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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctttatccatattcaattaatgcacaaaaaatgggaggaagcagcaagaagctctacaaatatgtagacatttccaaaattgatccacttctttgcagGCTGTTGCTGCAGATGCACTATCAAAGTTTTACTACCCCCCAGTTGCGGCAGTGTCCATTTCATATCCAAAGGAAGCAATTCGGACAGAATGCTTGATAG

Basic information

species Vitis vinifera
transcript Vv07s0005g02540.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g02540.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA10G27890.1 (Glycine max), 3'ss of exon 6
ttctttatccatattcaattaatgcacaaaaaatgggaggaagcagcaagaagctctacaaatatg-tagacatttccaaaattgatccac--ttctttgcagGCTGTTGCTGCAGATGCACTATCAAAGTTTTACTACCCCCCAGTTGCGGCAGTGTCCATTTCATATCCAAAGGAAGCAATTCGGACAGAATGCTTGATAG
      ||   |  |     ||||  ||||   ||| | ||   | |  |||  |  ||    | |   |  |||  | | |    |  ||  |   |||||||||| ||||||||||||||| ||||||||||| ||||| |||||||| ||||| ||||| || |||||||| ||||| ||| |  |||||||||||||||
--aaaaattagttgtttggaaatggccaaattttggcatgata-atcctgaatgtaaacgttgagggctgttattcacgacaaccttttactatctcttgcagGCTGCTGCTGCAGATGCACTTTCAAAGTTTTATTACCCTCCAGTTGCTGCAGTTTCCATATCCTATCCAAAAGAAGCTATTAGATCAGAATGCTTGATAG

upper sequence: Vv07s0005g02540.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA02G01000.1 (Glycine max), 3'ss of exon 8
---ttctttatccatattcaattaatgcacaaaaaatgggaggaagcagcaagaagctctacaaatatgtagacatttccaaaattgatccacttctttgcagGCTGTTGCTGCAGATGCACTATCAAAGTTTTACTACCCCCCAGTTGCGGCAGTGTCCATTTCATATCCAAAGGAAGCAATTCGGACAGAATGCTTGATAG
   |  ||     ||   ||| |  ||     | |||          | |  || ||  |       ||| |    |  ||   ||     |  || | | |||||| |||||||||| | || ||||||||||| ||||| |||||||  ||||| ||||| || |||||||| ||||| ||| |  |||||||||||||||
tagtggttcgaaaatggccaaattttgtcatgataatcccctatgtaaacttga-gcattgagggc-tgttgtttatgacagccttttaatatctcgt-gtagGCTGCTGCTGCAGATACGCTTTCAAAGTTTTATTACCCTCCAGTTGTTGCAGTTTCCATATCCTATCCAAAAGAAGCTATTAGATCAGAATGCTTGATAG
















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|351045190|gb|FQ451638.1|FQ451638
EST:     TGATGACTGTTCCATCCCGCGTTGCAAGTAGTCTGTTGCATCCTCTTTCT                         GCTGTTGCTGCAGATGCACTATCAAAGATTTACTACCCCCCAGTTGCGGCA
genomic: TGATGACTGTTCCATCCCGCGTTGCAAGTAGTCTGTTGCATCCTCTTTCTgtatgtttca ... ttctttgcagGCTGTTGCTGCAGATGCACTATCAAAGTTTTACTACCCCCCAGTTGCGGCA
EST: gi|351054509|gb|FQ451985.1|FQ451985
EST:     TGATGACTGTTCCATCCCGCGTTGCAAGTAGTCTGTTGCATCCTCTTTCT                         GCTGTTGCTGCAGATGCACTATCAAAGTTTTACTACCCCCCAGTTGCGGCA
genomic: TGATGACTGTTCCATCCCGCGTTGCAAGTAGTCTGTTGCATCCTCTTTCTgtatgtttca ... ttctttgcagGCTGTTGCTGCAGATGCACTATCAAAGTTTTACTACCCCCCAGTTGCGGCA
EST: gi|110378936|gb|EC944096.1|EC944096
EST:     TGATGACTGTCCCATCCCGCGTTGCAAGTAGTCTGTTGCATCCTCTTTCT                         GCTGTTGCTGCAGATGCACTATCAAAGTTTTACTACCCCCCAGTTGCGGCA
genomic: TGATGACTGTTCCATCCCGCGTTGCAAGTAGTCTGTTGCATCCTCTTTCTgtatgtttca ... ttctttgcagGCTGTTGCTGCAGATGCACTATCAAAGTTTTACTACCCCCCAGTTGCGGCA
EST: gi|110381438|gb|EC934459.1|EC934459
EST:     TGATGACTGTTCCATCCCGCGTTGCAAGTAGTCTGTTGCATCCTCTTTCT                         GCTGTTGCTGCAGATGCACTATCAAAGTTTTACTACCCCCCAGTTGCGGCA
genomic: TGATGACTGTTCCATCCCGCGTTGCAAGTAGTCTGTTGCATCCTCTTTCTgtatgtttca ... ttctttgcagGCTGTTGCTGCAGATGCACTATCAAAGTTTTACTACCCCCCAGTTGCGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaagaagctctacaaatatgtagacatttccaaaattgatccacttctttgcagGCTGTTGCTGCAGATGCACTATCAAAGTTTTACTACCCCCCAGTTGCGGCAGTGTCCATTTCATATCCAAAGGAAGCAATTCGGACAGAATGCTTGATAG
                                  aattgat  putative branch site (score: 4)
                                        tccacttcttt  CT-rich tract
           tacaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctttatccatattcaattaatgcacaaaaaatgggaggaagcagcaagaagctctacaaatatgtagacatttccaaaattgatccacttctttgcagGCTGTTGCTGCAGATGCACTATCAAAGTTTTACTACCCCCCAGTTGCGGCAGTGTCCATTTCATATCCAAAGGAAGCAATTCGGACAGAATGCTTGATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - aatgcac
- - - - - - - - - - - - - -aaaaaat
- - - - - - - - - - - - - - - - - - - ggaagca
- - - - - - - - - - - - - - - - - - - - - - -gcaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -acaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaattga