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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggaactgacctgttaaataccatactcgggtaatctgatgtcgtgctcagctgatttactgaagtatttcccatttctctcttctttttttcggccatgctttcttagGGCACAACCATGTTGCTTCCTAGCACTGCCTCCAATCCTGCCAACATGATAGGTCAAGCTCTCACCATTTACAAAAGCTTGGTTGGAAACGTCAATGGTG

Basic information

species Vitis vinifera
transcript Vv09s0002g01630.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g01630.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA04G40420.1 (Glycine max), 3'ss of exon 8
gtaaggaactgacctgttaaataccatactcgggtaatctgatgtcgtgctcagctgatttactgaagtatttcccatttctctcttctttttttcggccatgctttcttagGGCACAACCATGTTGCTTCCTAGCACTGCCTCCAATCCTGCCAACATGATAGGTCAAGCTCTCACCATTTACAAAAGCTTGGTTGGAAACGTCAATGGTG
|| || || ||||| | | || |||| | || ||| | | | || || | |||| | | || |||| || | || || |||||||||| ||||||||||||||| |||| ||||||||||| |||||||| | |||||||| || || || |||||| || |||| || |||
-------------gtgatatatcccata---agcttat-tgatattcacctgcactgcataatttgtttagtttc-atttttttatttattttatctttactttttcctcagGGCACAACAATGTTGCTTCCTAGCTCTGCATCCAATCCTGCTAACATGATGGCCCAAGCTCTTACTATGTATAAAAGCCTGCTTGGTAATCCTTCCAGTG

upper sequence: Vv09s0002g01630.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA06G14340.1 (Glycine max), 3'ss of exon 8
gtaaggaactgacctgttaaataccatactcgggtaatctgatgtcgtgctcagctgatttactgaagtatttcccatttctctcttctttttttcggccatgctttcttagGGCACAACCATGTTGCTTCCTAGCACTGCCTCCAATCCTGCCAACATGATAGGTCAAGCTCTCACCATTTACAAAAGCTTGGTTGGAAACG---TCAATGGTG--------------------
||| || | || || | | | | || || | ||| ||| ||| | |||||| || |||||||||| ||||||||||||||| |||| ||||||||||| |||||||| | |||||||| || || || |||||| || |||| || ||||| |
----------------------ttgatattcaatttcctgcatttcataatttgtttggttcgaaaattgttttgattttatctttactttttc-------------ctcagggcacaacaatgttgcttcctagCTCTGCATCCAATCCTGCTAACATGATGGCCCAAGCTCTTACTATGTATAAAAGCCTGCTTGGTAATCCTTCCAATGATAAGCATAGTGGAACTGCACCC
















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|18458599|gb|BM436877.1|BM436877
EST:     TAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATTGCCAAGGAG                         GGCACAACCATGTTGCTTCCTAGCACTGCCTCCAATCCTGCCAACATGATA
genomic: TAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATTGCCAAGGAGgtaaggaact ... gctttcttagGGCACAACCATGTTGCTTCCTAGCACTGCCTCCAATCCTGCCAACATGATA
EST: gi|30324273|gb|CD007535.1|CD007535
EST:     TAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATTGCCAAGGAG                         GGCACAACCATGTTGCTTCCTAGCACTGCCTCCAATCCTGCCAACATGATA
genomic: TAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATTGCCAAGGAGgtaaggaact ... gctttcttagGGCACAACCATGTTGCTTCCTAGCACTGCCTCCAATCCTGCCAACATGATA
EST: gi|110377134|gb|EC942193.1|EC942193
EST:     TAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATTGCCAAGGAG                         GGCACAACCATGTTGCTTCCTAGCACTGCCTCCAATCCTGCCAACATGATA
genomic: TAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATTGCCAAGGAGgtaaggaact ... gctttcttagGGCACAACCATGTTGCTTCCTAGCACTGCCTCCAATCCTGCCAACATGATA
EST: gi|110393459|gb|EC958711.1|EC958711
EST:     TAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATTGCCAAGGAG                         GGCACAACCATGTTGCTTCCTAGCACTGCCTCCAATCCTGCCAACATGATA
genomic: TAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATTGCCAAGGAGgtaaggaact ... gctttcttagGGCACAACCATGTTGCTTCCTAGCACTGCCTCCAATCCTGCCAACATGATA
EST: gi|30320908|gb|CD004170.1|CD004170
EST:     TAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATTGCCAAGGAG                         GGCACAACCATGTTGCTTCCTAGCACTGCCTCCAATCCTGCCAACATGATA
genomic: TAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATTGCCAAGGAGgtaaggaact ... gctttcttagGGCACAACCATGTTGCTTCCTAGCACTGCCTCCAATCCTGCCAACATGATA
EST: gi|110385372|gb|EC949890.1|EC949890
EST:     TAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATTGCCAAGGAG                         GGCACAACCATGTTGCTTCCTAGCACTGCCTCCAATCCTGCCAACATGATA
genomic: TAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATTGCCAAGGAGgtaaggaact ... gctttcttagGGCACAACCATGTTGCTTCCTAGCACTGCCTCCAATCCTGCCAACATGATA
EST: gi|30325554|gb|CD008816.1|CD008816
EST:     TAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATTGCCAAGGAG                         GGCACAACCATGTTGCTTCCTAGCACTGCCTCCAATCCTGCCAACATGATA
genomic: TAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATTGCCAAGGAGgtaaggaact ... gctttcttagGGCACAACCATGTTGCTTCCTAGCACTGCCTCCAATCCTGCCAACATGATA
EST: gi|30327281|gb|CD010543.1|CD010543
EST:     TAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATTGCCAAGGAG                         GGCACAACCATGTTGCTTCCTAGCACTGCCTCCAATCCTGCCAACATGATA
genomic: TAAGAATAGCTGAGCAATATATCCAGGCTTTCAGTATGATTGCCAAGGAGgtaaggaact ... gctttcttagGGCACAACCATGTTGCTTCCTAGCACTGCCTCCAATCCTGCCAACATGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttactgaagtatttcccatttctctcttctttttttcggccatgctttcttagGGCACAACCATGTTGCTTCCTAGCACTGCCTCCAATCCTGCCAACATGATAGGTCAAGCTCTCACCATTTACAAAAGCTTGGTTGGAAACGTCAATGGTG
 agctgat  putative branch site (score: 4)
 tttcccatttctctct  putative PPT
 ttcttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggaactgacctgttaaataccatactcgggtaatctgatgtcgtgctcagctgatttactgaagtatttcccatttctctcttctttttttcggccatgctttcttagGGCACAACCATGTTGCTTCCTAGCACTGCCTCCAATCCTGCCAACATGATAGGTCAAGCTCTCACCATTTACAAAAGCTTGGTTGGAAACGTCAATGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT