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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcatgatcgactatgattctccaattccttatttgttaatatgttaaaaaatcttgtttagttgttcattggcctagttaacatacttgatggttgtagGAGTCGGGAATTTCTTTGGCAGGAGGGGCATACTGCTTTTGCTACAAAGGAAGAGGCAGATAAAGAG

Basic information

species Vitis vinifera
transcript Vv07s0005g02620.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g02620.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G094123_T01 (Zea mays), 3'ss of exon 5
ttcatgatcgactatgattctccaattccttatttgttaatatgttaaaaaatctt---gtttagttgttcattggcctagttaacatact-tgatggttgt----agGAGTCGGGAATTTCTTTGGCAGGAGGGGCATACTGCTTTTGCTACAAAGGAAGAGGCAGATAAAGAG
       |  | | | || ||    ||   |   | |   | |    |    ||     || |    ||   ||  ||| || ||||| || |  |  || |    ||||| || |||||||| ||||| |||||||||||||||||||| || || |||||||||||| |||||
-------tttaatgt-atcctttgtttatgtgcatatggctgtacccagtcctcccctggtgtgcgcgtgttttttccttgtgaacattctgtagttattctcttcagGAGCCGTGAATTTCTGTGGCAAGAGGGGCATACTGCTTTTGCGACTAAAGAAGAGGCAGATGAAGAG

upper sequence: Vv07s0005g02620.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA19G40930.1 (Glycine max), 3'ss of exon 6
ttcatgatcgactatgattctccaattcct-tatttgttaat--atgttaaaaaatcttgtttagttgttcattggcctagttaacatacttgatggttgtagGAGTCGGGAATTTCTTTGGCAGGAGGGGCATACTGCTTTTGCTACAAAGGAAGAGGCAGATAAAGAG
 | |  || |  |  ||| ||     |  | | |    ||||  || |||   ||  |||| ||||   |  |  |    | | | | |  |  || ||  |||||||| || ||||||||||| || ||||| ||||||||||| |||||||| || ||||||  ||||
-ttaatatggttttggatactgttgctgttatgtaaactaatttatattatggaactttgtctagtccattgtgtggt--gctcatagaagttttgatttcagGAGTCGCGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCAACAAAGGATGAAGCAGATGCAGAG

upper sequence: Vv07s0005g02620.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA03G38340.1 (Glycine max), 3'ss of exon 6
ttcatgatcgactatgattct-ccaattccttatttgttaat--atgttaaaaaatcttgtttagttgttcattg-gcctagttaacatacttgatggttgtagGAGTCGGGAATTTCTTTGGCAGGAGGGGCATACTGCTTTTGCTACAAAGGAAGAGGCAGATAAAGAG
 | |  || |  |  ||| ||     || | | |    || |  || ||    ||  ||||    | || ||||| |    | | | | |  |  || ||| |||||||| || ||||||||||| || ||||| |||||||||||| ||||||| || ||||||  ||||
-ttaatatggttttggatactgttgctttcatgtaaaatagtttatattctggaactttgtcc--tagtccattgtgtggtgcttatagaagtt-tgattgcagGAGTCGTGAGTTTCTTTGGCAAGAAGGGCACACTGCTTTTGCTTCAAAGGAGGAAGCAGATGCAGAG

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|352787275|gb|FQ477895.1|FQ477895
EST:     TGGTGCAATGTTGTTCGATGGGAGTTCAGCCATCCTACCCCGTTTATAAG                         GAGTCGGGAATTTCTTTGGCAGGAGGGGCATACTGCTTTTGCTAC
genomic: TGGTGCAACGTTGTTCGGTGGGAGTTCAGCCATCCTACCCCATTTATAAGgtagtttggt ... atggttgtagGAGTCGGGAATTTCTTTGGCAGGAGGGGCATACTGCTTTTGCTAC
EST: gi|30306282|gb|CB983076.1|CB983076
EST:     TGGTGCAACGTTGTTCGGGGGGAGTTCAGCCATCCTACCCCATTTATAAG                         GAGTCGGGAATTTCTT-GGCAGGAGGGGCATACTGCTTTTGCTAAAAAGGA
genomic: TGGTGCAACGTTGTTCGGTGGGAGTTCAGCCATCCTACCCCATTTATAAGgtagtttggt ... atggttgtagGAGTCGGGAATTTCTTTGGCAGGAGGGGCATACTGCTTTTGCTACAAAGGA
EST: gi|294964991|gb|GW838794.1|GW838794
EST:     TGGTGCAACGTTGTTCGGTGGGAGTTCAGCCATCCTACCCCATTTATAAG                         GAGTCGGGAATTTCTTTGGCAGGAGGGGCATACTGCTTTTGCTACAAAGGA
genomic: TGGTGCAACGTTGTTCGGTGGGAGTTCAGCCATCCTACCCCATTTATAAGgtagtttggt ... atggttgtagGAGTCGGGAATTTCTTTGGCAGGAGGGGCATACTGCTTTTGCTACAAAGGA
EST: gi|110712760|gb|EE088090.1|EE088090
EST:     TGGTGCAATGTTGTTCGGTGGGAGTTCAGCCATCCTACCCCGTTTATAAA                         GAGTCGGGAATTTCTTTGGCAGGAAGGGCATACTGCTTTTGCTACAAAGGA
genomic: TGGTGCAACGTTGTTCGGTGGGAGTTCAGCCATCCTACCCCATTTATAAGgtagtttggt ... atggttgtagGAGTCGGGAATTTCTTTGGCAGGAGGGGCATACTGCTTTTGCTACAAAGGA
EST: gi|29784140|gb|CB344515.2|CB344515
EST:     TGGTGCAACGTTGTTCGGTGGGAGTTCAGCCATCCTACCCCATTTATAAG                         GAGTCGGGAATTTCTTTGGCAGGAGGGGCATACTGCTTTTGCTACAAAGGA
genomic: TGGTGCAACGTTGTTCGGTGGGAGTTCAGCCATCCTACCCCATTTATAAGgtagtttggt ... atggttgtagGAGTCGGGAATTTCTTTGGCAGGAGGGGCATACTGCTTTTGCTACAAAGGA
EST: gi|161708997|gb|FC058789.1|FC058789
EST:     TGGTGCAATGTTGTTCGGTGGGAGTTCAGCCATCCTACCCCGTTTATAAG                         GAGTCGGGAATTTCTTTGGCAGGAGGGGCATACTGCTTTTGCTACAAAGGA
genomic: TGGTGCAACGTTGTTCGGTGGGAGTTCAGCCATCCTACCCCATTTATAAGgtagtttggt ... atggttgtagGAGTCGGGAATTTCTTTGGCAGGAGGGGCATACTGCTTTTGCTACAAAGGA
EST: gi|37190730|gb|CF610079.1|CF610079
EST:     TGGTGCAACGTTGTTCGGTGGGAGTTCAGCCATCCTACCCCGTTTATAAG                         GAGTCGGGAATTTCTTTGGCAGGAGGGGCATACTGCTTTTGCTACAAAGGA
genomic: TGGTGCAACGTTGTTCGGTGGGAGTTCAGCCATCCTACCCCATTTATAAGgtagtttggt ... atggttgtagGAGTCGGGAATTTCTTTGGCAGGAGGGGCATACTGCTTTTGCTACAAAGGA
EST: gi|110713336|gb|EE089170.1|EE089170
EST:     TGGTGCAATGTTGTTCGGTGGGAGTTCAGCCATCCTACCCCGTTTATAAG                         GAGTCAGGAATTTCTTTGGCAGGAGGGGCATACTGCTTTTGCTACAAAGGA
genomic: TGGTGCAACGTTGTTCGGTGGGAGTTCAGCCATCCTACCCCATTTATAAGgtagtttggt ... atggttgtagGAGTCGGGAATTTCTTTGGCAGGAGGGGCATACTGCTTTTGCTACAAAGGA
EST: gi|110712013|gb|EE089150.1|EE089150
EST:     TGGTGCAATGTTGTTCGGTGGGAGTTCAGCCATCCTACCCCGTTTATAAG                         GAGTCGGGAATTTCTTTTGCAGGAGGGGCAAACTGCTTTTGCTACAAAGGA
genomic: TGGTGCAACGTTGTTCGGTGGGAGTTCAGCCATCCTACCCCATTTATAAGgtagtttggt ... atggttgtagGAGTCGGGAATTTCTTTGGCAGGAGGGGCATACTGCTTTTGCTACAAAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaaaatcttgtttagttgttcattggcctagttaacatacttgatggttgtagGAGTCGGGAATTTCTTTGGCAGGAGGGGCATACTGCTTTTGCTACAAAGGAAGAGGCAGATAAAGAG
                                 ttaacata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcatgatcgactatgattctccaattccttatttgttaatatgttaaaaaatcttgtttagttgttcattggcctagttaacatacttgatggttgtagGAGTCGGGAATTTCTTTGGCAGGAGGGGCATACTGCTTTTGCTACAAAGGAAGAGGCAGATAAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- catgatc
- - - - - - - - - tctccaa
- - - - - - - - - - - - - - - - - - - - - - -taaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacatac