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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agctaaggtttctgcagcaatatcttttactgaagctaacttgttaacttatcaattcaaacaagaagaggttattctgtttctgattccctttctctagGTGCTATGTGCTTCCAATGAAGATCACACTGGTGTAGAGCCTTTGCTCCCTCCAGAAGGTGCCAAAATTGGGGAACGTGTTTCATTTTCTGG

Basic information

species Vitis vinifera
transcript Vv13s0067g03060.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0067g03060.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G166345_T02 (Zea mays), 3'ss of exon 8
-agctaaggtttctgcagcaatatcttttactg-aagctaact--tgttaacttatcaattcaaacaagaagaggttattctgtttctgattccctttctctagGTGCTATGTGCTTCCAATGAAGATCACACTGGTGTAGAGCCTTTGCTCCCTCCAGAAGGTGCCAAAATTGGGGAACGTGTTTCATTTTCTGG
 | || | ||||||  |    |       |||| | |   |||  |||||  ||     ||  |   ||| |   || || ||      ||  | | |  | |||| || |||||||| | |||||||||  ||| ||| ||||||||| | ||||||||||| ||||| ||||| |||||  |||||||| ||||
gaacttaagtttcttaactcctggtccaaactgtatgtgtacttctgttattttgaggtttttattgagatgt--ttgttttggcatcaat--cttatgcccagGTCCTTTGTGCTTCAACTGAAGATCATGCTGCTGTGGAGCCTTTGATTCCTCCAGAAGGAGCCAAGATTGGAGAACGCATTTCATTTGCTGG

upper sequence: Vv13s0067g03060.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA04G40090.1 (Glycine max), 3'ss of exon 9
------------agctaaggtttctgcagcaatatcttttactgaagctaactt--gttaacttatcaattcaaacaagaagaggttattctgtttctgattccctttctctagGTGCTATGTGCTTCCAATGAAGATCACACTGGTGTAGAGCCTTTGCTCCCTCCAGAAGGTGCCAAAATTGGGGAACGTGTTTCATTTTCTGG
            |     | |   ||    ||  | |||| |||    || |||  | |     | ||||   ||     | | || |||  | | |   ||||  ||  | ||||  |||||||||| ||||||| ||  ||   ||| ||||| ||||||||||||||||| || |||||||| |||| | |||| ||||||||
gtattgatgctcattcttgttgcatgtgttaaatttttttgctgtgtgtagcttttgatggtcaagcaatcttaagggacatatgt-atttggctccccgttcctctttac-agGTCTTATGTGCTTCGAATGAAGGTCCAACCATTGTGGAGCCCTTGCTCCCTCCAGAAGGAGCAAAAATTGGTGAACATATTTCTTTTTCTGG
















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|30329567|gb|CD012829.1|CD012829
EST:     TCACAAATGTTAAACCTGGAAAGCTACGAGATGTGATGTCAGAAGGACTG                         GTGCTATGTGCTTCCAATGAAGATCACACTGGTGTAGAGCCTTTGCTCCCT
genomic: TCACAAATGTTAAACCTGGAAAGCTACGAGATGTGATGTCAGAAGGACTGgtaatcattt ... ctttctctagGTGCTATGTGCTTCCAATGAAGATCACACTGGTGTAGAGCCTTTGCTCCCT
EST: gi|110374826|gb|EC939761.1|EC939761
EST:     TCACAAATGTTAAACCTGGAAAGCTACGAGATGTGATGTCAGAAGGACTG                         GTGCTATGTGCTTCCAATGAAGATCACACTGGTGTAGAGCCTTTGCTCCCT
genomic: TCACAAATGTTAAACCTGGAAAGCTACGAGATGTGATGTCAGAAGGACTGgtaatcattt ... ctttctctagGTGCTATGTGCTTCCAATGAAGATCACACTGGTGTAGAGCCTTTGCTCCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacttatcaattcaaacaagaagaggttattctgtttctgattccctttctctagGTGCTATGTGCTTCCAATGAAGATCACACTGGTGTAGAGCCTTTGCTCCCTCCAGAAGGTGCCAAAATTGGGGAACGTGTTTCATTTTCTGG
                          ttattctgtttctgat  CT-rich tract
        aattcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agctaaggtttctgcagcaatatcttttactgaagctaacttgttaacttatcaattcaaacaagaagaggttattctgtttctgattccctttctctagGTGCTATGTGCTTCCAATGAAGATCACACTGGTGTAGAGCCTTTGCTCCCTCCAGAAGGTGCCAAAATTGGGGAACGTGTTTCATTTTCTGG

- - - - - tctgcag
- - - - - - - - - - - - - - - tgaagct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaacaa