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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttgtatcattcattctatggctgttttgatgttccctttgctcgactgctgatttagaaatattgatcatgtgtcacagGGGTAACATACTTCTAAGTCGGAAAGATTCTGAAATGTTGCAGTTCACTCTTGAGGGAAAGAATATGTTTGTCAAAACATTTGGATTGTCAATATCCATA

Basic information

species Vitis vinifera
transcript Vv14s0060g00450.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g00450.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA19G41380.1 (Glycine max), 3'ss of exon 10
-------gttttgtatcattcattctatggctgttttgatgttccctttgctcgactgctgatttagaaatattgatcatgtgtcacagGGGTAACATACTTCTAAGTCGGAAAGATTCTGAAATGTTGCAGTTCACTCTTGAGGGAAAGAATATGTTTGTCAAAACATTTGGATTGTCAATATCCATA
        |  ||         |  |||   | |  ||   ||   ||||| ||| | || |||||  |||||    ||  |||  |||||| || |||||| |  | || |  |||||||||| ||||||||||||||| || || |||| |||||| ||||||||   ||||||   |||||| || 
gtgggtcatcatgcggtggcgttgttata--tatgctgtcattgtatttgcacgattactaatttatgaatatc---caattgtt-cagGGGAAATATACTTGTGGGCCGAAGTGATTCTGAAACGTTGCAGTTCACTCTCGATGGCAAGACTATGTTGGTCAAAACTCATGGATTAATAATATCTATT

upper sequence: Vv14s0060g00450.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA03G38780.1 (Glycine max), 3'ss of exon 1
------------------gttttgtatcattcattct-atggctgttttgatgt---tccctttgctcgactgctgatttagaaatattgatcatgtgtcacagGGGTAACATACTTCTAAGTCGGAAAGATTCTGAAATGTTGCAGTTCACTCTTGAGGGAAAGAATATGTTTGTCAAAACATTTGGATTGTCAATATCCATA
                   |     ||  ||| || | ||||    ||    ||   |   ||||   || | || |||||  |||||  |     |  | |||||| || |||||| |  | || |  |||||||||| |||||||||||||||  | || |||||||||||  |||||||   ||||||   |||||| || 
caagattaacaattatgtctgcaaaatagttccttttgatggggacttcagagtgaatgtatttgtatgattactaatttatgaatatcca----attgctcagGGGAAATATACTTGTGGGCCGAAGTGATTCTGAAACGTTGCAGTTCACTCTCAATGGCAAGAATATGTTAATCAAAACGCATGGATTAATAATATCTATT
















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|351014738|gb|FQ437938.1|FQ437938
EST:     TTGGCTGTGGCAGAAGCTGCATATGAATTTGAACATCGTGATCTACACTG                         GGGTAACATACTTCTAAGTCGGAAAGATTCTGAAATGTTGCAGTTCACTCT
genomic: TTGGCTGTGGCAGAAGCTGCATATGAATTTGAACATCGTGATCTACACTGgttttgtatc ... tgtgtcacagGGGTAACATACTTCTAAGTCGGAAAGATTCTGAAATGTTGCAGTTCACTCT
EST: gi|122688897|gb|EC927503.1|EC927503
EST:     TTGGCTGTGGCAGAAGCTGCATATGAATTTGAACATCGTGATCTACACTG                         GGGTAACATACTTCTAAGTCGGAAAGATTCTGAAATGTTGCAGTTCACTCT
genomic: TTGGCTGTGGCAGAAGCTGCATATGAATTTGAACATCGTGATCTACACTGgttttgtatc ... tgtgtcacagGGGTAACATACTTCTAAGTCGGAAAGATTCTGAAATGTTGCAGTTCACTCT
EST: gi|349830931|gb|FQ418215.1|FQ418215
EST:     TTGGCTGTGGCAGAAGCTGCATATGAATTTGAACATCGTGATCTACACTG                         GGGTAACATACTTCTAAGTCGGAAAGATTCTGAAATGTTGCAGTTCACTCT
genomic: TTGGCTGTGGCAGAAGCTGCATATGAATTTGAACATCGTGATCTACACTGgttttgtatc ... tgtgtcacagGGGTAACATACTTCTAAGTCGGAAAGATTCTGAAATGTTGCAGTTCACTCT
EST: gi|351041418|gb|FQ447545.1|FQ447545
EST:     TTGGCTGTGGCAGAAGCTGCATATGAATTTGAACATCGTGATCTACACTG                         GGGTAACATACTTCTAAGTCGGAAAGATTCTGAAATGTTGCAGTTCACTCT
genomic: TTGGCTGTGGCAGAAGCTGCATATGAATTTGAACATCGTGATCTACACTGgttttgtatc ... tgtgtcacagGGGTAACATACTTCTAAGTCGGAAAGATTCTGAAATGTTGCAGTTCACTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgatgttccctttgctcgactgctgatttagaaatattgatcatgtgtcacagGGGTAACATACTTCTAAGTCGGAAAGATTCTGAAATGTTGCAGTTCACTCTTGAGGGAAAGAATATGTTTGTCAAAACATTTGGATTGTCAATATCCATA
                                    tattgat  putative branch site (score: 3)
                           atttagaaatattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttgtatcattcattctatggctgttttgatgttccctttgctcgactgctgatttagaaatattgatcatgtgtcacagGGGTAACATACTTCTAAGTCGGAAAGATTCTGAAATGTTGCAGTTCACTCTTGAGGGAAAGAATATGTTTGTCAAAACATTTGGATTGTCAATATCCATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA