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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAGgtatgatttgcttcttaattcctagccgttatctccaagtacatctcatttgtagttgcataaatgtttatatttgagatttatattaataggtaataca...

Basic information

species Vitis vinifera
transcript Vv17s0000g06230.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g06230.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os09g24650.4 (Oryza sativa), 5'ss of exon 3
TTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAGgtatgatttgcttcttaattcctagccgttatctccaagtacatctcatttgtagttgcataaatgtttatatttgagatttatattaataggtaataca
| ||||||| ||   ||||| |||||||||||||||||||||||||||||||| || || || |||||| ||||   ||||   |   |||   |   | ||   |||        | ||   | | |  | | ||| || |  | |  || | | |||| |          
TATGCTCATCGGGCTTGTGTGCAACGATGGTGCAATGAGAAAGGAGATGTAACGTGTGAAATTTGTCATGAGgtg-aatttatgttcaaatgattcatctttccttcct------ccacaggagcaat--cctgaat-ttgacctgttggaatgacattactgcag------

upper sequence: Vv17s0000g06230.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os02g36740.3 (Oryza sativa), 5'ss of exon 2
TTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAGgtatgatttgcttcttaattcctagccgttatctccaagtacatctcatttgtagttgcataaatgtttatatttgagatttatattaataggtaataca---
|  ||||||||  ||||||| ||| ||||||||||||||||||||||  |||  || || ||||| ||   |||| |   | |||      |      | || |  |  | |   |  | | | |      | |   ||  ||||  | |    ||  |||||| |    ||   
TACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATAATCTGTGAAATCTGCCACGTGgtaagtaattcttgcatgctttagttccttgtggcataatttgttccttctattcaacaacaggggtgaatatggggg---catcctaatagttggctcactc

upper sequence: Vv17s0000g06230.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G113619_T04 (Zea mays), 5'ss of exon 5
TTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAGgtatgatttgcttcttaattcctagccgttatctccaagtacatctcatttgtagttgcataaatgtttatatttgagatttatattaataggtaataca
| |||||||||||  ||||| |||||||||||||||||||||||||||||||| || || || |||||| ||||    ||   || | |      | | |||||  |||| | ||        ||   | | ||||| ||  |     | |  | | |  |           
TATGCTCATAGGACTTGTGTACAACGATGGTGCAATGAGAAAGGAGATGTAACATGTGAAATATGTCATGAGgtgattttgagttatgagcaaagaactgttatg-ccaatttcacaatgacagttaatac-taaattttgttgaaaaaaaactttctgcag----------

upper sequence: Vv17s0000g06230.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G118957_T04 (Zea mays), 5'ss of exon 4
TTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAGgta-tgatttgcttctt--aattcctagccgttatctccaagtacatctcatttgtagttgcataaatgtttatatttgagatttatattaataggtaataca
| |||||| ||| ||||||| ||||| ||||||||||||||||||||| |||  || || ||||| ||| |||||   | ||| ||| |  || | |||  |   |  |   |  |  | |  ||| | |    |       |    |    | |  | ||  || | |||    
TATGCTCACAGGGAATGTGTGCAACGTTGGTGCAATGAGAAAGGAGATATAATCTGTGAAATCTGCCATGAGgtaaccaattgtttccttcaactactactccaaacgtagcaaaatgtattgttt-tggcgaaagggcctctagcgtaatggttaaaaatgtattgttaagg--

upper sequence: Vv17s0000g06230.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G156734_T01 (Zea mays), 5'ss of exon 2
TTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAGgtatg-atttgcttcttaattcctagccgttatctccaagtacatctcatttgtagttgcataaatgtttatatttgagatttatatt--aataggtaataca----
| |||||| ||  ||||||| ||||||||||||||||||||||| |||  ||  || || ||||| ||| |||||   | ||| ||| |       |||   || ||| || || |||  | | | | ||  ||  |||      ||||  |||| |  |  |||| |   || |    
TATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAGgtaaacaattgtttcct-----tcagctacta-ctctaaatatatcaaaatggaaatta-atgcatgcactgttttgtaatttcttgtataataagacttaaagatt

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|161714671|gb|FC062664.1|FC062664
EST:     AACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAG                         CCTTATCAACCTGGCTATACTGCTCCACCACCTCCTCCACAGTCTGAGGAT
genomic: AACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAGgtatgatttg ... taatttgcagCCTTATCAACCTGGCTATACTGCTCCACC---TCCTCCACAGTCTGAGGAT
EST: gi|294966509|gb|GW837644.1|GW837644
EST:     AACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAG                         CCTCATCAACCTGGCTATACTGCTCCACCACCTCCTCCACAGTCCGAGGAT
genomic: AACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAGgtatgatttg ... taatttgcagCCTTATCAACCTGGCTATACTGCTCCACC---TCCTCCACAGTCTGAGGAT
EST: gi|71869497|gb|DT018552.1|DT018552
EST:     AACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAG                         CCTTATCAACCTGGCTATACTGCTCCACCACCTCCTCCACAGTCTGAGGAT
genomic: AACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAGgtatgatttg ... taatttgcagCCTTATCAACCTGGCTATACTGCTCCACC---TCCTCCACAGTCTGAGGAT
EST: gi|110685783|gb|EE062815.1|EE062815
EST:     AACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAG                         CCTTATCAACCTGGCTATACTGCTCCACCTCCTCCACAGTCTGAGGATGCT
genomic: AACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAGgtatgatttg ... taatttgcagCCTTATCAACCTGGCTATACTGCTCCACCTCCTCCACAGTCTGAGGATGCT
EST: gi|32248014|gb|CD713833.1|CD713833
EST:     AACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAG                         CCTTATCAACCTGGCTATACTGCTCCACCTCCTCCACAGTCTGAGGATGCT
genomic: AACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAGgtatgatttg ... taatttgcagCCTTATCAACCTGGCTATACTGCTCCACCTCCTCCACAGTCTGAGGATGCT
EST: gi|294965360|gb|GW837075.1|GW837075
EST:     AACGATGGTCCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAG                         CCTTATCAACCTGGCTATACTGCTCCAACTCCTCCACAGTCTGAGGATGCT
genomic: AACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAGgtatgatttg ... taatttgcagCCTTATCAACCTGGCTATACTGCTCCACCTCCTCCACAGTCTGAGGATGCT
EST: gi|110417057|gb|EC983083.1|EC983083
EST:     AACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAG                         CCTTATCAACCTGGCTATACTGCTCCACCTCCTCCACAGTCTGAGGATGCT
genomic: AACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAGgtatgatttg ... taatttgcagCCTTATCAACCTGGCTATACTGCTCCACCTCCTCCACAGTCTGAGGATGCT
EST: gi|161712599|gb|FC062201.1|FC062201
EST:     AACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAG                         CCTTATCAACCTGGCTATACTGCTCCACCACCTCCTCCACAGTCTGAGGAT
genomic: AACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAGgtatgatttg ... taatttgcagCCTTATCAACCTGGCTATACTGCTCCACC---TCCTCCACAGTCTGAGGAT
EST: gi|110376460|gb|EC941525.1|EC941525
EST:     AACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAG                         CCTTATCAACCTGGCTATACTGCTCCACCTCCTCCACAGTCTGAGGATGCT
genomic: AACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAGgtatgatttg ... taatttgcagCCTTATCAACCTGGCTATACTGCTCCACCTCCTCCACAGTCTGAGGATGCT
EST: gi|110400334|gb|EC966892.1|EC966892
EST:     ATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAG                         CCTTATCAACCTGGCTATACTGCTCCACCACCTCCTCCACAGTCTGAGGAT
genomic: ATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAGgtatgatttg ... taatttgcagCCTTATCAACCTGGCTATACTGCT---CCACCTCCTCCACAGTCTGAGGAT
EST: gi|110712693|gb|EE087960.1|EE087960
EST:     AACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAG                         CCTTATCAACCTGGCTATACTGCTCCACCACCTCCTCCACAGTCCGAGGAT
genomic: AACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAGgtatgatttg ... taatttgcagCCTTATCAACCTGGCTATACTGCTCCACC---TCCTCCACAGTCTGAGGAT
EST: gi|110718657|gb|EE095738.1|EE095738
EST:     AACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAG                         CCTTATCAACCTGGCTATACTGCTCCACCACCTCCTCCACAGTCCGAGGAT
genomic: AACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAGgtatgatttg ... taatttgcagCCTTATCAACCTGGCTATACTGCTCCACC---TCCTCCACAGTCTGAGGAT
EST: gi|110686225|gb|EE063635.1|EE063635
EST:     AACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAG                         CCTTATCAACCTGGCTATACTGCTCCACCACCTCCTCCACAGTCCGAGGAT
genomic: AACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAGgtatgatttg ... taatttgcagCCTTATCAACCTGGCTATACTGCTCCACC---TCCTCCACAGTCTGAGGAT
EST: gi|110695017|gb|EE072554.1|EE072554
EST:     AACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAG                         CCTTATCAACCTGGCTATACTGCTCCACCTCCTCCACAGTCTGAGGATGCT
genomic: AACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAGgtatgatttg ... taatttgcagCCTTATCAACCTGGCTATACTGCTCCACCTCCTCCACAGTCTGAGGATGCT
EST: gi|161711275|gb|FC060363.1|FC060363
EST:     AACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAG                         CCTTATCAACCTGGCTATACTGCTCCACCTCCTCCACAGTCTGAGGATGCT
genomic: AACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAGgtatgatttg ... taatttgcagCCTTATCAACCTGGCTATACTGCTCCACCTCCTCCACAGTCTGAGGATGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGCTCATAGGAAATGTGTTCAACGATGGTGCAATGAGAAAGGAGATGTAACTTGCGAGATCTGTCATCAGgtatgatttgcttcttaattcctagccgttatctccaagtacatctcatttgtagttgcataaatgtttatatttgagatttatattaataggtaataca

- - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcataaa