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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGGTTCTGGTTGGAAGAGCAGCTTTTGTTTTTCCCCTATCCTTTTTATCCAACTTAGCCAAGAAGAACCCAACTGAAAAAATCACTTTCAGGCAGCAAgtgggtgcttccttttttccttgatgtttggagttcatcattctaacttaccaattgaattaccaaatcttatcaacatttttcattgtgtag

Basic information

species Vitis vinifera
transcript Vv14s0030g00710.t01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0030g00710.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA03G40290.1 (Glycine max), 5'ss of exon 11
TTTGGTTCTGGTTGGAAGAGCAGCTTTTGTTTTTCCCCTATCCTTTTTATCCAACTTAGCCAAGAAGAACCCAACTGAAAAAATCACTTTCAGGCAGCAAgtgggtgcttccttttttccttgatgtttggagttcatcattctaacttaccaattgaattaccaaatcttatcaacat-ttttcattgtgtag
| | || || | |||||||||||| |||||||||||||||||||| ||||||||| |  | || ||||  | || ||||||||| | ||||||| |||| ||  | ||| | ||| |  |   | || |        ||  ||    || |   ||| |||  ||  |  | |  |||  |||||    | |||
TCTAGTGCTTGCTGGAAGAGCAGCCTTTGTTTTTCCCCTATCCTTCTTATCCAACCTCACTAAAAAGACGCAAAGTGAAAAAATAAGTTTCAGGGAGCAGgtatg-gctacatttctgtcaataagtat------tttctctcaggatttc---ttggattgtcaggttatgttgacaagttttctcactttag

upper sequence: Vv14s0030g00710.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA19G42900.1 (Glycine max), 5'ss of exon 11
TTTGGTTCTGGTTGGAAGAGCAGCTTTTGTTTTTCCCCTATCCTTTTTATCCAACTTAGCCAAGAAGAACCCAACTGAAAAAATCACTTTCAGGCAGCAAgtgggtgcttccttttttccttgatgtttggagttcatcattctaacttaccaattgaattaccaaatcttatcaaca--tttttcattgtgtag
| | || || | |||||||||||| |||||||||||||||||||| ||||||||| |  | || ||||  | || ||||||||| | ||||||| |||| ||  | |||   ||| | |    ||  |  |   |||   || | |          | |||  ||  |  | |  |||  ||||||||| |    
TCTAGTACTTGCTGGAAGAGCAGCCTTTGTTTTTCCCCTATCCTTCTTATCCAACCTCACTAAAAAGACGCAAAGTGAAAAAATAAGTTTCAGGGAGCAGgtatg-gctagatttctgcaagtattctctg---tcagggttttta----------ggattgtcaggttatgttgacaaatttttcattctag--

upper sequence: Vv14s0030g00710.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA10G30020.1 (Glycine max), 5'ss of exon 12
TTTGGTTCTGGTTGGAAGAGCAGCTTTTGTTTTTCCCCTATCCTTTTTATCCAACTTAGCCAAGAAGAACCCAACTGAAAAAATCACTTTCAGGCAGCAAgtgggtgcttccttttttccttgatgtttggagttcatcattctaacttaccaattgaattaccaaatcttatcaaca--tttttcattgtgtag---------
| |  ||||  |||||||||||||||||||||| ||| |||||||  |||||||||| || || ||    |||| ||| |||||||  ||||| ||||||||   || ||   | |||    |       |||| |    ||  |  || |   |   | |||||| | |||   | |  ||| || |||| |           
TCTAATTCTTCTTGGAAGAGCAGCTTTTGTTTTCCCCTTATCCTTCATATCCAACTTGGCTAAAAAATCACCAAATGAGAAAATCAGCTTCAGACAGCAAgta--tggttaaatatttgtcagt------gagtgccctttttcagatttcttgtgttactaccaagttttactgataggtttctcgttgtttctcaattctag

upper sequence: Vv14s0030g00710.t01 (Vitis vinifera), 5'ss of exon 11
lower sequence: GLYMA20G37370.1 (Glycine max), 5'ss of exon 12
TTTGGTTCTGGTTGGAAGAGCAGCTTTTGTTTTTCCCCTATCCTTTTTATCCAACTTAGCCAAGAAGAACCCAACTGAAAAAATCACTTTCAGGCAGCAAgtgggtgcttccttttttccttgatgtttggagttcatcattctaacttaccaattgaattaccaaatcttatcaaca--tttttcattgtgtag---------
| |  ||||  |||||||||||||||||||||| ||| |||||||  |||||||||| || || ||    |||| ||| |||||||  ||||| ||||||||   || ||   | | | |  |       ||||||    ||  |  || |       | |||||  | |||   | |  ||| ||||||| |           
TCTAATTCTTCTTGGAAGAGCAGCTTTTGTTTTCCCCTTATCCTTCCTATCCAACTTGGCTAAAAAATCACCAAATGAGAAAATCAGCTTCAGACAGCAAgta--tggttaaatatctgccagt------gagttccctttttcaggtttcttgcgctactaccatgttttactgataggtttctcattgtttctcaattctag

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|26263890|gb|CA814953.1|CA814953
EST:     CCAGCTTAGCCAAGAAGAACCCAACTGAAAAAATCACTTTCAGGCAGCAA                         GTTATAATATGGTGGGCTGGTCTCATGAGGGGTGCTGTGTCTGTGGCCCTT
genomic: CCAACTTAGCCAAGAAGAACCCAACTGAAAAAATCACTTTCAGGCAGCAAgtgggtgctt ... cattgtgtagGTTATAATATGGTGGGCTGGTCTCATGAGGGGTGCTGTGTCTGTGGCCCTT
EST: gi|33403305|gb|CF208932.1|CF208932
EST:     CCAACTTAGCCAAGAAGAACCCAACTGAAAAAATCACTTTCAGGCAGCAA                         GTTATAATATGGTGGGCTGGTCTCATGAGGGGTGCTGTGTCTGTGGCCCTT
genomic: CCAACTTAGCCAAGAAGAACCCAACTGAAAAAATCACTTTCAGGCAGCAAgtgggtgctt ... cattgtgtagGTTATAATATGGTGGGCTGGTCTCATGAGGGGTGCTGTGTCTGTGGCCCTT
EST: gi|161720457|gb|FC070569.1|FC070569
EST:     CCAACTTAGCCAAGAAGAACCCAACTGAAAAAATCACTTTCAGGCAGCAA                         GTTATAATATGGTGGGCTGGTCTCATGAGGGGTGCTGTGTCTGTGGCCCTT
genomic: CCAACTTAGCCAAGAAGAACCCAACTGAAAAAATCACTTTCAGGCAGCAAgtgggtgctt ... cattgtgtagGTTATAATATGGTGGGCTGGTCTCATGAGGGGTGCTGTGTCTGTGGCCCTT
EST: gi|161720623|gb|FC070233.1|FC070233
EST:     CCAACTTAGCCAAGAAGAACCCAACTGAAAAAATCACTTTCAGGCAGCAA                         GTTATAATATGGTGGGCTGGTCTCATGAGGGGTGCTGTGTCTGTGGCCCTT
genomic: CCAACTTAGCCAAGAAGAACCCAACTGAAAAAATCACTTTCAGGCAGCAAgtgggtgctt ... cattgtgtagGTTATAATATGGTGGGCTGGTCTCATGAGGGGTGCTGTGTCTGTGGCCCTT
EST: gi|26265801|gb|CA816864.1|CA816864
EST:     CAAGAAGAACCCAACTGAAAAAATCACTTTCAGGCAGCAA                         GTTATAATATGGTGGGCTGGTCTCATGAGGGGTGCTGTGTCTGTGGCCCTT
genomic: CAAGAAGAACCCAACTGAAAAAATCACTTTCAGGCAGCAAgtgggtgctt ... cattgtgtagGTTATAATATGGTGGGCTGGTCTCATGAGGGGTGCTGTGTCTGTGGCCCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGGTTCTGGTTGGAAGAGCAGCTTTTGTTTTTCCCCTATCCTTTTTATCCAACTTAGCCAAGAAGAACCCAACTGAAAAAATCACTTTCAGGCAGCAAgtgggtgcttccttttttccttgatgtttggagttcatcattctaacttaccaattgaattaccaaatcttatcaacatttttcattgtgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC