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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctttgcatcccaactctgaggctttatggattaaaagtgcaggattatgccttttgttccatctgcgtattttctaatgccaggatgtgccttaatagGTTGCTTGGATCCTGAAAACTTCAAGGAGTTCAAACTTATAAAACGCACCCAGCTCAGCCATAATGTGGCTAAATTTATATTTGCTCTTCCAACACCAAC

Basic information

species Vitis vinifera
transcript Vv06s0009g01710.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0009g01710.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G133213_T01 (Zea mays), 3'ss of exon 1
ttctttgcatcccaactctgaggcttta----tggattaaaagtgcaggatta-tgcctttt-gttccatctgcgtatttt-ctaatgccaggatgtgccttaatagGTTGCTTGGATCCTGAAAACTTCAAGGAGTTCAAACTTATAAAACGCACCCAGCTCAGCCATAATGTGGCTAAATTTATATTTGCTCTTCCAACACCAAC
||  |  |     || | |  |   |||    ||  |    | | || | ||| ||| || | | || || ||  | || | ||  ||    |   |       |||| |||||||||||||| ||||||| | ||||||||||| |  ||   |  ||  | || |||||||| || |  || |  || ||||||||||| |||||
tttatcacccaaaaaatatttgtgcttaagtttgcttctgcaattcaaggttaatgcgttatagctcaatttgattgttgtgctgttgttttggcat-------tagGCTGCTTGGATCCTGAGAACTTCAGGAAGTTCAAACTTGTTGAAAAGAAGCAAATAAGTCATAATGTTGCCAGGTTCAAGTTCGCTCTTCCAACTCCAAC

upper sequence: Vv06s0009g01710.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA20G05640.1 (Glycine max), 3'ss of exon 1
---ttctttgcatcccaactctgaggctttatggattaaaagtgcaggattatgccttttgttccatctgcgtattttctaatgccaggatgtgccttaatagGTTGCTTGGATCCTGAAAACTTCAAGGAGTTCAAACTTATAAAACGCACCCAGCTCAGCCATAATGTGGCTAAATTTATATTTGCTCTTCCAACACCAAC
   || ||  |||       |       || || || |  ||   |     | |  ||||  | | |  |  ||  | |   | |     | |  | |  |||| |||||||||||||| |||||||| || || |||||| | |||||||| || |||||||||||||| || |  ||   ||||| |||||| || || | 
ggatttttatcattttgttaccatcttcttctgaataactagcataatgggaggggtttttgttcttgagaataaatacaggttctg---tatttcgtggtagGGTGCTTGGATCCTGAGAACTTCAAAGAATTTAAACTTGTTAAACGCACTCAACTCAGCCATAATGTTGCCACGTTCCGATTTGATCTTCCTACTCCTAA
















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|110720681|gb|EE096826.1|EE096826
EST:     CATTGGCGCCGGAACCGCCTACTATTTCTATTTCATCAAAAAACCTAAAG                         GTTGCTTGGATCCTGAAAACTTCAAGGAGTTCAAACTTATAAAACGCACCC
genomic: CATTGGCGCCGGAACCGCCTATTATTTCTATTTCATCAAAAAACCTAAAGgtttcctcct ... gccttaatagGTTGCTTGGATCCTGAAAACTTCAAGGAGTTCAAACTTATAAAACGCACCC
EST: gi|71864812|gb|DT013867.1|DT013867
EST:     CATTGGCGCCGGAACCGCCTATTATTTCTATTTCATCAAAAAACCTAAAG                         GTTGCTTGGATCCTGAAAACTTCAAGGAGTTCAAACTTATAAAACGCACCC
genomic: CATTGGCGCCGGAACCGCCTATTATTTCTATTTCATCAAAAAACCTAAAGgtttcctcct ... gccttaatagGTTGCTTGGATCCTGAAAACTTCAAGGAGTTCAAACTTATAAAACGCACCC
EST: gi|110688836|gb|EE067844.1|EE067844
EST:     CATTGGCGCCGGAACCGCCTATTATTTCTATTTCATCAAAAAACCTAAAG                         GTTGCTTGGATCCTGAAAACTTCAAGGAGTTCAAACTTATAAAACG--CCC
genomic: CATTGGCGCCGGAACCGCCTATTATTTCTATTTCATCAAAAAACCTAAAGgtttcctcct ... gccttaatagGTTGCTTGGATCCTGAAAACTTCAAGGAGTTCAAACTTATAAAACGCACCC
EST: gi|110718332|gb|EE095045.1|EE095045
EST:     CATTGGCGCCGGAGCCGCCTATTATTTCTATTTCATCAAAAAACCTAAAG                         GTTGCTTGGATCCTGAAAACTTCAAGGAGTTCAAACTTATAAAACGCACCC
genomic: CATTGGCGCCGGAACCGCCTATTATTTCTATTTCATCAAAAAACCTAAAGgtttcctcct ... gccttaatagGTTGCTTGGATCCTGAAAACTTCAAGGAGTTCAAACTTATAAAACGCACCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatgccttttgttccatctgcgtattttctaatgccaggatgtgccttaatagGTTGCTTGGATCCTGAAAACTTCAAGGAGTTCAAACTTATAAAACGCACCCAGCTCAGCCATAATGTGGCTAAATTTATATTTGCTCTTCCAACACCAAC
                            ttctaat  putative branch site (score: 2)
                        tattttctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctttgcatcccaactctgaggctttatggattaaaagtgcaggattatgccttttgttccatctgcgtattttctaatgccaggatgtgccttaatagGTTGCTTGGATCCTGAAAACTTCAAGGAGTTCAAACTTATAAAACGCACCCAGCTCAGCCATAATGTGGCTAAATTTATATTTGCTCTTCCAACACCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - -catccca
- - - - - - - - - - - - - - - -attaaaa
- - - - - - - - - - - - - - - - - - - -tgcagga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taatgcc