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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctttgtctcattgagatataattttccttggctatactgttggatgccctgattgatatctgctattaatcctctgccttcataactgagatccttagGTGGATAGGAAACTGGTGAAGCAGACAGTGATGACATCAGTATATGGAGTTACTTATATTGGTGCTCGTGACCAAATCAAGAGGAGATTAAAAGAACGTT

Basic information

species Vitis vinifera
transcript Vv01s0010g00690.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0010g00690.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: PP1S256_41V6.1 (Physcomitrella patens), 3'ss of exon 13
---------------------atctttgtctcattgagatat-aattttccttggctatactgttggatgccctgattgatatctgctattaatcctctgc---------cttcataactgagatccttagGTGGATAGGAAACTGGTGAAGCAGACAGTGATGACATCAGTATATGGAGTTACTTATATTGGTGCTCGTGACCAAATCAAGAGGAGATTAAAAGAACGTT
                     || ||  | | | ||  ||   || | |     |  ||| |  | |   |  |  |    |  | ||     |  | ||          |||   |  |   ||   ||| | ||||| || || || ||||||||||||||||||||||| ||||||||||||| | |||| || ||    |||||    |  ||||| || || ||| 
gtatgaaccgaacgactactcattttgttgttactgctatgccaagtgttaaaagtaatatt--taggctcttttttctggacatactgcaggttttttgtggtactgatctttgcatattctatgtgtagATTGATAGAAAGCTTGTCAAGCAGACAGTGATGACATCAGTGTATGGAGTTACTTTTGTTGGCGCCCGCATGCAAATATTTAATAGATTGAAGGAGCGTG

upper sequence: Vv01s0010g00690.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: EFJ20792 (Selaginella moellendorffii), 3'ss of exon 12
atctttgtctcattgagatataattttccttggctatactgttggatgccctgattgatatctgctattaatcctctgccttcataactgagatccttagGTGGATAGGAAACTGGTGAAGCAGACAGTGATGACATCAGTATATGGAGTTACTTATATTGGTGCTCGTGACCAAATCAAGAGGAGATTAAAAGAACGTT
                                          ||  |  ||   | | | |    ||     ||| |  | |||   ||  | ||   |||||||||||||||| ||||| |||||||||||||| || || || || || || ||  |||| || ||| ||||||| |  |  ||| | |  ||     
-----------------------------------------gtgagtatccatttcggttttcttta-----cctttctcatcaattcttcggtcac-agGTGGATAGGAAACTAGTGAAACAGACAGTGATGACTTCGGTTTACGGCGTGACATACGTTGGAGCACGTAACCAAATAACAAACAGACTTAGGGACAAGG

upper sequence: Vv01s0010g00690.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: EFJ32457 (Selaginella moellendorffii), 3'ss of exon 12
atctttgtctcattgagatataattttccttggctatactgttggatgccctgattgatatctgctattaatcctctgccttcataactgagatccttagGTGGATAGGAAACTGGTGAAGCAGACAGTGATGACATCAGTATATGGAGTTACTTATATTGGTGCTCGTGACCAAATCAAGAGGAGATTAAAAGAACGTT
                                          ||  |  ||   | | | |    || |     | |  | |||   ||  | ||   |||||||||||||||| ||||| |||||||||||||| || || || || || || ||  |||| || ||| ||||||| |  |  ||| | |  ||     
-----------------------------------------gtgagtatccatttcggttttctttact-----tttctcatcaattcttcggtcac-agGTGGATAGGAAACTAGTGAAACAGACAGTGATGACTTCGGTTTACGGCGTGACATACGTTGGAGCACGTAACCAAATAACAAACAGACTTAGGGACAAGG

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|27581209|gb|CB003904.1|CB003904
EST:     ATCCTGCTACTGAACCAAATGCCTTGCGTGCTAGACTTTTAATCAGTCAG                         GTGGATAGGAAACTGGTGAAGCAGACAGTGATGACATCAGTATATGGAGTT
genomic: ATCCTGCTACTGAACCAAATGCCTTGCGTGCTAGACTTTTAATCAGTCAGgtttttttta ... agatccttagGTGGATAGGAAACTGGTGAAGCAGACAGTGATGACATCAGTATATGGAGTT
EST: gi|27581087|gb|CB003782.1|CB003782
EST:     ATCCTGCTACTGAACCAAATGCCTTGCGTGCTAGACTTTTAATCAGTCAG                         GTGGATAGGAAACTGGTGAAGCAGACAGTGATGACATCAGTATATGGAGTT
genomic: ATCCTGCTACTGAACCAAATGCCTTGCGTGCTAGACTTTTAATCAGTCAGgtttttttta ... agatccttagGTGGATAGGAAACTGGTGAAGCAGACAGTGATGACATCAGTATATGGAGTT
EST: gi|27579010|gb|CB001705.1|CB001705
EST:     ATCCTGCTACTGAACCAAATGCCTTGCGTGCTAGACTTTTAATCAGTCAG                         GTGGATAGGAAACTGGTGAAGCAGACAGTGATGACATCAGTATATGGAGTT
genomic: ATCCTGCTACTGAACCAAATGCCTTGCGTGCTAGACTTTTAATCAGTCAGgtttttttta ... agatccttagGTGGATAGGAAACTGGTGAAGCAGACAGTGATGACATCAGTATATGGAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgccctgattgatatctgctattaatcctctgccttcataactgagatccttagGTGGATAGGAAACTGGTGAAGCAGACAGTGATGACATCAGTATATGGAGTTACTTATATTGGTGCTCGTGACCAAATCAAGAGGAGATTAAAAGAACGTT
                                    tcataac  putative branch site (score: 2)
                                                tcctt  putative PPT
                    tattaat  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atctttgtctcattgagatataattttccttggctatactgttggatgccctgattgatatctgctattaatcctctgccttcataactgagatccttagGTGGATAGGAAACTGGTGAAGCAGACAGTGATGACATCAGTATATGGAGTTACTTATATTGGTGCTCGTGACCAAATCAAGAGGAGATTAAAAGAACGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - -tgtctca
- - - - - - - - - - - - -ttccttg
- - - - - - - - - - - - - - - - - - - ctgttgg
- - - - - - - - - - - - - - - - - - - - - - - tgccctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgctat