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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcacttgttcttatgtgttttttgttagataattatgtagattttgtgttatttattgaaagggaactttcagcacttattattgtatgcaatgttactgattcagCTGATATTGGATCAAAGGGGGTGGCAAAGATTAGTAACAGTGATGTTTGTGGCATTGGAAGGTCAAGCAGAACACTGCCAAGCTCTGAGTTACAGAAGCA

Basic information

species Vitis vinifera
transcript Vv08s0040g03220.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0040g03220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G05560.2 (Glycine max), 3'ss of exon 4
gtatgcac-ttgttcttatgtgttttttgttaga---taattatgtagattttgtgttatttattgaaagggaactttcagcacttattattgtatgcaatgttactgattcagCTGATATTGGATCAAAGGGGGTGGCAAAGATTAGTAACAGTGATGTTTGTGGCATTGGAAGGTCAAGCAGAACACTGCCAAGCTCTGAGTTACAGAAGCA
| |||||   |  | || | |||| |||||| ||    |||  | || ||||  | |  | || | || |  |   | || |||||||||   |||   | ||||||||||||||||||||||||||||||||| | ||| ||||||  |||||   | |  ||||  | ||||  || |   || |||| || |  |||||| |||  |||||
gcatgcatactccttttgtttgttgtttgtttgaagtcaatagtctacattt-atttactatactaaatgcaactgtccaccacttattacgttatatgacgttactgattcagCTGATATTGGATCAAAGGGGATAGCACAGATTACCAACAGCAGTCTCAGTGGTGTAGGAAATTCTACTGGAGCACTACCGACTTCTGAGATACCCAAGCA

upper sequence: Vv08s0040g03220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G19910.1 (Glycine max), 3'ss of exon 4
gtatgcac-ttgttcttatgtgttttttgttagataattat-gtagat-tttgtgttatttattgaaagggaactttcagcacttattattgtatgcaatgttactgattcagCTGATATTGGATCAAAGGGGGTGGCAAAGATTAGTAACAGTGATGTTTGTGGCATTGGAAGGTCAAGCAGAACACTGCCAAGCTCTGAGTTACAGAAGCA
| |||||   |  | || | |||| |||||| ||     || ||  |  ||| | |  | || | || || |   | || ||||||||||  |||   | ||||||||||||||||||||||||||||||||| |  || ||||||  |||||   | |  ||||  ||||||  || |  |||||||| |  |  |||||| |||  |||||
gcatgcatactccttttgtttgttgtttgtttgaagtccatagtctacatttatttgctatactaaatggaactgtccaccacttattatgttatatgacgttactgattcagCTGATATTGGATCAAAGGGGATAACACAGATTACCAACAGCAGTCTCAGTGGTGTTGGAAATTCTACTAGAACACTACTGACTTCTGAGATACCAAAGCA

upper sequence: Vv08s0040g03220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA03G33440.1 (Glycine max), 3'ss of exon 4
gtatgcacttgttcttatgtgtttt-ttgttagataattatgtagattttgtgttatttat-tgaaagggaactt--tcagcacttatt-attgtatgcaatgttactgattcagCTGATATTGGATCAAAGGGGGTGGCAAAGATTAGTAACAGTGATGTTTGTGGCATTGGAAGGTCAAGCAGAACACTGCCAAGCTCTGAGTTACAGAAGCA
    |  ||| |  |||   |||   ||| | | |   ||||   ||| ||   |   | |   ||| |||||||   || |||||||| ||  |||   | ||||||||||||||||||||||||||||||||| |  ||   ||| || ||||   | || ||||  |||| |  || |  ||||  |||||     ||||| |    || ||
----gttcttatatttactggttcaattgcttgtttgatatg---attctgcaatggctgtactaaatggaacttgtccaccacttatttatgttatatgacgttactgattcagCTGATATTGGATCAAAGGGGATAACACGAATTGGTCACAGCAGTCTTAGTGGTGTTGGGAACTCTACTAGAAATCTGCCTGCTACTGAGATGGCAAAACA

upper sequence: Vv08s0040g03220.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA19G36170.1 (Glycine max), 3'ss of exon 5
--------------------------------------------------gtatgcacttgttcttatgtgtttt-ttgttagataattatgtagattttgtgttatttat-tgaaagggaacttt--cagcactta-ttattgtatgcaatgttactgattcagCTGATATTGGATCAAAGGGGGTGGCAAAGATTAGTAACAGTGATGTTTGTGGCATTGGAAGGTCAAGCAGAACACTGCCAAGCTCTGAGTTACAGAAGCA
                                                   |  |  ||| |  || |  |||   ||| | | |   |||| ||| | |||| |   | |   ||| ||||||||  || |||||| ||||  |||   | ||||||||||||||||||||||||||||||||| |  ||   |||    ||||   | || ||||  |||| |  || |  ||||  |||||     ||||| | |  || ||
gtaaggatgagctcgccaatcttcttggaaatgaaggcacgcacacttcttttagttcttatatttgttggttcaattgcttgtttgatatgaagagtctgtgatggctgtactaaatggaacttttccaccacttaattatgttatatgacgttactgattcagCTGATATTGGATCAAAGGGGATAACACGAATTGACCACAGCAGTCTTAGTGGTGTTGGGAACTCTACTAGAAATCTGCCTGCTACTGAGATGCCAAAACA

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|110377422|gb|EC942485.1|EC942485
EST:     AAGTGGAATCGCTCCACCACAAGATGAATACAGTCTTCACATGGTTGAAG                         CTGATATTGGATCAAAGGGGGTGGCAAAGATTAGTAACAGTGATGTTTGTG
genomic: AAGTGGAATCGCTCCACCCCAAGATGAATACAGTCTTCACATGGTTGAAGgtatgcactt ... actgattcagCTGATATTGGATCAAAGGGGGTGGCAAAGATTAGTAACAGTGATGTTTGTG
EST: gi|349821355|gb|FQ410976.1|FQ410976
EST:     AAGTGGAATCGCTCCACCCCAAGATGAATACAGTCTTCACATGGTTGAAG                         CTGATATTGGATCAAAGGGGTTGGCAAAGATTAGTAACAGTGATGTTTGTG
genomic: AAGTGGAATCGCTCCACCCCAAGATGAATACAGTCTTCACATGGTTGAAGgtatgcactt ... actgattcagCTGATATTGGATCAAAGGGGGTGGCAAAGATTAGTAACAGTGATGTTTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttattgaaagggaactttcagcacttattattgtatgcaatgttactgattcagCTGATATTGGATCAAAGGGGGTGGCAAAGATTAGTAACAGTGATGTTTGTGGCATTGGAAGGTCAAGCAGAACACTGCCAAGCTCTGAGTTACAGAAGCA
                                            tactgat  putative branch site (score: 2)
                       acttattattgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcacttgttcttatgtgttttttgttagataattatgtagattttgtgttatttattgaaagggaactttcagcacttattattgtatgcaatgttactgattcagCTGATATTGGATCAAAGGGGGTGGCAAAGATTAGTAACAGTGATGTTTGTGGCATTGGAAGGTCAAGCAGAACACTGCCAAGCTCTGAGTTACAGAAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC