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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattgtcaaacaaaatatcaatagctactccattccagggattaggtcaaatgctcatctgtataacttgatttctgatgatatatttatgtgattttagGCTGCACAACTGAATTTCAGAGGACAGCGTATCTGGTCAGCTGCTATAGAAGATTTAATGTCCAAGGGAATGCGCTATGCCAACCAG

Basic information

species Vitis vinifera
transcript Vv14s0060g00230.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g00230.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA03G38650.1 (Glycine max), 3'ss of exon 4
aattgtcaaacaaaatatcaatagctactccattc-cagggattaggtcaaatgctcatctgtataacttgatttctgatgatatatttat--gtgattttagGCTGCACAACTGAATTTCAGAGGACAGCGTATCTGGTCAGCTGCTATAGAAGATTTAATGTCCAAGGGAATGCGCTATGCCAACCAG
  ||| || |       | |||        |||||  |   ||  | |||| ||    | | |   |||  ||||      ||| | || |  || |   ||| ||||| ||||| | ||||||||||||||||| ||| ||||||| || |||||||| ||||| ||||||||||| | |||||  |||
--ttgacatatgccccttgaattcacttgacattcatatatatatgatcaattgagggt-tattccactatatttacctccataaaattgtttgtcaaaatagACTGCAGAACTGCAATTCAGAGGACAGCGTATTTGGGCAGCTGCAATGGAAGATTTGATGTCAAAGGGAATGCGTTTTGCCAGTCAG

upper sequence: Vv14s0060g00230.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA19G41240.1 (Glycine max), 3'ss of exon 4
aattgtcaaacaaaatatcaatagctactccattccagggattaggtcaaatgctcatctgtataacttgatttctgatgatatatttatgtgattttagGCTGCACAACTGAATTTCAGAGGACAGCGTATCTGGTCAGCTGCTATAGAAGATTTAATGTCCAAGGGAATGCGCTATGCCAACCAG
|  | |    |   |  | | | |  | ||   |  |   ||  | |||| ||    |   |  |   |  || ||      |  | | |||     ||| ||||| ||||| | ||||||||||||||||| ||| ||||||| || |||||||| ||||| || |||||||| | |||||| |||
acatatgccccttgaattgacttgacattcatatatatatatatgatcaattgagggttattccacgatatttacttgcataaattgtttgtccaaatagACTGCAGAACTGCAATTCAGAGGACAGCGTATTTGGGCAGCTGCAATGGAAGATTTGATGTCAAAAGGAATGCGTTTTGCCAATCAG

upper sequence: Vv14s0060g00230.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G28230.1 (Glycine max), 3'ss of exon 4
aattgtcaaacaaaatatcaatagctactccattccagggat--taggtcaaatgctca--tctgtataacttgatttctgatgatatat-ttatgtgattt--tagGCTGCACAACTGAATTTCAGAGGACAGCGTATCTGGTCAGCTGCTATAGAAGATTTAATGTCCAAGGGAATGCGCTATGCCAACCAG
           || |||| || | ||    |||      |||   |  |||    || |  | |  ||      ||   |  ||  | || |||| || |     ||||||| |||||| | || |||||||||||||| ||||| || || || |||||||| ||||| ||||||||||| | |||||  |||
-------ttttaacatataaaaaactgaggcatgatgttgatgacacttcacgcacttaattttacattggacaatacttactggcaaatattatctgttgagacagGCTGCGCAACTGCAATTTAGAGGACAGCGTATTTGGTCGGCAGCAATCGAAGATTTGATGTCAAAGGGAATGCGATTTGCCAGGCAG

upper sequence: Vv14s0060g00230.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G22210.1 (Glycine max), 3'ss of exon 4
aattgtcaaacaaaatatcaatagctactccattccagggattaggtcaaatgctcatctgtataacttgatttctgatgat--atatt-tatgtgattttagGCTGCACAACTGAATTTCAGAGGACAGCGTATCTGGTCAGCTGCTATAGAAGATTTAATGTCCAAGGGAATGCGCTATGCCAACCAG
  || | | | | || | |    || |     ||   |  | |    |  |      | |  ||      ||   |  |     ||||| | |||      |||  || |||||| | || |||||||||||||| ||||  ||||| || |||||||| | ||| ||||||||||| | |||||| |||
--ttttaacatataaaaactgaggc-atgatgttgatgacacttcaacgcacttaactttacattggacaatacttacttgcgaatattgtctgttgacacagGTGGCGCAACTGCAATTTAGAGGACAGCGTATTTGGTTGGCTGCAATGGAAGATTTGAAGTCAAAGGGAATGCGATTTGCCAAGCAG

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|32271244|gb|CD720403.1|CD720403
EST:     AGCTTCGTTATTGTGATGGTGCCTCTTTTACTGGTGACAGCCAAAATCAG                         GCTGCACAACTGAATTTCAGAGGACAGCGTATCTGGTCAGCTGCTATAGAA
genomic: AGCTTCGTTATTGTGATGGTGCCTCTTTTACTGGTGACAGCCAAAATCAGgttggtggta ... gtgattttagGCTGCACAACTGAATTTCAGAGGACAGCGTATCTGGTCAGCTGCTATAGAA
EST: gi|30324545|gb|CD007807.1|CD007807
EST:     AGCTTCGTTATTGTGATGGTGCCTCTTTTACTGGTGACAGCCAAAATCAG                         GCTGCACAACTGAATTTCAGAGGACAGCGTATCTGGTCAGCTGCTATAGAA
genomic: AGCTTCGTTATTGTGATGGTGCCTCTTTTACTGGTGACAGCCAAAATCAGgttggtggta ... gtgattttagGCTGCACAACTGAATTTCAGAGGACAGCGTATCTGGTCAGCTGCTATAGAA
EST: gi|71864790|gb|DT013845.1|DT013845
EST:     AGCTTCGTTATTGTGATGGTGCCTCTTTTACTGGTGACAGCCAAAATCAG                         GTTGGCTGCACAACTGAATTTCAGAGGACAGCGTATCTGGTCAGCTGCTAT
genomic: AGCTTCGTTATTGTGATGGTGCCTCTTTTACTGGTGACAGCCAAAATCAGgttggtggta ... gtgattttagG----CTGCACAACTGAATTTCAGAGGACAGCGTATCTGGTCAGCTGCTAT
EST: gi|110373337|gb|EC937563.1|EC937563
EST:     AGCTTCGTTATTGTGATGGTGCCTCTTTTACTGGTGACAGCCAAAATCAG                         GCTGCACAACTGAATTTCAGAGGACAGCGTATCTGGTCAGCTGCTATAGAA
genomic: AGCTTCGTTATTGTGATGGTGCCTCTTTTACTGGTGACAGCCAAAATCAGgttggtggta ... gtgattttagGCTGCACAACTGAATTTCAGAGGACAGCGTATCTGGTCAGCTGCTATAGAA
EST: gi|18458238|gb|BM436516.1|BM436516
EST:     AGCTTCGTTATTGTGATGGTGCCTCTTTTACTGGTGACAGCCAAAATCAG                         GCTGCACAACTGAATTTCAGAGGACAGCGTATCTGGTCAGCTGCTATAGAA
genomic: AGCTTCGTTATTGTGATGGTGCCTCTTTTACTGGTGACAGCCAAAATCAGgttggtggta ... gtgattttagGCTGCACAACTGAATTTCAGAGGACAGCGTATCTGGTCAGCTGCTATAGAA
EST: gi|30327012|gb|CD010274.1|CD010274
EST:     AGCTTCGTTATTGTGATGGTGCCTCTTTTACTGGTGACAGCCAAAATCAG                         GCTGCACAACTGAATTTCAGAGGACAGCGTATCTGGTCAGCTGCTATAGAA
genomic: AGCTTCGTTATTGTGATGGTGCCTCTTTTACTGGTGACAGCCAAAATCAGgttggtggta ... gtgattttagGCTGCACAACTGAATTTCAGAGGACAGCGTATCTGGTCAGCTGCTATAGAA
EST: gi|30327090|gb|CD010352.1|CD010352
EST:     AGCTTCGTTATTGTGATGGTGCCTCTTTTACTGGTGACAGCCAAAATCAG                         GCTGCACAACTGAATTTCAGAGGACAGCGTATCTGGTCAGCTGCTATAGAA
genomic: AGCTTCGTTATTGTGATGGTGCCTCTTTTACTGGTGACAGCCAAAATCAGgttggtggta ... gtgattttagGCTGCACAACTGAATTTCAGAGGACAGCGTATCTGGTCAGCTGCTATAGAA
EST: gi|30321442|gb|CD004704.1|CD004704
EST:     AGCTTCGTTATTGTGATGGTGCCTCTTTTACTGGTGACAGCCAAAATCAG                         GCTGCACAACTGAATTTCAGAGGACAGCGTATCTGGTCAGCTGCTATAGAA
genomic: AGCTTCGTTATTGTGATGGTGCCTCTTTTACTGGTGACAGCCAAAATCAGgttggtggta ... gtgattttagGCTGCACAACTGAATTTCAGAGGACAGCGTATCTGGTCAGCTGCTATAGAA
EST: gi|32268077|gb|CD717236.1|CD717236
EST:     AGCTTCGTTATTGTGATGGTGCCTCTTTTACTGGTGACAGCCAAAATCAG                         GCTGCACAACTGAATTTCAGAGGACAGCGTATCTGGTCAGCTGCTATAGAA
genomic: AGCTTCGTTATTGTGATGGTGCCTCTTTTACTGGTGACAGCCAAAATCAGgttggtggta ... gtgattttagGCTGCACAACTGAATTTCAGAGGACAGCGTATCTGGTCAGCTGCTATAGAA
EST: gi|110696063|gb|EE074792.1|EE074792
EST:     AGCTTCGTTATTGTGATGGTGCCTCTTTTACTGGTGACAGCCAAAATCAG                         GCTGCACAACTGAATTTCAGAGGACAGCGTATCTGGTCAGCTGCTATAGAA
genomic: AGCTTCGTTATTGTGATGGTGCCTCTTTTACTGGTGACAGCCAAAATCAGgttggtggta ... gtgattttagGCTGCACAACTGAATTTCAGAGGACAGCGTATCTGGTCAGCTGCTATAGAA
EST: gi|161714504|gb|FC062954.1|FC062954
EST:     AGCTTCGTTATTGTGATGGTGCCTCTTTTACTGGTGACAGCCAAAATCAG                         GCTGCACAACTGAATTTCAGAGGACAGCGTATCTGGTCAGCTGCTATAGAA
genomic: AGCTTCGTTATTGTGATGGTGCCTCTTTTACTGGTGACAGCCAAAATCAGgttggtggta ... gtgattttagGCTGCACAACTGAATTTCAGAGGACAGCGTATCTGGTCAGCTGCTATAGAA
EST: gi|30326319|gb|CD009581.1|CD009581
EST:     AGCTTCGTTATTGTGATGGTGCCTCTTTTACTGGTGACAGCCAAAATCAG                         GCTGCACAACTGAATTTCAGAGGACAGCGTATCTGGTCAGCTGCTATAGAA
genomic: AGCTTCGTTATTGTGATGGTGCCTCTTTTACTGGTGACAGCCAAAATCAGgttggtggta ... gtgattttagGCTGCACAACTGAATTTCAGAGGACAGCGTATCTGGTCAGCTGCTATAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcaaatgctcatctgtataacttgatttctgatgatatatttatgtgattttagGCTGCACAACTGAATTTCAGAGGACAGCGTATCTGGTCAGCTGCTATAGAAGATTTAATGTCCAAGGGAATGCGCTATGCCAACCAG
                           ttctgat  putative branch site (score: 3)
                                atgatatatttatgtg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattgtcaaacaaaatatcaatagctactccattccagggattaggtcaaatgctcatctgtataacttgatttctgatgatatatttatgtgattttagGCTGCACAACTGAATTTCAGAGGACAGCGTATCTGGTCAGCTGCTATAGAAGATTTAATGTCCAAGGGAATGCGCTATGCCAACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - -aaacaaa
- - - - - - - - - - - - - - -ccattcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgatga