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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttctatgttctccattattagatctaccctaagaactactacagatgggttcctgttttacagggaggtgggtttaataattctcttcctctttctcagCTGATGTTGGAAATTACCTTGGTGACTTTCGTCCTGATTGGGGTTCAATGAGCTTCCTTATAGACTTCCTGCGACCAACTACTACTGACGGGTCATGGTA

Basic information

species Vitis vinifera
transcript Vv18s0072g00410.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0072g00410.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G43580.1 (Arabidopsis thaliana), 3'ss of exon 2
gttctatgttctccattattagatctaccctaagaactactacagatgggttcctgttttacagggaggtgggtttaataattctcttcct-ctttctcagCTGATGTTGGAAATTACCTTGGTGACTTTCGTCCTGATTGGGGTTCAATGAGCTTCCTTATAGACTTCCTGCGACCAACTACTACTGACGGGTCATGGTA
| ||| ||| | | | |||| | ||| | || | ||| || | || || | ||| |||||||| |||| |||| ||||||||| | | ||||||||||||||||||||||||||| || ||| || |||| | | |||| ||||| | |
------------gtaatatctagtctccttcacttattact-----taggtatttattgctta----------cttattagtactttttttgttttaacagCTGATCCAGGAAGTTACATTGGTGACTATAGAGCTGATTGGGGTTCAATGAGCTTCCTTAGTGAGTTCTTGAGACCGAGTTACTCTGAAGGGTCTTCTTG
















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|32265206|gb|CD716795.1|CD716795
EST:     TTCGGATCCAGCTGCTATTCGTCAAGTAATAGAACGTGATATAGCCTATG                         CTGATGTTGGAAATTACCTTGGTGACTTTCGTCCTGATTGGGGTTCAATGA
genomic: TTCGGATCCAGCTGCTATTCGTCAAGTAATAGAACGTGATATAGCCTATGgtatgtgttt ... tctttctcagCTGATGTTGGAAATTACCTTGGTGACTTTCGTCCTGATTGGGGTTCAATGA
EST: gi|32247973|gb|CD713792.1|CD713792
EST:     TTCGGATCCAGCTGCTATTCGTCAAGTAATAGAACGTGATATAGCCTATG                         CTGATGTTGGAAATTACCTTGGTGACTTTCGTCCTGATTGGGGTTCAATGA
genomic: TTCGGATCCAGCTGCTATTCGTCAAGTAATAGAACGTGATATAGCCTATGgtatgtgttt ... tctttctcagCTGATGTTGGAAATTACCTTGGTGACTTTCGTCCTGATTGGGGTTCAATGA
EST: gi|32249764|gb|CD715583.1|CD715583
EST:     TTCGGATCCAGCTGCTATTCGTCAAGTAATAGAACGTGATATAGCCTATG                         CTGATGTTGGAAATTACCTTGGTGACTTTCGTCCTGATTGGGGTTCAATGA
genomic: TTCGGATCCAGCTGCTATTCGTCAAGTAATAGAACGTGATATAGCCTATGgtatgtgttt ... tctttctcagCTGATGTTGGAAATTACCTTGGTGACTTTCGTCCTGATTGGGGTTCAATGA
EST: gi|110428995|gb|EC995481.1|EC995481
EST:     TTCGGATCCAGCTGCTATTCGTCAAGTAATAGAACGTGATATAGCCTATG                         CTGATGTTGGAAATTACCTTGGTGACTTTCGTCCTGATTGGGGTTCAATGA
genomic: TTCGGATCCAGCTGCTATTCGTCAAGTAATAGAACGTGATATAGCCTATGgtatgtgttt ... tctttctcagCTGATGTTGGAAATTACCTTGGTGACTTTCGTCCTGATTGGGGTTCAATGA
EST: gi|32268478|gb|CD717637.1|CD717637
EST:     TTCGGATCCAGCTGCTATTCGTCAAGTAATAGAACGTGATATAGCCTATG                         CTGATGTTGGAAATTACCTTGGTGACTTTCGTCCTGATTGGGGTTCAATGA
genomic: TTCGGATCCAGCTGCTATTCGTCAAGTAATAGAACGTGATATAGCCTATGgtatgtgttt ... tctttctcagCTGATGTTGGAAATTACCTTGGTGACTTTCGTCCTGATTGGGGTTCAATGA
EST: gi|110689139|gb|EE065104.1|EE065104
EST:     TTCGGATCCAGCTGCTATTCGTCAAGTAATAGAACGTGATATAGCCTATG                         CTGATGTTGGAAATTACCTTGGTGACTTTCGTCCTGATTGGGGTTCA
genomic: TTCGGATCCAGCTGCTATTCGTCAAGTAATAGAACGTGATATAGCCTATGgtatgtgttt ... tctttctcagCTGATGTTGGAAATTACCTTGGTGACTTTCGTCCTGATTGGGGTTCA
EST: gi|110376951|gb|EC942020.1|EC942020
EST:     TTCGGATCCAGCTGCTATTCGTCAAGTAATAGAACGTGATATAGCCTATG                         CTGATGTTGGAAATTACCTTGGTGACTTTCGTCCTGATTGGGGTTCAATGA
genomic: TTCGGATCCAGCTGCTATTCGTCAAGTAATAGAACGTGATATAGCCTATGgtatgtgttt ... tctttctcagCTGATGTTGGAAATTACCTTGGTGACTTTCGTCCTGATTGGGGTTCAATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgggttcctgttttacagggaggtgggtttaataattctcttcctctttctcagCTGATGTTGGAAATTACCTTGGTGACTTTCGTCCTGATTGGGGTTCAATGAGCTTCCTTATAGACTTCCTGCGACCAACTACTACTGACGGGTCATGGTA
                           gtttaat  putative branch site (score: 4)
 taattctcttcctctt  CT-rich tract
 tttaataattctctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctatgttctccattattagatctaccctaagaactactacagatgggttcctgttttacagggaggtgggtttaataattctcttcctctttctcagCTGATGTTGGAAATTACCTTGGTGACTTTCGTCCTGATTGGGGTTCAATGAGCTTCCTTATAGACTTCCTGCGACCAACTACTACTGACGGGTCATGGTA

- - - - -tctccat
- - - - - - - - - - - - - accctaa
- - - - - - - - - - - - - - - - - - - - - cagatgg
- - - - - - - - - - - - - - - - - - - - - - - - - ttcctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtgggt