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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgtgttcttgcaacccgggctctcacacaaatccagatgtcgaataattctctaaatgcatagttgtaacttggcaacactgttggacatccttgcagGCTCTGTCAAAGAGAATCCACTATGGCAAGTTCGTGGCAGAGGCAAAATTCCAAGCCTCCCCAGATGCATACGAAGCTGCCATCAAAGCACAA

Basic information

species Vitis vinifera
transcript Vv14s0108g01330.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0108g01330.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G29200.1 (Arabidopsis thaliana), 3'ss of exon 4
--------tatgtgttcttgcaacccgggctctcacacaaatccagat----gtcgaataattctctaaatgcat----agttg--taacttggca-acactgttggacatcc-ttgcagGCTCTGTCAAAGAGAATCCACTATGGCAAGTTCGTGGCAGAGGCAAAATTCCAAGCCTCCCCAGATGCATACGAAGCTGCCATCAAAGCACAA
          | | ||| |       ||  ||  | ||||     |||    ||  || || |    |  |   |    ||| |  |||| |  ||   | | || ||  ||| ||||||  ||| |||||||||||||| || || || || || ||||| || ||||| |||||||| || || ||||||||  | |||||||||||||||
gtttgttcctttttttccttttgttaggtatcagaaacaagcttggatatttgtttaaaaacttgtcacctcttttctaagtcgattaacgtctcatgtagtttttgatgtccattgcagTGTCTCTCAAAGAGAATCCATTACGGTAAATTTGTTGCAGAAGCTAAATTTCAAGCCTCACCCGAAGCATACGAGTCCGCCATCAAAGCACAA
















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|33405272|gb|CF210899.1|CF210899
EST:     TGTGACACAATTTGCTTGCAG                         GCTCTGTCAAAGAGACTCCACTATGGCAAGTTCGTGGCAGAGGCAAAATTC
genomic: TGTGACACAATTTGCTTGCAGgtatgaattt ... atccttgcagGCTCTGTCAAAGAGAATCCACTATGGCAAGTTCGTGGCAGAGGCAAAATTC
EST: gi|33407291|gb|CF212918.1|CF212918
EST:     ATGATGGAAACTATGGATCAGCAGCTGTTTGTGACACAATTTGCTTGCAG                         GCTCTGTCAAAGAGAATCCACTATGGCAAGTTCGTGGCAGAGGCAAAATTC
genomic: ATGATGGAAACTATGGATCAGCAGCTGTTTGTGACACAATTTGCTTGCAGgtatgaattt ... atccttgcagGCTCTGTCAAAGAGAATCCACTATGGCAAGTTCGTGGCAGAGGCAAAATTC
EST: gi|351041739|gb|FQ455949.1|FQ455949
EST:     ATGATGGAAACTATGGATCAGCAGCTGTTTGTGACACAATTTGCTTGCAG                         GCTCTGTCAAAGAGAATCCACTATGGCAAGTTCGTGGCAGAGGCAAAATTC
genomic: ATGATGGAAACTATGGATCAGCAGCTGTTTGTGACACAATTTGCTTGCAGgtatgaattt ... atccttgcagGCTCTGTCAAAGAGAATCCACTATGGCAAGTTCGTGGCAGAGGCAAAATTC
EST: gi|161715858|gb|FC065189.1|FC065189
EST:     ATGATGGAAACTATGGATCAGCAGCTGTTTGTGACACAATTTGCTTGCAG                         GCTCTGTCAAAGAGAATCCACTATGGCAAGTTCGTGGCAGAGGCAAAATTC
genomic: ATGATGGAAACTATGGATCAGCAGCTGTTTGTGACACAATTTGCTTGCAGgtatgaattt ... atccttgcagGCTCTGTCAAAGAGAATCCACTATGGCAAGTTCGTGGCAGAGGCAAAATTC
EST: gi|351026402|gb|FQ428414.1|FQ428414
EST:     ATGATGGAAACTATGGATCAGCAGCTGTTTGTGACACAATTTGCTTGCAG                         GCTCTGTCAAAGAGAATCCACTATGGCAAGTTCGTGGCAGAGGCAAAATTC
genomic: ATGATGGAAACTATGGATCAGCAGCTGTTTGTGACACAATTTGCTTGCAGgtatgaattt ... atccttgcagGCTCTGTCAAAGAGAATCCACTATGGCAAGTTCGTGGCAGAGGCAAAATTC
EST: gi|351040113|gb|FQ425199.1|FQ425199
EST:     ATGATGGAAACTATGGATCAGCAGCTGTTTGTGACACAATTTGCTTGCAG                         GCTCTGTCAGAGAGAATCCACTATGGCAAGTTCGTGGCAGAGGCAAAAATC
genomic: ATGATGGAAACTATGGATCAGCAGCTGTTTGTGACACAATTTGCTTGCAGgtatgaattt ... atccttgcagGCTCTGTCAAAGAGAATCCACTATGGCAAGTTCGTGGCAGAGGCAAAATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataattctctaaatgcatagttgtaacttggcaacactgttggacatccttgcagGCTCTGTCAAAGAGAATCCACTATGGCAAGTTCGTGGCAGAGGCAAAATTCCAAGCCTCCCCAGATGCATACGAAGCTGCCATCAAAGCACAA
                    ttgtaac  putative branch site (score: 2)
                                            catcctt  putative PPT
       tctaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgtgttcttgcaacccgggctctcacacaaatccagatgtcgaataattctctaaatgcatagttgtaacttggcaacactgttggacatccttgcagGCTCTGTCAAAGAGAATCCACTATGGCAAGTTCGTGGCAGAGGCAAAATTCCAAGCCTCCCCAGATGCATACGAAGCTGCCATCAAAGCACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- tgtgttc
- - - - - -gcaaccc
- - - - - - - - - - -ctctcac
- - - - - - - - - - - - - - - aaatcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcaacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgga