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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttatgtagcaattgcatttatttataaaatatcaatgttctctgatgggatttctgggtatatgatttatagtattgattactaagttaactggatcagGTTCATGAGGAGCTTATTTGGGCAATCAAAGATGCAGAAGAAGGGCTTTTTCACCTGAAACGGGCACGTTTATTGCGAGAAGCTGATTCAGCGCTACATG

Basic information

species Vitis vinifera
transcript Vv04s0008g07000.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g07000.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G43320.1 (Glycine max), 3'ss of exon 1
gttatgtagcaattgcatttatttataaa-atatcaatgttctctgatgggatttctgggtatatgatttatagtattgattactaagttaactggat----cagGTTCATGAGGAGCTTATTTGGGCAATCAAAGATGCAGAAGAAGGGCTTTTTCACCTGAAACGGGCACGTTTATTGCGAGAAGCTGATTCAGCGCTACATG
| | |  ||||      |    | || |  || ||||     ||| ||   |||||   |  || | |||||| |     ||  |||  |   | |||    |||||||||||||||||| ||  |||||| || |||||||||||||| ||| ||||||| ||||| ||||| || || |  ||||| ||||||| ||| ||| 
gatctagagcatgattttgacctcatgattatgtcaac-caatctaat---atttccaaggcta-gttttatacttaaatttcttaaaattgtttgatattccagGTTCATGAGGAGCTTGTTCAGGCAATTAAGGATGCAGAAGAAGGACTTCTTCACCTAAAACGTGCACGATTGTTACAGGAAGCAGATTCAGTGCTGCATA

upper sequence: Vv04s0008g07000.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA18G10210.1 (Glycine max), 3'ss of exon 1
gttatgtagcaattgcatttatttataaaatatcaatgttctctga--tgggatttctgggtatatgatttatagtattgattactaagttaactggat----cagGTTCATGAGGAGCTTATTTGGGCAATCAAAGATGCAGAAGAAGGGCTTTTTCACCTGAAACGGGCACGTTTATTGCGAGAAGCTGATTCAGCGCTACATG
   || |||    ||  |||      |  ||    ||||   |  |  |   |||||   |  || | |||||| |     ||  |||  |   | |||    |||||||||||||||||| ||  |||||| || |||||||||||||| ||| ||||||| ||||| ||||| || || |  ||||| ||||||| ||| ||| 
--gatctagagcatgattttgacctcatgatt---atgtcaaccaatctactatttccaaggcta-gttttatacttaaatttcttaaaattgtttgatatcccagGTTCATGAGGAGCTTGTTCAGGCAATTAAGGATGCAGAAGAAGGACTTCTTCACCTAAAACGTGCACGATTGTTACAGGAAGCAGATTCAGTGCTGCATA
















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|37186604|gb|CF605957.1|CF605957
EST:     TTCTCAAAGAAGCCCTTGTTTCCGACCCTACAAACTCGGAGCTCCTCTCG                         GTTCATGAGGAGCTTATTTGGGCAATCAAAGATGCAGAAGAAGGGCTTTTT
genomic: TTCTCAAAGAAGCCCTTGTTTCCGACCCTACAAACTCGGAGCTCCTCTCGgtacaactct ... actggatcagGTTCATGAGGAGCTTATTTGGGCAATCAAAGATGCAGAAGAAGGGCTTTTT
EST: gi|26259436|gb|CA810499.1|CA810499
EST:     TTCTCAAAGAAGCCCTTGTTTCCGACCCTACAAACTCGGAGCTCCTCTCG                         GTTCATGAGGAGCTTATTTGGGCAATCAAAGATGCAGAAGAAGGGCTTTTT
genomic: TTCTCAAAGAAGCCCTTGTTTCCGACCCTACAAACTCGGAGCTCCTCTCGgtacaactct ... actggatcagGTTCATGAGGAGCTTATTTGGGCAATCAAAGATGCAGAAGAAGGGCTTTTT
EST: gi|110712504|gb|EE090201.1|EE090201
EST:     TTCTCAAAGAAGCCCTTGTTTCCGACCCTACAAACTCGGAGCTCCTGTCG                         GTTCATGAGGAGCTTGTTTGGGCAATCAAAGATGCAGAAGAAGGGCTTTTT
genomic: TTCTCAAAGAAGCCCTTGTTTCCGACCCTACAAACTCGGAGCTCCTCTCGgtacaactct ... actggatcagGTTCATGAGGAGCTTATTTGGGCAATCAAAGATGCAGAAGAAGGGCTTTTT
EST: gi|110718718|gb|EE095871.1|EE095871
EST:     TTCTCAAAGAGGCCCTTGTTTCCGACCCTACAAACTCGGAGCTCCTGTCG                         GTTCATGAGGAGCTTGTTTGGGCAATCAAAGATGCAGAAGAAGGGCTTTTT
genomic: TTCTCAAAGAAGCCCTTGTTTCCGACCCTACAAACTCGGAGCTCCTCTCGgtacaactct ... actggatcagGTTCATGAGGAGCTTATTTGGGCAATCAAAGATGCAGAAGAAGGGCTTTTT
EST: gi|37190291|gb|CF609640.1|CF609640
EST:     TTCTCAAAGAAGCCCTTGTTTCCGACCCTACAAACTCGGAGCTCCTCTCG                         GTTCATGAGGAGCTTATTTGGGCAATCAAAGATGCAGAAGAAGGGCTTTTT
genomic: TTCTCAAAGAAGCCCTTGTTTCCGACCCTACAAACTCGGAGCTCCTCTCGgtacaactct ... actggatcagGTTCATGAGGAGCTTATTTGGGCAATCAAAGATGCAGAAGAAGGGCTTTTT
EST: gi|110702309|gb|EE080873.1|EE080873
EST:     TTCTCAAAGAAGCCCTTGTTTCCGACCCTACAAACTCGGAGCTCCTGTCG                         GTTCATGAGGAGCTTGTTTGGGCAATCAAAGATGCAGAAGAAGGGCTTTTT
genomic: TTCTCAAAGAAGCCCTTGTTTCCGACCCTACAAACTCGGAGCTCCTCTCGgtacaactct ... actggatcagGTTCATGAGGAGCTTATTTGGGCAATCAAAGATGCAGAAGAAGGGCTTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgggatttctgggtatatgatttatagtattgattactaagttaactggatcagGTTCATGAGGAGCTTATTTGGGCAATCAAAGATGCAGAAGAAGGGCTTTTTCACCTGAAACGGGCACGTTTATTGCGAGAAGCTGATTCAGCGCTACATG
                                        agttaac  putative branch site (score: 3)
              tatatgatttatagta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatgtagcaattgcatttatttataaaatatcaatgttctctgatgggatttctgggtatatgatttatagtattgattactaagttaactggatcagGTTCATGAGGAGCTTATTTGGGCAATCAAAGATGCAGAAGAAGGGCTTTTTCACCTGAAACGGGCACGTTTATTGCGAGAAGCTGATTCAGCGCTACATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - tgtagca
- - - - - - - - - - - - ataaaat
- - - - - - - - - - - - - - - - -caatgtt
- - - - - - - - - - - - - - - - - - - - - -tgatggg