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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctctcttgatacattctcaaactaaagagaatcggtttttagtaaaggctttgttgatggtgatatttttgtatggtatctaagataaaactctgcagGAAAAACTTTGCAGCATGCTTAAAGATGTGCTAAAGAACAAACCTAATGTGGATGTCGTGAAACTTCAAAAGTCAGGTGGTGTTGTATCCAGGGGTGCAA

Basic information

species Vitis vinifera
transcript Vv14s0066g02630.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0066g02630.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA20G38670.1 (Glycine max), 3'ss of exon 6
----atctctcttgata-cattctcaaactaaagagaatcggtttttagtaaaggctttgttgatggtgatatttttgtatggtatctaagataaaactctgcagGAAAAACTTTGCAGCATGCTTAAAGATGTGCTAAAGAACAAACCTAATGTGGATGTCGTGAAACTTCAAAAGTCAGGTGGTGTTGTATCCAGGGGTGCAA
    || | | |  ||| ||| ||     ||   | | | | |  ||  |      | ||| || | | |     |       |   |   ||    |  || |||||||||| ||||||||||| ||||||||||| ||||   | || || || || || || |||||||| | ||||||||| |||||||| |||  |||||
tcatatttttttgaatatcatactttccttatgcatagttgttaattcttgcc--ttctgtagaagctcagtgactcaggctttgctttgaatt---ccttgtagGAAAAACTGTGCAGCATGCTCAAAGATGTGCTCAAGAGTGAGCCCAAAGTAGACGTAGTTAAACTTCAGAGGTCAGGTGGAGTTGTATCTAGGAATGCAA
















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|351037774|gb|FQ464215.1|FQ464215
EST:     TCCATGCTATAGATACATTCAATGCCAATGTTGTTTTGGTTTCGGGTCAG                         GAAAAACTTTGCAGCATGCTTAAAGATGTGCTAAAGAACAAACCTAATGTG
genomic: TCCATGCTATAGATACATTCAATGCCAATGTTGTTTTGGTTTCGGGTCAGgtaagtggct ... aactctgcagGAAAAACTTTGCAGCATGCTTAAAGATGTGCTAAAGAACAAACCTAATGTG
EST: gi|351053260|gb|FQ459128.1|FQ459128
EST:     CCATGCTATAGATACATTTCA-TGCCAATGTTGTTTTGGTTTCGGGTCAG                         GAAAAACTTTGC
genomic: CCATGCTATAGATACATT-CAATGCCAATGTTGTTTTGGTTTCGGGTCAGgtaagtggct ... aactctgcagGAAAAACTTTGC
EST: gi|352789973|gb|FQ479583.1|FQ479583
EST:     TCCATGCTATAGATACATTCAATGCCAATGTTGTTTTGGTTTCGGGTCAG                         GAAAAACTTTGCAGCATGCTTAA
genomic: TCCATGCTATAGATACATTCAATGCCAATGTTGTTTTGGTTTCGGGTCAGgtaagtggct ... aactctgcagGAAAAACTTTGCAGCATGCTTAA
EST: gi|351046157|gb|FQ442535.1|FQ442535
EST:     TCCATGCTATAGATACATTCAATGCCAATGTTGTTTTGGTTTCGGGTCAG                         GAAAAACTTTGCAGCATGCTTAAAGATGTGCTAAAGAACAAACCTAATGTG
genomic: TCCATGCTATAGATACATTCAATGCCAATGTTGTTTTGGTTTCGGGTCAGgtaagtggct ... aactctgcagGAAAAACTTTGCAGCATGCTTAAAGATGTGCTAAAGAACAAACCTAATGTG
EST: gi|30130802|gb|CB916141.1|CB916141
EST:     GATACATTCAATGCCAATGTTGTTTTGGTTTCGGGTCAG                         GAAAAACTTTGCAGCATGCTTAAAGATGTGCTAAAGAACAAACCTAATGTG
genomic: GATACATTCAATGCCAATGTTGTTTTGGTTTCGGGTCAGgtaagtggct ... aactctgcagGAAAAACTTTGCAGCATGCTTAAAGATGTGCTAAAGAACAAACCTAATGTG
EST: gi|351042381|gb|FQ442848.1|FQ442848
EST:     TCCATGCTATAGATACATTCAATGCCAATGTTGTTTTGGTTTCGGGTCAG                         GAAAAACTTTGCAGCATACTTAAAGATGTGCTAAAGAACAAACCTAATGTG
genomic: TCCATGCTATAGATACATTCAATGCCAATGTTGTTTTGGTTTCGGGTCAGgtaagtggct ... aactctgcagGAAAAACTTTGCAGCATGCTTAAAGATGTGCTAAAGAACAAACCTAATGTG
EST: gi|110398356|gb|EC964659.1|EC964659
EST:     GATACATTCAATGCCAATGTTGTTTTGGTTTCGGGTCAG                         GAAAAACTTTGCAGCATGCTTAAAGATGTGCTAAAGAACAAACCTAATGTG
genomic: GATACATTCAATGCCAATGTTGTTTTGGTTTCGGGTCAGgtaagtggct ... aactctgcagGAAAAACTTTGCAGCATGCTTAAAGATGTGCTAAAGAACAAACCTAATGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaggctttgttgatggtgatatttttgtatggtatctaagataaaactctgcagGAAAAACTTTGCAGCATGCTTAAAGATGTGCTAAAGAACAAACCTAATGTGGATGTCGTGAAACTTCAAAAGTCAGGTGGTGTTGTATCCAGGGGTGCAA
        tgttgat  putative branch site (score: 4)
                 tgatatttttgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atctctcttgatacattctcaaactaaagagaatcggtttttagtaaaggctttgttgatggtgatatttttgtatggtatctaagataaaactctgcagGAAAAACTTTGCAGCATGCTTAAAGATGTGCTAAAGAACAAACCTAATGTGGATGTCGTGAAACTTCAAAAGTCAGGTGGTGTTGTATCCAGGGGTGCAA

-tctctct
- - - - - - -cattctc
- - - - - - - - - - aaactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagataa