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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATGCTCATAGGAAGTGTGTTCAACGATGGTGCAATGAGAAAGGAGACATAATTTGTGAGATCTGCCATCAGgtatactcgttattttttttcctttccactttctgtcctcaggaggctgcatatgtgctttttaaatcacatttcctttgatgggcccaaacctgcaagt...

Basic information

species Vitis vinifera
transcript Vv01s0026g02470.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0026g02470.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os02g36740.3 (Oryza sativa), 5'ss of exon 2
TATGCTCATAGGAAGTGTGTTCAACGATGGTGCAATGAGAAAGGAGACATAATTTGTGAGATCTGCCATCAGgta-----tactcgt-tattttttttcctttc--cactttctgtcctcaggaggctgcatatgtgctttttaaatcacatttcctttgatgggcccaaacctgcaagt
|| ||||||||  | ||||| ||| |||||||||||||||||||||||||||| ||||| ||||||||   ||||     | || |  |  |||  ||||||    ||   | ||| |     |  |  ||   | | |   ||        | |   |  | ||| ||  |        
TACGCTCATAGAGAATGTGTGCAAAGATGGTGCAATGAGAAAGGAGACATAATCTGTGAAATCTGCCACGTGgtaagtaattcttgcatgctttagttccttgtggcataatttgttccttctattcaacaacaggggtgaatatgggggcatcctaatagttggctcactc--------

upper sequence: Vv01s0026g02470.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os09g24650.4 (Oryza sativa), 5'ss of exon 3
TATGCTCATAGGAAGTGTGTTCAACGATGGTGCAATGAGAAAGGAGACATAATTTGTGAGATCTGCCATCAGgtatactcgttattttttttcctttccactttctgtcctcaggag----gctgcatatgtgctttttaaatcacatttcctttgatgggcccaaacctgcaagt
||||||||| ||   ||||| ||||||||||||||||||||||||||  |||  ||||| || || ||| ||||  | |  |  |    |      ||     |   ||| ||||||     ||| || ||  || ||  ||| ||||| |    |                    
TATGCTCATCGGGCTTGTGTGCAACGATGGTGCAATGAGAAAGGAGATGTAACGTGTGAAATTTGTCATGAGgtgaatttatgttcaaatgattcatctttccttcctccacaggagcaatcctgaatttgacctgttggaatgacattactgcag--------------------

upper sequence: Vv01s0026g02470.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os11g38800.1 (Oryza sativa), 5'ss of exon 3
TATGCTCATAGGAAGTGTGTTCAACGATGGTGCAATGAGAAAGGAGACATAATTTGTGAGATCTGCCATCAGgtatactcgttattttttttcctttccactttctgtcctcaggaggctg---catatgt-gctttttaaatcacatttcctttgatgggcccaaacctgcaagt
|||||||||||    ||||| ||||| ||||||||||||||||||||||| |  ||||| ||||| ||| ||||      | | | || | | ||   |  || ||   |   |    ||    | ||| | |    | | ||  ||  |  ||||||  |     | |       
TATGCTCATAGAGCTTGTGTGCAACGCTGGTGCAATGAGAAAGGAGACATTACATGTGAAATCTGTCATGAGgtcagtaagatttcttctctactactccattactacgcattgctttctagttcttatctagaggctaagatagcacctattttgatatgtgtgcatccaa----

upper sequence: Vv01s0026g02470.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G118957_T04 (Zea mays), 5'ss of exon 4
TATGCTCATAGGAAGTGTGTTCAACGATGGTGCAATGAGAAAGGAGACATAATTTGTGAGATCTGCCATCAGgtatactcgttattttttttcctttccactttctgtcctcaggaggctgcatatgtgctttttaaatcacatttcctttgatgggcccaaacctgcaagt----
|||||||| ||| | ||||| ||||| |||||||||||||||||||| ||||| ||||| ||||||||| ||||| ||   || |||  ||    | | |||  |    |  || |   || || |||  |    |||   | | |    | ||||    |||  |     |    
TATGCTCACAGGGAATGTGTGCAACGTTGGTGCAATGAGAAAGGAGATATAATCTGTGAAATCTGCCATGAGgta-accaattgtttccttcaactactact--ccaaacgtagcaaaatgtat-tgttttggcgaaagggcctctagcgtaatggttaaaaatgtattgttaagg

upper sequence: Vv01s0026g02470.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G113619_T04 (Zea mays), 5'ss of exon 5
TATGCTCATAGGAAGTGTGTTCAACGATGGTGCAATGAGAAAGGAGACATAATTTGTGAGATCTGCCATCAGgtatactcgttattttttttcctttccactttctgtcctcaggaggctgcatatgtgctttttaaatcacatttcctttgatgggcccaaacctgcaagt
|||||||||||||  ||||| ||||||||||||||||||||||||||  |||  ||||| || || ||| ||||    | |  | || |   |         || || |          | || |    |  || | |  | ||||  ||  |      |    |||||   
TATGCTCATAGGACTTGTGTACAACGATGGTGCAATGAGAAAGGAGATGTAACATGTGAAATATGTCATGAGgtgattttg--agttatgagcaaagaactgttatgcc-------aatttcacaatgacagttaatactaaattttgttgaaaaaaaactt-tctgcag--

upper sequence: Vv01s0026g02470.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G156734_T01 (Zea mays), 5'ss of exon 2
TATGCTCATAGGAAGTGTGTTCAACGATGGTGCAATGAGAAAGGAGACATAATTTGTGAGATCTGCCATCAGgtatactcgttattttttttcctttccactttc--tgtcctcaggaggctgcatatgtgctttttaaatcacatttcctttgatgggcccaaacctgcaagt-
|||||||| ||  | ||||| ||||||||||||||||||||||| || | ||| ||||| ||||||||| ||||| ||   || |||  ||    | | ||| |   | |    |   ||      |||       |   |   | || |||  ||      | || |  |  | 
TATGCTCACAGAGAATGTGTGCAACGATGGTGCAATGAGAAAGGGGATACAATCTGTGAAATCTGCCATGAGgtaaaca-attgtttccttcagctactactctaaatatatcaaaatggaaattaatgcatgcactgttttgtaatttcttgtataa--taagacttaaagatt

upper sequence: Vv01s0026g02470.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA07G35750.2 (Glycine max), 5'ss of exon 2
TATGCTCATAGGAAGTGTGTTCAACGATGGTGCAATGAGAAAGGAGACATAATTTGTGAGATCTGCCATCAGgtatactcgttattttttttcctttccactttctg---tcctcaggaggctgcatatgtgctttt---taaatcacatttcctttgatgggc-----ccaaacctgcaagt----------------------------------------------------------------------------------
||||||||||| ||||| ||||| || ||||||||||||||||||||||||||||||||||| || ||| ||||||  |  ||||   | |   |||    ||| ||   |     | |   |  || |||| |  |   || || |   |    | |    ||        |||  | |||                                                                                   
TATGCTCATAGAAAGTGCGTTCAGCGTTGGTGCAATGAGAAAGGAGACATAATTTGTGAGATATGTCATAAGgtatggttcttatacatgtgatttttacttttgtgaaatttatggtattttaaatttgtggtgatggttagataatgctaatatggtcatgcattgttttaactagtaagctttattgaacaattattttgttcaattgtgtgtctcagtggtgtgtactaaattctttcaattttatatatgtaattctcag

upper sequence: Vv01s0026g02470.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA20G04870.1 (Glycine max), 5'ss of exon 2
TATGCTCATAGGAAGTGTGTTCAACGATGGTGCAATGAGAAAGGAGACATAATTTGTGAGATCTGCCATCAGgtatactcgttattttttttcctttcc----------actttctgtcctcaggaggctgcat--atgtgcttttta-aatcacatttcctttgatgggcccaa----acctgcaagt--------------------------------------------------------------
||||||||||| ||||| ||||| || ||||||||||||||||||||||||| ||||||||| || ||  ||||||  |  || | | | |   ||||           | ||| |||  |  | |   ||     |||  ||  | |   | |   |||  ||  |  |  |||    | ||     |                                                              
TATGCTCATAGAAAGTGCGTTCAGCGTTGGTGCAATGAGAAAGGAGACATAACTTGTGAGATATGTCACAAGgtatgattcttttgtatgtgattttcgcatatagtgaaatttttgttatttgaaatttgtgatgatggtctggtcatggtaatgattcaattattctgtacaatggtatctctggattgaaccaaatgctctgtgtgtgtgtactgaatttctttcaattttgtatatgtaattctcag

upper sequence: Vv01s0026g02470.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA04G26830.1 (Glycine max), 5'ss of exon 2
TATGCTCATAGGAAGTGTGTTCAACGATGGTGCAATGAGAAAGGAGACATAATTTGTGAGATCTGCCATCAGgtatactcgtt-----attttttttcctttcc---actttctg-tcctcaggaggctgcatatgt-gctttttaaatca-catttcctttg-atgggcccaaacctgcaagt-------------------
|||||||| || |||||||| ||||  |||||  |||||||||||||||||| ||||||||| || ||||| |||| ||  ||     ||  ||||    ||||   ||||| || |  |    ||| |       | |    ||| || |   |||  |||| | | | | ||   |    ||                   
TATGCTCACAGAAAGTGTGTCCAACATTGGTGTGATGAGAAAGGAGACATAACTTGTGAGATATGTCATCATgtatgctttttgcacaatagttttcatattccggtactttttggttattgtaaggttatgaggataggaaattatataagtgtttattttgtaagtgtctaactttattggtttataatttggcgcatcag

upper sequence: Vv01s0026g02470.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA02G11960.1 (Glycine max), 5'ss of exon 3
TATGCTCATAGGAAGTGTGTTCAACGATGGTGCAATGAGAAAGGAGACATAATTTGTGAGATCTGCCATCAGgtatactcgttattttttttcctttccactttctgtcctcaggaggctgcatatgtgctttttaaatcacatttcctttgatgggcccaaacctgcaagt----
|||||||| || |||||||| || |  |||||  |||||||||||||||||| ||||||||| || |||||||||| ||  ||      |    ||   | || | || ||     |      || | | | |    ||   |  |  | | |  |     |   || ||||    
TATGCTCACAGAAAGTGTGTCCAGCATTGGTGTGATGAGAAAGGAGACATAACTTGTGAGATATGTCATCAGgtatgctttttgcacaatagttttcata-ttccggtactttttggttattgtaag-gttatgaggataggaaattatataagtgttt--attttgtaagtgtct

upper sequence: Vv01s0026g02470.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA01G05800.1 (Glycine max), 5'ss of exon 3
TATGCTCATAGGAAGTGTGTTCAACGATGGTGCAATGAGAAAGGAGACATAATTTGTGAGATCTGCCATCAGgtatactcgttat----tttttttcctttc----cactttctg-tcctcaggaggctgca--tatgtgctttttaaatcacatttcctttg-atgggcccaaacctgcaagt
|||||||| || |||||||| || |  |||||  |||||||||||||||||| ||||||||| || |||||||||| ||  || |    |  ||||| | |      ||||| || |  |    ||| |      ||| |   ||  |   || |||  |||| ||| | |             
TATGCTCACAGAAAGTGTGTCCAGCATTGGTGTGATGAGAAAGGAGACATAACTTGTGAGATATGTCATCAGgtatgctttttgtacaatagttttcatattacattactttttggttattgtaaggttatgatgatgggaaattatatgaacgtttattttgtatgtgtct------------

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|351030409|gb|FQ432347.1|FQ432347
EST:     AACGATGGTGCAATGAGAAAGGAGACATAATTTGTGAGATCTGCCATCAG                         CCTTACCAACCGGGCTACACTGCTCCTCCCCCACCACCTCATCCTGAAGAT
genomic: AACGATGGTGCAATGAGAAAGGAGACATAATTTGTGAGATCTGCCATCAGgtatactcgt ... tgatgcacagCCTTACCAACCGGGCTACACTGCTCCTCCCCCACCACCTCATCCTGAAGAT
EST: gi|110685836|gb|EE062903.1|EE062903
EST:     AACGATGGTGCAATGAGAAAGGAGACATAATTTGTGAGATCTGCCATCAG                         CCTTACCAACCGGGCTACACTGCTCCTCCCCCACCACCTCATCCTGAAGAT
genomic: AACGATGGTGCAATGAGAAAGGAGACATAATTTGTGAGATCTGCCATCAGgtatactcgt ... tgatgcacagCCTTACCAACCGGGCTACACTGCTCCTCCCCCACCACCTCATCCTGAAGAT
EST: gi|110689841|gb|EE066416.1|EE066416
EST:     AACGATGGTGCAATGAGAAAGGAGACATAATTTGTGAGATCTGCCATCAG                         CCTTACCAACCGGGCTACACTGCTCCTCCCCCACCACCTCATCCTGAAGAT
genomic: AACGATGGTGCAATGAGAAAGGAGACATAATTTGTGAGATCTGCCATCAGgtatactcgt ... tgatgcacagCCTTACCAACCGGGCTACACTGCTCCTCCCCCACCACCTCATCCTGAAGAT
EST: gi|110713173|gb|EE088860.1|EE088860
EST:     AACGATGGTGCAATGAGAAAGGAGACATAATTTGTGAGATCTGCCATCAG                         CCTTACCAACCGGGCTACACTGCTCCTCCCCCACCACCTCATCCTGAAGAT
genomic: AACGATGGTGCAATGAGAAAGGAGACATAATTTGTGAGATCTGCCATCAGgtatactcgt ... tgatgcacagCCTTACCAACCGGGCTACACTGCTCCTCCCCCACCACCTCATCCTGAAGAT
EST: gi|30298557|gb|CB975351.1|CB975351
EST:     AACGATGGTGCAATGAGAAAGGAGACATAATTTGTGAGATCTGCCATCAG                         CCTTACCAACCAGGCTACACTGCTCCTCCCCCACCACCTCATTCGGAAGAT
genomic: AACGATGGTGCAATGAGAAAGGAGACATAATTTGTGAGATCTGCCATCAGgtatactcgt ... tgatgcacagCCTTACCAACCGGGCTACACTGCTCCTCCCCCACCACCTCATCCTGAAGAT
EST: gi|110715491|gb|EE093604.1|EE093604
EST:     AACGATGGTGCAATGAGAAAGGAGACGTAATTTGTGAGATCTGCCATCAG                         CCTTACCAACCGGGCTACACTGCTCCTCCCCCACCACCTCATTCTGAAGAT
genomic: AACGATGGTGCAATGAGAAAGGAGACATAATTTGTGAGATCTGCCATCAGgtatactcgt ... tgatgcacagCCTTACCAACCGGGCTACACTGCTCCTCCCCCACCACCTCATCCTGAAGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATGCTCATAGGAAGTGTGTTCAACGATGGTGCAATGAGAAAGGAGACATAATTTGTGAGATCTGCCATCAGgtatactcgttattttttttcctttccactttctgtcctcaggaggctgcatatgtgctttttaaatcacatttcctttgatgggcccaaacctgcaagt

- - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaatcaca