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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acacccacccactcacagacatgggaaaaatgtttaatgtgttggttctttggaattatttcctagactagtaccaaactgacacctctgtctcatccagTTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAG

Basic information

species Vitis vinifera
transcript Vv17s0000g06230.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g06230.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os09g24650.3 (Oryza sativa), 3'ss of exon 3
--acacccacccactcacagacatgggaaaaatgtttaatgtgttggttctttggaattatttcct-agactagtaccaaactgacacctctgtctcatccagTTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAG
   | ||       |   |   |     ||  |    ||| | | | | | | |  |     |    | | |  |   | | |   |  | |||   || |||| ||||||| ||   ||||| |||||||||||||||||||||||||||||||| || || || |||||| ||
gcgctcctgattttttttatgtaactataagtttccgaatttat-gatccctagataccgcatgtggatattgctcatacatttttagttttgtg--atacagTATGCTCATCGGGCTTGTGTGCAACGATGGTGCAATGAGAAAGGAGATGTAACGTGTGAAATTTGTCATGAG

upper sequence: Vv17s0000g06230.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g36740.3 (Oryza sativa), 3'ss of exon 1
acacccacccactcacagacatgggaaaaatgtttaatgtgttggttctttggaattatttcctaga---ctagtaccaaactgacacctctgtctcatccagTTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAG
  |   |  |  | |  ||  |        | |||| ||| ||  |  |||| |  |  |  ||| |   ||| |     |   |||    | | |  | ||||  ||||||||  ||||||| ||| ||||||||||||||||||||||  |||  || || ||||| ||   |
tgattgaatctgttaaggattttttttttgt-tttactgtatt--tcttttgtacgtcatgtctatatttctactttttgatctacaagattttattgtgcagTACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATAATCTGTGAAATCTGCCACGTG

upper sequence: Vv17s0000g06230.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G113619_T04 (Zea mays), 3'ss of exon 4
----acacccacccactcacagacatgggaaa-aatgtttaatgtgttggttctttggaattatttcctagactagtaccaaactgacacctctgtctcatccagTTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAG
    |||   | |   | | | | |||    |  || ||| ||| | |   | ||  ||    ||||     |    | |  | |   |  | | ||| || |||| |||||||||||  ||||| |||||||||||||||||||||||||||||||| || || || |||||| ||
tcagacaaaaatctgttaaaatagatgtaccatgattttttatgcgattacttttaaga----tttctatatcctccaactcagttttagttttttct-atgcagTATGCTCATAGGACTTGTGTACAACGATGGTGCAATGAGAAAGGAGATGTAACATGTGAAATATGTCATGAG

upper sequence: Vv17s0000g06230.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G118957_T04 (Zea mays), 3'ss of exon 3
acacccacccactcacagacatgggaaaaatgtt-taatgtgttggtt--ctttggaattatttcctagactagtaccaaactgacacctctgtctcatccagTTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAG
    | | |  || ||  |  |  |     ||   |  |||    |       | | || | |   |   ||| |       |  ||| | ||| |    |||| |||||| ||| ||||||| ||||| ||||||||||||||||||||| |||  || || ||||| ||| ||
--gtctaactgcttacctaagtttgtcttttgccatcctgtacgagccaagcattgcataaatctgtttgctaatttttttataccacatttgttt-gcacagTATGCTCACAGGGAATGTGTGCAACGTTGGTGCAATGAGAAAGGAGATATAATCTGTGAAATCTGCCATGAG

upper sequence: Vv17s0000g06230.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G156734_T01 (Zea mays), 3'ss of exon 1
--acacccacccactcacagacatgggaaaaatgtttaatgtgttggttctttggaattatttcctagactagtaccaaactgacacctctgtctcatccagTTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAG
    | || || ||  |      |     |    |    | |||     |  | | || | |   |   ||| |       |   || ||||| ||   |||| |||||| ||  ||||||| ||||||||||||||||||||||| |||  ||  || || ||||| ||| ||
gtctaaccgcctacctaagtttgtcttttac-catcctgtatgtgcaaaccattgcataaatctgtttgctaattttgttatactacatctgt-tcgcacagTATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAG

upper sequence: Vv17s0000g06230.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G20860.2 (Glycine max), 3'ss of exon 2
-acacccacccactcacagacatgggaaaaatgtttaatgtgttggttctttggaattatttcctagactagtacca-aactgacacctctgtctcatccagTTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAG
  |||    | | |   |  | ||        ||| | | |  |  || |      |       | ||| | | | | ||  |     ||| | |   |||||||||||||| |||||||||||||  ||||||| | ||||| || |||  || ||| ||||||||  |||||
gtcacttgactattatta--cttgatctcccggttcactctcgtcattgtaaactctgcccaatttgacaattgcaataataggggtttctttttataccagTTTGCTCATACGAAATGTGTTCAAATATGGTGCTACGAGAAGGGTGATACAATTTGTGAGATCTGCAATCAG

upper sequence: Vv17s0000g06230.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G33580.2 (Glycine max), 3'ss of exon 2
----acacccacccactcacagacatgggaaaaatgtttaatgtgttggttctttggaattatttcctagactagtacca-aactgacacctctgtctcatccagTTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAG
    ||| |         | | | ||       || | | || |||||||   |||  | |||| | | ||| | | | | ||  |     ||| | |   |||||||||||||| ||||||| |||||| ||||||| | ||||| || |||  || ||| || |||||  || ||
actaacaacaggtattctataaa-atattttggatttattat-tgttggtcacttg--actattgctt-gacaattgcaataataggggtttctttttataccagTTTGCTCATACGAAATGTATTCAACTATGGTGCTACGAGAAGGGTGATACAATTTGTGAAATCTGCAATAAG

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|161711392|gb|FC059127.1|FC059127
EST:     ATAGCATCAAGAATTTGGAGGTACCTTGTGCTTGCAGTGGCAGTTTGAAG                         TTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTA
genomic: ATAGCATCAAGAATTTGGAGGTACCTTGTGCTTGCAGTGGCAGTTTGAAGgtaatttccc ... tctcatccagTTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTA
EST: gi|161714671|gb|FC062664.1|FC062664
EST:     ATAGCATCAAGAATTTGGAGGTACCTTGTGCTTGCAGTGGCAGTTTGAAG                         TTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTA
genomic: ATAGCATCAAGAATTTGGAGGTACCTTGTGCTTGCAGTGGCAGTTTGAAGgtaatttccc ... tctcatccagTTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTA
EST: gi|294966509|gb|GW837644.1|GW837644
EST:     ATAGCATCAAGAATTTGGAGATACCTTGTGCTTGCAGTGGCAGTTTGAAG                         TTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTA
genomic: ATAGCATCAAGAATTTGGAGGTACCTTGTGCTTGCAGTGGCAGTTTGAAGgtaatttccc ... tctcatccagTTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTA
EST: gi|71869497|gb|DT018552.1|DT018552
EST:     ATAGCATCAAGAATTTGGAGGTACCTTGTGCTTGCAGTGGCAGTTTGAAG                         TTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTA
genomic: ATAGCATCAAGAATTTGGAGGTACCTTGTGCTTGCAGTGGCAGTTTGAAGgtaatttccc ... tctcatccagTTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTA
EST: gi|110685783|gb|EE062815.1|EE062815
EST:     ATAGCATCAAGAATTTGGAGGTACCTTGTGCTTGCAGTGGCAGTTTGAAG                         TTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTA
genomic: ATAGCATCAAGAATTTGGAGGTACCTTGTGCTTGCAGTGGCAGTTTGAAGgtaatttccc ... tctcatccagTTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTA
EST: gi|32248014|gb|CD713833.1|CD713833
EST:     ATAGCATCAAGAATTTGGAGGTACCTTGTGCTTGCAGTGGCAGTTTGAAG                         TTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTA
genomic: ATAGCATCAAGAATTTGGAGGTACCTTGTGCTTGCAGTGGCAGTTTGAAGgtaatttccc ... tctcatccagTTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTA
EST: gi|294965360|gb|GW837075.1|GW837075
EST:     ATAGCATCAAGAATTTGGAGGTACCTTGTGCTTGCAGTGGCAGTTTGAAG                         TTTGCTCATAGGAAATGTGTTCAACGATGGTCCAATGAGAAAGGAGATGTA
genomic: ATAGCATCAAGAATTTGGAGGTACCTTGTGCTTGCAGTGGCAGTTTGAAGgtaatttccc ... tctcatccagTTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTA
EST: gi|110417057|gb|EC983083.1|EC983083
EST:     ATAGCATCAAGAATTTGGAGGTACCTTGTGCTTGCAGTGGCAGTTTGAAG                         TTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTA
genomic: ATAGCATCAAGAATTTGGAGGTACCTTGTGCTTGCAGTGGCAGTTTGAAGgtaatttccc ... tctcatccagTTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTA
EST: gi|161712599|gb|FC062201.1|FC062201
EST:     ATAGCATCAAGAATTTGGAGGTACCTTGTGCTTGCAGTGGCAGTTTGAAG                         TTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTA
genomic: ATAGCATCAAGAATTTGGAGGTACCTTGTGCTTGCAGTGGCAGTTTGAAGgtaatttccc ... tctcatccagTTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTA
EST: gi|110376460|gb|EC941525.1|EC941525
EST:     ATAGCATCAAGAATTTGGAGGTACCTTGTGCTTGCAGTGGCAGTTTGAAG                         TTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTA
genomic: ATAGCATCAAGAATTTGGAGGTACCTTGTGCTTGCAGTGGCAGTTTGAAGgtaatttccc ... tctcatccagTTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTA
EST: gi|110712693|gb|EE087960.1|EE087960
EST:     ATAGCATCAAGAATTTGGAGATACCTTGTGCTTGCAGTGGCAGTTTGAAG                         TTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTA
genomic: ATAGCATCAAGAATTTGGAGGTACCTTGTGCTTGCAGTGGCAGTTTGAAGgtaatttccc ... tctcatccagTTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTA
EST: gi|110718657|gb|EE095738.1|EE095738
EST:     ATAGCATCAAGAATTTGGAGATACCTTGTGCTTGCAGTGGCAGTTTGAAG                         TTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTA
genomic: ATAGCATCAAGAATTTGGAGGTACCTTGTGCTTGCAGTGGCAGTTTGAAGgtaatttccc ... tctcatccagTTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTA
EST: gi|110686225|gb|EE063635.1|EE063635
EST:     ATAGCATCAAGAATTTGGAGATACCTTGTGCTTGCAGTGGCAGTTTGAAG                         TTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTA
genomic: ATAGCATCAAGAATTTGGAGGTACCTTGTGCTTGCAGTGGCAGTTTGAAGgtaatttccc ... tctcatccagTTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTA
EST: gi|110695017|gb|EE072554.1|EE072554
EST:     ATAGCATCAAGAATTTGGAGGTACCTTGTGCTTGCAGTGGCAGTTTGAAG                         TTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTA
genomic: ATAGCATCAAGAATTTGGAGGTACCTTGTGCTTGCAGTGGCAGTTTGAAGgtaatttccc ... tctcatccagTTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTA
EST: gi|161711275|gb|FC060363.1|FC060363
EST:     ATAGCATCAAGAATTTGGAGGTACCTTGTGCTTGCAGTGGCAGTTTGAAG                         TTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTA
genomic: ATAGCATCAAGAATTTGGAGGTACCTTGTGCTTGCAGTGGCAGTTTGAAGgtaatttccc ... tctcatccagTTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctttggaattatttcctagactagtaccaaactgacacctctgtctcatccagTTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAG
                               aactgac  putative branch site (score: 2)
                                       cctctgtctcatcc  CT-rich tract
        aattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acacccacccactcacagacatgggaaaaatgtttaatgtgttggttctttggaattatttcctagactagtaccaaactgacacctctgtctcatccagTTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- -cccaccc
- - - - - - -cacagac
- - - - - - - - - - - -ggaaaaa
- - - - - - - - - - - - - - - - - - - gtgttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaaact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacctct