtactattttatgcctagttccataatgcaattgtggagactctaatttgttagtaaagtttgttctttttctgacaagttcttctattgttttacagGAAACTCAAGAAGCTGAGATTAAGATGCTTAGGAAGAGTTTGACCTTTAAAGCAACGCCCATGCCAAGCTTCTATCAGGAACCCCCACCTCCTAAAGTGG
||  || | |||||    |   |    ||||  |        |   |   |||   ||   |  || |  | ||      ||||  | |||  ||  |||||| ||| ||||||||||  | || ||||||||||||||||||| ||| || ||||| || ||||| |||||||| ||||||||  | ||||| || ||||
gtaatattgttttactttt--cttggaaatgttacccc----atcttgcattgcatgtgttgcctgctaatatt------agtttctttat-attgcacagGAGACTGAAGAAGCTGAACTCAAAATGCTTAGGAAGAGTTTGAACTTCAAGGCAACACCAATGCCCAGCTTCTACCAGGAACCAACTCCTCCAAAGGTGG

upper sequence: Vv04s0008g05480.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G090935_T01 (Zea mays), 3'ss of exon 5
gttgtactattttatgcctagttccataatgcaattgtggagactctaatttgttagtaaagtttgttctttttctgacaagttcttctattgttttacagGAAACTCAAGAAGCTGAGATTAAGATGCTTAGGAAGAGTTTGACCTTTAAAGCAACGCCCATGCCAAGCTTCTATCAGGAACCCCCACCTCCTAAAGTGG
   ||||  || | ||||   |||  |     |||  ||    ||   |    |   |    | ||||  |   |||| |  ||    ||   |   |||||||||| ||||||| ||  | || ||||| || |||||||||| ||| || ||||| || ||||||||||||||| |||||||  | |||   || || |
---gtacccttatttgccc--ttcttttggaaaatgatgc---cttccaacgatgcatcctttatgttgctca-ctgatatatttcggtaaaatgc-acagGAAACTGAAGAAGCAGAACTCAAAATGCTGAGAAAGAGTTTGAACTTCAAGGCAACACCAATGCCAAGCTTCTATAAGGAACCAACTCCTGTCAAGGTTG

upper sequence: Vv04s0008g05480.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA17G31990.1 (Glycine max), 3'ss of exon 7
gttgtactattttatgcctagttccataatgcaattgtggagactctaatttgttagt--aaagtttgttctttt-tctgacaagttcttctattgttttacagGAAACTCAAGAAGCTGAGATTAAGATGCTTAGGAAGAGTTTGACCTTTAAAGCAACGCCCATGCCAAGCTTCTATCAGGAACCCCCACCTCCTAAAGTGG
                         | ||| |  |  |    |  |||| |||| | |  | | ||| |  |||  ||     | |  |||     ||||| ||||||| |||||||| |||||||||||||||||||||||| |||  ||||||||||| || |||||||| || || ||||| ||  | ||| |||| | ||
----------------------gtgagaatact-tcatatctaggctaaattgtgaattgagaatttatcttttaatcatgtcaatcattcaccccttttatagGAAACCCAAGAAGCCGAGATTAAGATGCTTAGGAAGAGTCTGAATTTTAAAGCAACTCCAATGCCAAGTTTTTACCAGGAGCCTGCTCCTGCTAAGGCGG

upper sequence: Vv04s0008g05480.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA14G14400.2 (Glycine max), 3'ss of exon 6
gttgtactattttatgcctagttccataatgcaattgtggagactctaatttgttagtaaagtttgttctttttctgacaagttcttctattgttttacagGAAACTCAAGAAGCTGAGATTAAGATGCTTAGGAAGAGTTTGACCTTTAAAGCAACGCCCATGCCAAGCTTCTATCAGGAACCCCCACCTCCTAAAGTGG
||   | || || ||  || |  | | || |  |||   |||| | ||  ||  || | | ||                 | |  |||     ||||| |||| || |||||||| |||||||||||||||||||||||| |||  ||||||||||| || |||||||| || || ||||| ||  | ||| |||| | ||
gtgagagtacttgatatctggg-ctaaaacgtgattt--gagaatttatctt-ctaatcatgtc----------------aatcattcaccccttttatagGAGACCCAAGAAGCCGAGATTAAGATGCTTAGGAAGAGTCTGAATTTTAAAGCAACTCCAATGCCAAGTTTTTACCAGGAGCCTGCTCCTGCTAAGGCGG

upper sequence: Vv04s0008g05480.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA04G07100.1 (Glycine max), 3'ss of exon 7
gttgtactattttatgcctagttccataatgcaattgtggagactctaatttgttagtaaagtttgttctttttctgacaagttcttctattgttttacagGAAACTCAAGAAGCTGAGATTAAGATGCTTAGGAAGAGTTTGACCTTTAAAGCAACGCCCATGCCAAGCTTCTATCAGGAACCCCCACCTCCTAAAGTGG
||  || ||||| ||   |||    | |    |||||  || | |   ||||  |   |                   | |    |||   | ||||| |||| || |||||||||||||||||||||||| | || ||| |    ||||||||||| || |||||||||||||| ||||| || || |||||||  ||||
gtgataatatttgatatgtaggatgaaatgtaaattgcagatattgccatttaatcaca-------------------ccaacctttcaccttttttatagGAGACCCAAGAAGCTGAGATTAAGATGCTTCGAAAAAGTCTAGGATTTAAAGCAACTCCAATGCCAAGCTTCTACCAGGAGCCTCCTCCTCCTAGGGTGG

upper sequence: Vv04s0008g05480.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA06G07190.1 (Glycine max), 3'ss of exon 7
gttgtactattttatgcctagttccataatgcaattgtggagactctaatttgttagtaaagtttgttctttttctgacaagttcttctattgttttacagGAAACTCAAGAAGCTGAGATTAAGATGCTTAGGAAGAGTTTGACCTTTAAAGCAACGCCCATGCCAAGCTTCTATCAGGAACCCCCACCTCCTAAAGTGG
||  || ||||| ||  |||||      ||| |||           ||| |||    ||   || |   ||  ||  || |    |||   | ||||| |||| |  |||||||| ||||||||||||||||| || ||| |    ||||||||||| || |||||||||||||| ||||| || || |||||||  | ||
gtgataatatttgatatctagt------atgaaatg----------taacttgcagata---ttggcatttaatcacaccaacctttcaccttttttatagGAGAACCAAGAAGCCGAGATTAAGATGCTTAGAAAAAGTCTAGGATTTAAAGCAACTCCAATGCCAAGCTTCTACCAGGAGCCTCCTCCTCCTAGGGCGG

upper sequence: Vv04s0008g05480.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT2G25480.1 (Arabidopsis thaliana), 3'ss of exon 7
gttgtactattttatgcctagtt--ccataatgcaat-tgtggagactctaatttgttagtaaagtttgttctttttctgacaagttcttctattgt-tttacagGAAACTCAAGAAGCTGAGATTAAGATGCTTAGGAAGAGTTTGACCTTTAAAGCAACGCCCATGCCAAGCTTCTATCAGGAACCCCCACCTCCTAAAGTGG
|||||  | | |     || |||   | |||       | |      | |||  |||   ||  | |   |||| | |||  ||  || |||    |  || ||||||||||||||||||||| |||||||||| ||||||||| ||| ||| ||||| || || ||||| | ||||||||| ||||| |  |  ||||||   |
gttgtgttctatgccctcttgtttttcttaaaatgtcctattattcatttaaagtgtctatat-gctcagtcttctactgtaaatatcatctggaatacttgcagGAAACTCAAGAAGCTGAGCTTAAGATGCTAAGGAAGAGTCTGAACTTCAAAGCCACACCTATGCCTACCTTCTATCAAGAACCTCAGCTACCTAAAACAG

upper sequence: Vv04s0008g05480.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT4G32330.3 (Arabidopsis thaliana), 3'ss of exon 7
gttgtactattttatgcctagttccataatgcaattgtggagactctaatttgttagtaaagtttgttctttttctgacaagttcttctattgttttacagGAAACTCAAGAAGCTGAGATTAAGATGCTTAGGAAGAGTTTGACCTTTAAAGCAACGCCCATGCCAAGCTTCTATCAGGAACCCCCACCTCCTAAAGTGG
                  | ||  | ||   | |   ||   | | | ||    |    | | |||  ||  | |  |  |    |  |  | | |  |||||||| |||||||||||| ||| |||||| ||||||||||||| ||| ||||| || || ||||| ||||| ||||| ||||| |  || ||||||   |
-----------------gttgtctcctatacccaccctgtttattgtcatagtgtttagatgcttggcctcctccaaaacaaaattcttggtttctcgcagGAAACACAAGAAGCTGAGCTTAGGATGCTAAGGAAGAGTTTGAACTTCAAAGCCACACCTATGCCTAGCTTTTATCAAGAACCTCAGCCGCCTAAAACAG

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|34547172|gb|CF515404.1|CF515404
EST:     GAAATAGAGCGGACTAGCTTGCAAGCTAAGTCCAAG                         GAAACTCAAGAAGCTGAGATTAAGATGCTTAGGAAGAGTTTGACCTTTAAA
genomic: GAAATAGAGCGGACTAACTTGCAAGCTAAGTCCAAGgttgtactat ... tgttttacagGAAACTCAAGAAGCTGAGATTAAGATGCTTAGGAAGAGTTTGACCTTTAAA
EST: gi|110711956|gb|EE089029.1|EE089029
EST:     AGACTCATGCNAAGGAAATAGAGCGGACTAACTTGCAAGCTAAGTCCAAG                         GAAACTCAAGAAGCTGAGATTAAGATGCTTAGGAAGAGTTTGACCTTTAAA
genomic: AGACTCATGCAAAGGAAATAGAGCGGACTAACTTGCAAGCTAAGTCCAAGgttgtactat ... tgttttacagGAAACTCAAGAAGCTGAGATTAAGATGCTTAGGAAGAGTTTGACCTTTAAA
EST: gi|110732118|gb|EE107126.1|EE107126
EST:     AGACTCATGCAAAGGAAATAGAGCGGACTAACTTGCAAGCTAAGTCCAAG                         GAAACTCAAGAAGCTGAGATTAAGATGCTTAGGAAGAGTTTGACCTTTAAA
genomic: AGACTCATGCAAAGGAAATAGAGCGGACTAACTTGCAAGCTAAGTCCAAGgttgtactat ... tgttttacagGAAACTCAAGAAGCTGAGATTAAGATGCTTAGGAAGAGTTTGACCTTTAAA
EST: gi|37183656|gb|CF603010.1|CF603010
EST:     AGACTCATGCAAAGGAAATAGAGCGGACTAACTTGCAAGCTAAGTCCAAG                         GAAACTCAAGAAGCTGAGATTAAGATGCTTAGGAAGAGTTTGACCTTTAAA
genomic: AGACTCATGCAAAGGAAATAGAGCGGACTAACTTGCAAGCTAAGTCCAAGgttgtactat ... tgttttacagGAAACTCAAGAAGCTGAGATTAAGATGCTTAGGAAGAGTTTGACCTTTAAA
EST: gi|110372845|gb|EC937039.1|EC937039
EST:     AGACTCATGCAAAGGAAATAGAGCGGACTAACTTGCAAGCTAAGTCCAAG                         GAAACTCAAGAAGCTGAGATTAAGATGCTTAGGAAGAGTTTGACCTTTAAA
genomic: AGACTCATGCAAAGGAAATAGAGCGGACTAACTTGCAAGCTAAGTCCAAGgttgtactat ... tgttttacagGAAACTCAAGAAGCTGAGATTAAGATGCTTAGGAAGAGTTTGACCTTTAAA
EST: gi|110713754|gb|EE089952.1|EE089952
EST:     AGACTCATGCAAAGGAAATAGAGCGGACTGACTTGCAAGCTAAGTCCAAG                         GAAACTCAAGAAGCTGAGATTAAGATGCTTAGGAGGAGTTTGACCTTTTAA
genomic: AGACTCATGCAAAGGAAATAGAGCGGACTAACTTGCAAGCTAAGTCCAAGgttgtactat ... tgttttacagGAAACTCAAGAAGCTGAGATTAAGATGCTTAGGAAGAGTTTGACCTTT-AA
EST: gi|34547260|gb|CF515492.1|CF515492
EST:     GACTCATGCAAAGGAAATAGAGCGGACTAGCTTGCAAGCTAAGTCCAAG                         GAAACTCAAGAAGCTGAGATTAAGATGCTTAGGAAGAGTTTGACCTTTAAA
genomic: GACTCATGCAAAGGAAATAGAGCGGACTAACTTGCAAGCTAAGTCCAAGgttgtactat ... tgttttacagGAAACTCAAGAAGCTGAGATTAAGATGCTTAGGAAGAGTTTGACCTTTAAA
EST: gi|294964234|gb|GW838037.1|GW838037
EST:     GACTCATGGCAA-GGAAATAGAGCGGACTAACTTGCAAGCTAAGTCCAAG                         GAAACTCAAGAAGCTGA
genomic: GACTCATG-CAAAGGAAATAGAGCGGACTAACTTGCAAGCTAAGTCCAAGgttgtactat ... tgttttacagGAAACTCAAGAAGCTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatttgttagtaaagtttgttctttttctgacaagttcttctattgttttacagGAAACTCAAGAAGCTGAGATTAAGATGCTTAGGAAGAGTTTGACCTTTAAAGCAACGCCCATGCCAAGCTTCTATCAGGAACCCCCACCTCCTAAAGTGG
                          ttctgac  putative branch site (score: 2)
                                    ttcttctattgtttt  putative PPT
                                          tattgtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgtactattttatgcctagttccataatgcaattgtggagactctaatttgttagtaaagtttgttctttttctgacaagttcttctattgttttacagGAAACTCAAGAAGCTGAGATTAAGATGCTTAGGAAGAGTTTGACCTTTAAAGCAACGCCCATGCCAAGCTTCTATCAGGAACCCCCACCTCCTAAAGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT