Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccgataatcatcttgacttgggttttgtcatcatttgattgctctttctgcattcttttaatgaatgttccatcctgatgtcattgaactctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCTATGCCCAAAATGCTCATCGATGGTGCTGTTGAGTATGAAGATGGTACCC

Basic information

species Vitis vinifera
transcript Vv09s0002g05950.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g05950.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os05g23620.1 (Oryza sativa), 3'ss of exon 6
ccgataatcatcttgacttgggttttgtcatcatttgattgctctttctgcattcttttaatgaatgttccatcctgatg---tcattga---actctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCTATGCCCAAAATGCTCATCGATGGTGCTGTTGAGTATGAAGATGGTACCC
    | ||  |  |  ||    |||| |||  |  || |||   | | |   ||  |||    | ||| | |   |  |    ||  ||    | |  |  | ||||| || || ||  |||| || ||||| || ||||||||||| || |||||||||||||| ||||| || ||||| |||||||| |||||||||||||| |
---gttatttttctagctgtaatttt-tca--agctggttgtgttctgttatttgctttctgcagtgtgcaacattagtaaactctctggttgatttgtattctagATCCGTGAGGGTTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCTATGCCCAAGATGCTTATAGATGGAGCTGTTGAATATGAAGATGGTACTC

upper sequence: Vv09s0002g05950.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g70960.1 (Oryza sativa), 3'ss of exon 5
ccgataatcatcttgacttgggttttgtca-tcatttgattgctctttctgcattcttttaatgaatgttccatcctgatgtcattgaactctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCTATGCCCAAAATGCTCATCGATGGTGCTGTTGAGTATGAAGATGGTACCC
  |      |   ||  |  | | |||| | || |   | ||| ||  ||  |||   ||    | ||| | | |||  || | ||||  |     | |||||||| || ||  |||| || ||||| || ||||||||||| || ||||| |||||||| ||||| || ||||| || || |||||||||||||| || |
ttgcctgctaaagtgcttctgttattgttactcctcctagtgcactccctaaatttgcttttgcagtgtcctaaccttctggcgttgatttgaaatt-tagATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTTATTGATGGAGCAGTCGAGTATGAAGATGGCACTC

upper sequence: Vv09s0002g05950.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G032367_T01 (Zea mays), 3'ss of exon 5
---ccgata-atcatcttgacttgggttttgtcatcatttgattgctctttctgcattcttttaatgaatgttccatcctgatgtcattgaactctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCTATGCCCAAAATGCTCATCGATGGTGCTGTTGAGTATGAAGATGGTACCC
     |||  || |||||  | |    |||  | |  |||  |   |   | | |  ||||  ||  || | |  |      ||   |||| || | ||  |||||||| || || |||||||| || || || ||||||||||| || ||||| |||||||| |||||||  ||||| |||||||||||||| |||||||| |
ttaaggatgtattatcttt-catactcttttccttttttttgtgtttgcctttactatcttacaagtaacgataaaaaacattg--gttgatctgtatcc-tagATTCGTGAGGGTCTGCACTACAACCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTCAATGATGGAGCTGTTGAGTATGAGGATGGTACTC

upper sequence: Vv09s0002g05950.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G158479_T04 (Zea mays), 3'ss of exon 5
----ccgataatcatcttgacttgggttttgtcatcatttga-ttgctctttctgcattcttttaatgaatgttccatcctgatgtcattgaactctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCTATGCCCAAAATGCTCATCGATGGTGCTGTTGAGTATGAAGATGGTACCC
     | |   ||| ||||  |||    |||||  | ||  |        |  ||   |||  |||| ||    ||||    |  |   |  | |       |||||||| || || |||||||| ||||| || ||||||||||| || ||||| ||||| || ||||| |  ||||| |||||||||||||| |||||||| |
gcataccaaggtcaccttggtttg--ccttgtcgcctttgaaaccatggctcttgttatctcgtaatcaaa---ccataaaaactttggtttatttgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCGAAGATGCTTAATGATGGAGCTGTTGAGTATGAGGATGGTACAC

upper sequence: Vv09s0002g05950.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA19G22530.2 (Glycine max), 3'ss of exon 5
-ccgataatcatcttgacttgggttttgtcatcatttgattgctctttctgcatt---cttttaatgaatgttccatcctgatgtcattgaactctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCTATGCCCAAAATGCTCATCGATGGTGCTGTTGAGTATGAAGATGGTACCC
     |||| ||  |  ||    |||    |    |  |    |||   |  |||   |||  | ||||  || |       | |  || ||     |  ||||||| |||| || |||||||||||||||||||| ||||||||||| || |||||||| |||||||| |  ||||| |||||||| ||||||||||||||||
gaacttaattatactttctcaactttc--taattctcaacaaatctaaatatattgcacttaaagtgaaaatttcgattgtttttttttaaaaaaaat--gtagATTAGAGAAGGACTGCACTATAATCCTTATTTTCCTGGTGGGGCTATTGCTATGCCTAAAATGCTTAATGATGGCGCTGTTGAATATGAAGATGGTACCC

upper sequence: Vv09s0002g05950.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G07020.1 (Glycine max), 3'ss of exon 5
ccgataatcatcttgacttgggttttgtcatcatttgattgctctttctgcatt---cttttaatgaatgttccatcctgatgtcattgaactctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCTATGCCCAAAATGCTCATCGATGGTGCTGTTGAGTATGAAGATGGTACCC
    |||| ||  |  ||    |||    |    |  |    |||   |  |||   |||  | ||||  ||      |   ||  |  || |  |  |||||||| |||| || |||||||||||||||||||| ||||| ||||| || |||||||| |||||||| |  |||||||||||||| ||||||||||||||||
aacttaattatactttctcaactttc--tagttctcaacaaatctaaatatattgcacttaaagtgaaaattttgat-tatggttctctaaataataatgtagATTAGAGAAGGACTGCACTATAATCCTTATTTTCCTGGCGGGGCTATTGCTATGCCTAAAATGCTTAATGATGGTGCTGTTGAATATGAAGATGGTACCC

upper sequence: Vv09s0002g05950.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA19G24620.2 (Glycine max), 3'ss of exon 5
---ccgataatcatcttgacttgggttttgtcatcatttgattgctctttctgcattcttttaatgaatgttccatcctga-tgtcattgaactctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCTATGCCCAAAATGCTCATCGATGGTGCTGTTGAGTATGAAGATGGTACCC
     | || |  |    |  |   |||||||   ||   |  | | |      ||| | ||  | ||  |    || ||| | |  |  || |  |  |||||||  |||| || || || ||||||||||| || |||||||| ||||| || ||||| |||||||| |  ||||||||||| || ||||||||||||||||
tatatggtactagttcatatatca-ttttgtccctat---accgatgtactgatattgtgttcttaaacttcttttcatgactatgttcaaaataataatgtagATAAGAGAGGGACTTCATTATAATCCTTACTTTCCTGGTGGAGCAATTGCCATGCCTAAAATGCTTAATGATGGTGCTGTGGAATATGAAGATGGTACCC

upper sequence: Vv09s0002g05950.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA16G06700.2 (Glycine max), 3'ss of exon 5
-ccgataatcatcttgacttgggttttgtcatcat-ttgat-tgctctttctgcattcttttaatgaatgttccatcctgatgtcattgaactctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCTATGCCCAAAATGCTCATCGATGGTGCTGTTGAGTATGAAGATGGTACCC
    |  |  |  |    |    |||||||   ||   ||| | ||  |  ||  |||||  ||    | || |||    ||||  |  || |  |  |||||||  |||| || || || ||||||||||| || |||||||| ||||| || ||||| |||||||| |  ||||||||||| || |||||||||||||| |
atttagtactagttcatatatcattttgtccctataccgatgtactgatattgtgttctta-aacctttttttcatggctatgt--tcaaaataataatgtagATAAGAGAGGGACTTCATTATAATCCTTACTTTCCTGGTGGAGCAATTGCCATGCCTAAAATGCTTAATGATGGTGCTGTGGAATATGAAGATGGTACTC

upper sequence: Vv09s0002g05950.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G40810.2 (Arabidopsis thaliana), 3'ss of exon 4
ccgataatcatcttgacttgggttttgtcatcatttgattgctctttctgcattcttttaatgaatgttccatcctgatgtcattgaactctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCTATGCCCAAAATGCTCATCGATGGTGCTGTTGAGTATGAAGATGGTACCC
       | |  ||  ||    ||||  | | |     ||| | || |  | |    ||  || | |||  |   | ||    | ||        |  ||||  |||| ||||| ||||| |||||||||||||||||||| ||||| |||||||| |||||||||| |||||  ||||| || ||||||||||| || |
------gtaaatttctctcctatttttgctttagac--ttgttattacaacttcaaattgttggaagttagaaa-taatcctgt-gactaacgggtacagATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGCAATCGCTATGCCAAAAATGCTCAACGATGAAGCTGTGGAATATGAAGATGGAACTC

upper sequence: Vv09s0002g05950.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G27240.1 (Arabidopsis thaliana), 3'ss of exon 5
ccgataatcatcttgacttgggttttgtcatcatttgattgctctttctgcattcttttaatgaatgttccatcctgatgtcattgaactctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCTATGCCCAAAATGCTCATCGATGGTGCTGTTGAGTATGAAGATGGTACCC
                 |  | || | ||||  |     |     |||| |    |   | ||   |||  ||    |   |  |||  |   | |  ||||| |||| ||| | ||||| ||||||||||||||||| || ||||| |||||||| ||||||||||  ||||  |||||||||||||||||||||  ||
----------------gtaagtttctctcattttccacattgaacttcttcgaattcaaagtgctggtt--atgaaaaatccgatga--taactgtacagATTAGAGAGGGGTTACACTACAATCCTTATTTCCCTGGGGGAGCAATTGCTATGCCGAAAATGCTCAATGATGAAGCTGTTGAGTATGAAGATGGTGTCC

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|110377968|gb|EC943074.1|EC943074
EST:     ATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCA                         ATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCT
genomic: ATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCAgtaagttctt ... ctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCT
EST: gi|30321061|gb|CD004323.1|CD004323
EST:     ATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCA                         ATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCT
genomic: ATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCAgtaagttctt ... ctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCT
EST: gi|110698992|gb|EE077122.1|EE077122
EST:     ATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCA                         ATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCT
genomic: ATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCAgtaagttctt ... ctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCT
EST: gi|34550509|gb|CF518727.1|CF518727
EST:     ATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCA                         ATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCT
genomic: ATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCAgtaagttctt ... ctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCT
EST: gi|349813644|gb|FQ413878.1|FQ413878
EST:     ATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCA                         ATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCT
genomic: ATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCAgtaagttctt ... ctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCT
EST: gi|351028222|gb|FQ426123.1|FQ426123
EST:     ATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCA                         ATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCT
genomic: ATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCAgtaagttctt ... ctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCT
EST: gi|110428516|gb|EC994990.1|EC994990
EST:     ATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCA                         ATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCT
genomic: ATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCAgtaagttctt ... ctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCT
EST: gi|34547391|gb|CF515623.1|CF515623
EST:     ATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCA                         ATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCT
genomic: ATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCAgtaagttctt ... ctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCT
EST: gi|34550428|gb|CF518646.1|CF518646
EST:     ATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCA                         ATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCT
genomic: ATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCAgtaagttctt ... ctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCT
EST: gi|351033244|gb|FQ462016.1|FQ462016
EST:     ATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCA                         ATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCT
genomic: ATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCAgtaagttctt ... ctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCT
EST: gi|34547301|gb|CF515533.1|CF515533
EST:     ATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCA                         ATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCT
genomic: ATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCAgtaagttctt ... ctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCT
EST: gi|30320467|gb|CD003729.1|CD003729
EST:     ATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCA                         ATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCT
genomic: ATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCAgtaagttctt ... ctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCT
EST: gi|349808524|gb|FQ405668.1|FQ405668
EST:     ATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCA                         ATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCT
genomic: ATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCAgtaagttctt ... ctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCT
EST: gi|110417035|gb|EC983057.1|EC983057
EST:     ATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCA                         ATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCT
genomic: ATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCAgtaagttctt ... ctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCT
EST: gi|351017876|gb|FQ436229.1|FQ436229
EST:     ATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCA                         ATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCT
genomic: ATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCAgtaagttctt ... ctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCT
EST: gi|110378867|gb|EC944022.1|EC944022
EST:     ATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCA                         ATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCT
genomic: ATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCAgtaagttctt ... ctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCT
EST: gi|349809896|gb|FQ398521.1|FQ398521
EST:     ATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCA                         ATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCT
genomic: ATGTATTTGCTCTTTTAACTGGTTACCGTGATCCTCCAGCTGGTGTTTCAgtaagttctt ... ctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgcattcttttaatgaatgttccatcctgatgtcattgaactctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCTATGCCCAAAATGCTCATCGATGGTGCTGTTGAGTATGAAGATGGTACCC
                           tcctgat  putative branch site (score: 3)
                                           ctctttctgt  putative PPT
      attcttttaatgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccgataatcatcttgacttgggttttgtcatcatttgattgctctttctgcattcttttaatgaatgttccatcctgatgtcattgaactctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCTATGCCCAAAATGCTCATCGATGGTGCTGTTGAGTATGAAGATGGTACCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - -tgacttg
- - - - - - - - - - - - - gtcatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatcct