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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaaatatttgactgtcatcatcactcaaaactgttataatctggctttaccctgagttttcatgccatctgatgttctttttcttcttgtttctaacagAGCTCTCTGGCATCCCATCTGATATCCGCACACGGCTTATTCCAGAACATGCACGAAAGCAAAACTTATTCATGGCTCTGCACACCTAAGCAAAATCCTG

Basic information

species Vitis vinifera
transcript Vv12s0035g01060.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 11
acaaatatttgactgtcatca---tcactcaaaactgttataatctggctttaccctgagttttcatgccatctgatgttctttttcttcttgtttctaacagAGCTCTCTGGCATCCCATCTGATATCCGCACACGGCTTATTCCAGAACATGCACGAAAGCAAAACTTATTCATGGCTCTGCACACCTAAGCAAAATCCTG--
| | |    ||| || || ||   | |||||    | ||| |         ||   ||  |||     |  | | || |  | ||| || ||  |||   |||| || |||||  | ||  ||||| ||  ||  |||||||||||||| ||||| || || || |||||||| |||||| ||||||||||    || ||| |  
atacaggagtgaatgacaccagatttactcacttgtcttaaatctaaatgataatttgcatttat---ctctttaatttcgtgtttgttgttcattcatgcagAACTTTCTGGTGTACCCCCTGATGTCATCAATCGGCTTATTCCAGAGCATGCGCGTAAACAGAACTTATTTATGGCTTTGCACACCTAGC--AATTCCCGTA
















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|30126156|gb|CB911495.1|CB911495
EST:     TCTTCCTAATGGCCGCCCTCTTCCTCCCCTCTTTAATTTCAA-CCTCAAG                         AGCTCTCTGGCATCCCATCTG
genomic: TCTTCCTAATGGCCGTCCTCTTCCTCCCCTCTTTAATTTCAAACCTCAAGgtaagtttga ... tttctaacagAGCTCTCTGGCATCCCATCTG
EST: gi|110726124|gb|EE101641.1|EE101641
EST:     TCTTCCTAATGGCCGTCCTCTTCCTCCCCTCTTTAATTTCAAACCTCAAG                         AGCTCTCTGGCATCCCATCTGATATCCGCACACGGCTTATTCCAGAACATG
genomic: TCTTCCTAATGGCCGTCCTCTTCCTCCCCTCTTTAATTTCAAACCTCAAGgtaagtttga ... tttctaacagAGCTCTCTGGCATCCCATCTGATATCCGCACACGGCTTATTCCAGAACATG
EST: gi|27580396|gb|CB003091.1|CB003091
EST:     TCTTCCTAATGGCCGCCCTCTTCCTCCCCTCTTTAATTTCAAACCTCAAG                         AGCTCTCTGGCATCCCATCTGATATCCGCACACGGCTTATTCCAGAACATG
genomic: TCTTCCTAATGGCCGTCCTCTTCCTCCCCTCTTTAATTTCAAACCTCAAGgtaagtttga ... tttctaacagAGCTCTCTGGCATCCCATCTGATATCCGCACACGGCTTATTCCAGAACATG
EST: gi|27579322|gb|CB002017.1|CB002017
EST:     TCTTCCTAATGGCCGCCCTCTTCCTCCCCTCTTTAATTTCAAACCTCAAG                         AGCTCTCTGGCATCCCATCTGATATCCGCACACGGCTTATTCCAGAACATG
genomic: TCTTCCTAATGGCCGTCCTCTTCCTCCCCTCTTTAATTTCAAACCTCAAGgtaagtttga ... tttctaacagAGCTCTCTGGCATCCCATCTGATATCCGCACACGGCTTATTCCAGAACATG
EST: gi|27581595|gb|CB004290.1|CB004290
EST:     TCTTCCTAATGGCCGCCCTCTTCCTCCCCTCTTTAATTTCAAACCTCAAG                         AGCTCTCTGGCATCCCATCTGATATCCGCACACGGCTTATTCCAGAACATG
genomic: TCTTCCTAATGGCCGTCCTCTTCCTCCCCTCTTTAATTTCAAACCTCAAGgtaagtttga ... tttctaacagAGCTCTCTGGCATCCCATCTGATATCCGCACACGGCTTATTCCAGAACATG
EST: gi|27581007|gb|CB003702.1|CB003702
EST:     TCTTCCTAATGGCCGCCCTCTTCCTCCCCTCTTTAATTTCAAACCTCAAG                         AGCTCTCTGGCATCCCATCTGATATCCGCACACGGCTTATTCCAGAACATG
genomic: TCTTCCTAATGGCCGTCCTCTTCCTCCCCTCTTTAATTTCAAACCTCAAGgtaagtttga ... tttctaacagAGCTCTCTGGCATCCCATCTGATATCCGCACACGGCTTATTCCAGAACATG
EST: gi|30130728|gb|CB916067.1|CB916067
EST:     TCTTCCTAATGGCCGCCCTCTTCCTCCCCTCTTTAATTTCAAACCTCAAG                         AGCTCTCTGGCATCCCATCTGATATCCGCACACGGCTTATTCCAGAACATG
genomic: TCTTCCTAATGGCCGTCCTCTTCCTCCCCTCTTTAATTTCAAACCTCAAGgtaagtttga ... tttctaacagAGCTCTCTGGCATCCCATCTGATATCCGCACACGGCTTATTCCAGAACATG
EST: gi|110419339|gb|EC985557.1|EC985557
EST:     TCTTCCTAATGGCCGTCCTCTTCCTCCCCTCTTTAATTTCAAACCTCAAG                         AGCTCTCTGGCATCCCATCTGATATCCGCACACGGCTTATTCCAGAACATG
genomic: TCTTCCTAATGGCCGTCCTCTTCCTCCCCTCTTTAATTTCAAACCTCAAGgtaagtttga ... tttctaacagAGCTCTCTGGCATCCCATCTGATATCCGCACACGGCTTATTCCAGAACATG
EST: gi|27579129|gb|CB001824.1|CB001824
EST:     TCTTCCTAATGGCCGCCCTCTTCCTCCCCTCTTTAATTTCAAACCTCAAG                         AGCTCTCTGGCATCCCATCTGATATCCGCACACGGCTTATTCCAGAACATG
genomic: TCTTCCTAATGGCCGTCCTCTTCCTCCCCTCTTTAATTTCAAACCTCAAGgtaagtttga ... tttctaacagAGCTCTCTGGCATCCCATCTGATATCCGCACACGGCTTATTCCAGAACATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttaccctgagttttcatgccatctgatgttctttttcttcttgtttctaacagAGCTCTCTGGCATCCCATCTGATATCCGCACACGGCTTATTCCAGAACATGCACGAAAGCAAAACTTATTCATGGCTCTGCACACCTAAGCAAAATCCTG
                      atctgat  putative branch site (score: 4)
                       tctgatgttctttttc  CT-rich tract
                              ttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaaatatttgactgtcatcatcactcaaaactgttataatctggctttaccctgagttttcatgccatctgatgttctttttcttcttgtttctaacagAGCTCTCTGGCATCCCATCTGATATCCGCACACGGCTTATTCCAGAACATGCACGAAAGCAAAACTTATTCATGGCTCTGCACACCTAAGCAAAATCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
acaaata
- - - - - - ctgtcat
- - - - - - - - - - -tcactca
- - - - - - - - - - - - - - - - - - - - - tggcttt
- - - - - - - - - - - - - - - - - - - - - - - - -accctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgcc