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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagctttatatgcagtgtcatgcttgaggaattcttactagcatcttctgtgaaatttttcaatgatattttacatttactttttcagGTTTGACCCGCAGACAGGGCTACTGACTGGAACAAATGATGGGACTGTTGTAAACCTATTTTTAAGACAATTTGGCAGGATGTCAGAAAAGTCACTTTGC

Basic information

species Vitis vinifera
transcript Vv08s0007g05920.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g05920.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA10G16320.1 (Glycine max), 3'ss of exon 9
gtagctttatatgcagtgtcatgcttgaggaattcttactagcatcttctgtgaaatt-tttcaatgatatttta-----catttactttttcagGTTTGACCCGCAGACAGGGCTACTGACTGGAACAAATGATGGGACTGTTGTAAACCTATTTTTAAGACAATTTGGCAGGATGTCAGAAAAGTCACTTTGC
||||   |  ||  |      ||  | || | |  || |   ||||||   |  | || |||   ||| |  | |     ||| ||||  |||||||||||||| || || || ||||||||||| ||||||||||||||  |||| ||| | ||  ||||| | || |||   | ||| |||||| ||||||| 
gtaggcattgataga----tgtgtcttagtattggtt-cagacatcttgcatatacttgtttggttgaaacctcatataccatctactcattcagGTTTGACCCTCAAACTGGACTACTGACTGGGACAAATGATGGGACACTTGTTAACTTTTTCCTAAGAAATTTAGGCCAAAAGTCTGAAAAGACACTTTGT

upper sequence: Vv08s0007g05920.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA02G34640.1 (Glycine max), 3'ss of exon 9
gtagctttatatgcagtgtcatgcttgaggaattcttactagcatcttctgtgaaatttttcaat-gatattttac-------atttactttttcagGTTTGACCCGCAGACAGGGCTACTGACTGGAACAAATGATGGGACTGTTGTAAACCTATTTTTAAGACAATTTGGCAGGATGTCAGAAAAGTCACTTTGC
||||   |   |  |      |   | ||  |||  | |   ||||||   |  | || ||   | || |  | ||       || ||||  |||||||||||||| || || || ||||||||||| ||||||||||||||  |||| ||| | ||| ||||| | || ||| | | ||| |||||| ||||||| 
gtaggcattggtaga----tgtatcttagttattggttcagacatcttgcatatacttgtttggttgaaacctcacgtatatcatctactcattcagGTTTGACCCTCAAACTGGACTACTGACTGGGACAAATGATGGGACACTTGTTAACTTCTTTCTAAGAAATTTAGGCCGAAAGTCCGAAAAGGCACTTTGT
















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|156736397|gb|EV240511.1|EV240511
EST:     CTTTCTGGCTATGTGAAATGCCCACGGCATCGTCTGCCAAG                         GTTTGACCCGCAGACAGGGCTACTGACTGGAACAAATGATGGGACTGTTGT
genomic: CTTTCTGGCTATGTGAAATGCCCACGGCATCGTCTGCCAAGgtagctttat ... actttttcagGTTTGACCCGCAGACAGGGCTACTGACTGGAACAAATGATGGGACTGTTGT
EST: gi|33405215|gb|CF210842.1|CF210842
EST:     CTTTCTGGCTATGTGAAATGCCCACGGCATCGTCTGCCAAG                         GTTTGACCCGCAGACAGGGCTACTGACTGGAACAAATGATGGGACTGTTGT
genomic: CTTTCTGGCTATGTGAAATGCCCACGGCATCGTCTGCCAAGgtagctttat ... actttttcagGTTTGACCCGCAGACAGGGCTACTGACTGGAACAAATGATGGGACTGTTGT
EST: gi|33405130|gb|CF210757.1|CF210757
EST:     CTTTCTGGCTATGTGAAATGCCCACGGCATCGTCTGCCAAG                         GTTTGACCCGCAGACAGGGCTACTGACTGGAACAAATGATGGGACTGTTGT
genomic: CTTTCTGGCTATGTGAAATGCCCACGGCATCGTCTGCCAAGgtagctttat ... actttttcagGTTTGACCCGCAGACAGGGCTACTGACTGGAACAAATGATGGGACTGTTGT
EST: gi|349825767|gb|FQ421866.1|FQ421866
EST:     CTTTCTGGCTATGTGAAATGCCCACGGCATCGTCTGCCAAG                         GTTTGACCCGCAGACAGGGCTACTGACTGGAACAAATGATGGGACTGTTGT
genomic: CTTTCTGGCTATGTGAAATGCCCACGGCATCGTCTGCCAAGgtagctttat ... actttttcagGTTTGACCCGCAGACAGGGCTACTGACTGGAACAAATGATGGGACTGTTGT
EST: gi|22010048|gb|BQ795082.1|BQ795082
EST:     CTTTCTGGCTATGTGAAATGCCCACGGCATCGTCTGCCAAG                         GTTTGACCCGCAGACAGGGCTACTGACTGGAACAAATGATGGGACTGTTGT
genomic: CTTTCTGGCTATGTGAAATGCCCACGGCATCGTCTGCCAAGgtagctttat ... actttttcagGTTTGACCCGCAGACAGGGCTACTGACTGGAACAAATGATGGGACTGTTGT
EST: gi|110377471|gb|EC942537.1|EC942537
EST:     CTTTCTGGCTATGTGAAATGCCCACGGCATCGTCTGCCAAG                         GTTTGACCCGCAGACAGGGCTACTGACTGGAACAAATGATGGGACTGTTGT
genomic: CTTTCTGGCTATGTGAAATGCCCACGGCATCGTCTGCCAAGgtagctttat ... actttttcagGTTTGACCCGCAGACAGGGCTACTGACTGGAACAAATGATGGGACTGTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttactagcatcttctgtgaaatttttcaatgatattttacatttactttttcagGTTTGACCCGCAGACAGGGCTACTGACTGGAACAAATGATGGGACTGTTGTAAACCTATTTTTAAGACAATTTGGCAGGATGTCAGAAAAGTCACTTTGC
 ttcttac  putative branch site (score: 2)
                                          tttactttttc  putative PPT
                 tgaaatttttcaatga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagctttatatgcagtgtcatgcttgaggaattcttactagcatcttctgtgaaatttttcaatgatattttacatttactttttcagGTTTGACCCGCAGACAGGGCTACTGACTGGAACAAATGATGGGACTGTTGTAAACCTATTTTTAAGACAATTTGGCAGGATGTCAGAAAAGTCACTTTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG