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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttgcatttcctatttcttctttgtcgatagtgatgaatattttatagagtttttgtattggattatttaaaatgtttttgattgatttcattgtacagGGGTTCTTCAATTTTACTTCCCGAAGGCCTCGCCATCTGCTGAATATTTTGGAGCTTGGATATAATGTTATGTACAATGATGTTGATATGGTGTGGTTGG

Basic information

species Vitis vinifera
transcript Vv15s0046g01630.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0046g01630.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G09360.1 (Glycine max), 3'ss of exon 1
ctttgcatttcctatttct--tctttgtcgatagtgatgaatattttatagagtttttgtattggattatttaaaatgtttttgattgatttcattgtacagGGGTTCTTCAATTTTACTTCCCGAAGGCCTCGCCATCTGCTGAATATTTTGGAGCTTGGATATAATGTTATGTACAATGATGTTGATATGGTGTGGTTGG
  |||  |  | |  |  |  |  |||    |     | ||| | ||       | | ||  ||  || |  ||    || ||| || |||||| |||  |||| |||||||| |||||  |  |  ||||  ||||||||||||| ||||||||||||||||||| ||| ||||||||||||||||||||||| |||||||
-cttgtctgccgtggtgttgattattggaactgtctcttaatttctttctcgtgtgtggtgctgagttttaaaatccattcttgttt-atttcactgtctagGGTTTCTTCAACTTTACAGCAAGGCGGCCAAGCCATCTGCTGAAGATTTTGGAGCTTGGATATAGTGTGATGTACAATGATGTTGATATGGTTTGGTTGG

upper sequence: Vv15s0046g01630.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT1G56550.1 (Arabidopsis thaliana), 3'ss of exon 1
-ctttgcatttcctatttcttctttgtcgatagtgatgaatattttatagagtttttgtattggattatttaaaatgtt-tttgattgatttcattgtac-agGGGTTCTTCAATTTTACTTCCCGAAGGCCTCGCCATCTGCTGAATATTTTGGAGCTTGGATATAATGTTATGTACAATGATGTTGATATGGTGTGGTTGG
 | ||  |  || ||       |    | |  ||||| |    |  | ||| |||   || || |  ||   |  | ||   | ||| |||  ||| ||  |||| ||||||||| | || || || ||||| |  |||||  | || ||||||||||| || || ||||||||||||||||||||||||||||| ||| |  
acatta-acatcataaaagagttagaccaaatgtgataatatatgcaaagaatttgaatactgca--atccgatgttttacctaatttattatattatattagGGTTTCTTCAATCTGACATCTCGGAGGCCACAACATCTCTTAAACATTTTGGAGCTAGGTTACAATGTTATGTACAATGATGTTGATATGGTCTGGCTAC

upper sequence: Vv15s0046g01630.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G01770.1 (Arabidopsis thaliana), 3'ss of exon 1
ctttgcatttcctatttcttctttgtcgatagtgatgaatattttatagagtttttgtattg-gattatttaaaatgtttttgattgatt--tcat---tgtacagGGGTTCTTCAATTTTACTTCCCGAAGGCCTCGCCATCTGCTGAATATTTTGGAGCTTGGATATAATGTTATGTACAATGATGTTGATATGGTGTGGTTGG
  ||| |      |  |  |  | ||| |  |  ||   |  |||||    | | ||| |   ||  | |||   | |   | ||| | |  ||||    |   |||| ||||||||||| ||  | |||||||| |  |||||  || | ||||||||||| || || |||||||||||||| |||||||||||||| |||||| 
--ttgaaaaaaaaagat--tggtggtctagggccattgct--tttattatttctgtgtgtgaagaaaacttatgttttcactaatttactcatcatatccgactagGGTTTCTTCAATTTCACAGCTCGAAGGCCGCAACATCTCTTGCAAATTTTGGAGCTAGGTTACAATGTTATGTACAACGATGTTGATATGGTTTGGTTGC

upper sequence: Vv15s0046g01630.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G01750.1 (Arabidopsis thaliana), 3'ss of exon 1
ctttgcatttcctatttcttctttgtcgatagtgatgaatattttatagagtttttgtattggattatttaaaatgtttttgattgatt--tcat---tgtacagGGGTTCTTCAATTTTACTTCCCGAAGGCCTCGCCATCTGCTGAATATTTTGGAGCTTGGATATAATGTTATGTACAATGATGTTGATATGGTGTGGTTGG
   |   ||||  || |        || | |    |   |||    | |  | |||||| || |  |  || | | |   | ||| | |  ||||    |   |||| |||||||| || ||  | |||||||| |  |||||  || | ||||||||||| || || |||||||||||||| |||||||||||||| |||||| 
---tttctttcggatcttgatcaaatccaaatgattatgtatcccct-gtttctttgtaatgaaa-acatatattttcactaatttactcatcatatccgactagGGTTTCTTCAACTTCACAGCTCGAAGGCCACAACATCTCTTGCAAATTTTGGAGCTAGGTTACAATGTTATGTACAACGATGTTGATATGGTTTGGTTGC

upper sequence: Vv15s0046g01630.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G01220.1 (Arabidopsis thaliana), 3'ss of exon 1
ctttgcatttcctatttcttctttgtcgatagtgatgaatattttata----gagtttttgtattggattatttaaaatgtttttgattgatttcattgtacagGGGTTCTTCAATTTTACTTCCCGAAGGCCTCGCCATCTGCTGAATATTTTGGAGCTTGGATATAATGTTATGTACAATGATGTTGATATGGTGTGGTTGG
  | |||    | |||| | |  |||   |     ||| || | ||||     ||   |||||||  | |       ||  |||  | | ||||| ||||| |||| ||||||||||| ||  | || ||||| |  |||||  || | ||||||||| | || || |||||||||||||| |||||||||||||| |||||| 
--tagcagcagccatttttcccctgtttctgtatgtga-tactatatatgctaagagcttgtattacaatggaatcgattgtttaaactaatttc-ttgtatagGGATTCTTCAATTTCACAGCACGGAGGCCGCAACATCTCTTGGAAATTTTGGAGTTAGGTTACAATGTTATGTACAACGATGTTGATATGGTTTGGTTGC

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|351029945|gb|FQ427785.1|FQ427785
EST:     TGGTTCCGCCAGCCCCTGACGCCCAAACTGCCCATAAGTTTGGTTCTATG                         GGGTTCTTCAATTTTACTTCCCGAAGGCCTCGCCATCTACTGAATATTTTG
genomic: TGGTTCCGCCAGCCCCTGACGCCCAAACTGCCCATAAGTTTGGTTCTATGgtatataaca ... cattgtacagGGGTTCTTCAATTTTACTTCCCGAAGGCCTCGCCATCTGCTGAATATTTTG
EST: gi|352786171|gb|FQ478782.1|FQ478782
EST:     TGGTTCCGCCAGCCCCTGACGCCCAAACTGCCCATAAGTTTGGTTCTATG                         GGGTTCTTCAATTTTACTTCCCGAAGGCCTCGCCATCTACTGAATATTTTG
genomic: TGGTTCCGCCAGCCCCTGACGCCCAAACTGCCCATAAGTTTGGTTCTATGgtatataaca ... cattgtacagGGGTTCTTCAATTTTACTTCCCGAAGGCCTCGCCATCTGCTGAATATTTTG
EST: gi|351038208|gb|FQ460900.1|FQ460900
EST:     TGGTTCCGCCAGCCCCTGACGCCCAAACTGCCCATAAGTTTGGTTCTATG                         GGGTTCTTCAATTTTACTTCCCGAAGGCCTCGCCATCTACTGAATATTTTG
genomic: TGGTTCCGCCAGCCCCTGACGCCCAAACTGCCCATAAGTTTGGTTCTATGgtatataaca ... cattgtacagGGGTTCTTCAATTTTACTTCCCGAAGGCCTCGCCATCTGCTGAATATTTTG
EST: gi|351056219|gb|FQ453681.1|FQ453681
EST:     TGGTTCCGCCAGCCCCTGACGCCCAAACTGCCCATAAGTTTGGTTCTATG                         GGGTTCTTCAATTTTACTTCTCGAAGGCCTCGCCATCTACTGAATATTTTG
genomic: TGGTTCCGCCAGCCCCTGACGCCCAAACTGCCCATAAGTTTGGTTCTATGgtatataaca ... cattgtacagGGGTTCTTCAATTTTACTTCCCGAAGGCCTCGCCATCTGCTGAATATTTTG
EST: gi|161715714|gb|FC066821.1|FC066821
EST:     TGGTTCCGCCAGCCCCTGACGCCCAAACTGCCCATAAGTTTGGTTCTATG                         GGGTTCTTCAATTTTACTTCCCGAAGGCCTCGCCATCTGCTGAATATTTTG
genomic: TGGTTCCGCCAGCCCCTGACGCCCAAACTGCCCATAAGTTTGGTTCTATGgtatataaca ... cattgtacagGGGTTCTTCAATTTTACTTCCCGAAGGCCTCGCCATCTGCTGAATATTTTG
EST: gi|351012109|gb|FQ429915.1|FQ429915
EST:     TGGTTCCGCCAGCCCCTGACGCCCAAACTGCCCATAAGTTTGGTTCTATG                         GGGTTCTTCAATTTTACTTCCCGAAGGCCTCGCCATCTACTGAATATTTTG
genomic: TGGTTCCGCCAGCCCCTGACGCCCAAACTGCCCATAAGTTTGGTTCTATGgtatataaca ... cattgtacagGGGTTCTTCAATTTTACTTCCCGAAGGCCTCGCCATCTGCTGAATATTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagagtttttgtattggattatttaaaatgtttttgattgatttcattgtacagGGGTTCTTCAATTTTACTTCCCGAAGGCCTCGCCATCTGCTGAATATTTTGGAGCTTGGATATAATGTTATGTACAATGATGTTGATATGGTGTGGTTGG
                                    gattgat  putative branch site (score: 4)
                                          tttcatt  CT-rich tract
      tttttgtattggatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttgcatttcctatttcttctttgtcgatagtgatgaatattttatagagtttttgtattggattatttaaaatgtttttgattgatttcattgtacagGGGTTCTTCAATTTTACTTCCCGAAGGCCTCGCCATCTGCTGAATATTTTGGAGCTTGGATATAATGTTATGTACAATGATGTTGATATGGTGTGGTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - gcatttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taaaatg