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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagaaactagttcatgttggtttatgcatttcataaattatgtaagccttggaggggtatggacattcttggagaattctaattttcttcatttcaattagGGTGGTATAGTCCAAATTAGATTTCAACCTCGTCATGGAAGATATCTTGCAGCAGCTGCAGAGAACGTTGTATCAATACTGGATGTGGAGACACAAGCTT

Basic information

species Vitis vinifera
transcript Vv04s0008g04910.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g04910.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA14G16040.1 (Glycine max), 3'ss of exon 15
gtagaaactagttcatgttggtttatgcatttcataaattatgtaagccttggaggggtatggacattcttggagaattctaattttcttcatttcaattagGGTGGTATAGTCCAAATTAGATTTCAACCTCGTCATGGAAGATATCTTGCAGCAGCTGCAGAGAACGTTGTATCAATACTGGATGTGGAGACACAAGCTT
||||||  |    ||| | |  | ||||||||  | | ||   |  |  |||       ||   || | |   | | |   ||||||  | | |   |||||||||| | ||  ||||| ||||||||||||||||  || || || || || |||||||||||||| ||||| || ||||| |||||||| || ||||| |
gtagaattttag-catat-gcataatgcatttgtttacttggttgtgtattgagtttacattt-cagtttgctaaactgaaaatttttcttact--gattagGGTGGCACAGCTCAAATGAGATTTCAACCTCGTCTAGGGAGGTACCTAGCTGCAGCTGCAGAGAATGTTGTTTCTATACTTGATGTGGAAACTCAAGCAT

upper sequence: Vv04s0008g04910.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA17G30910.1 (Glycine max), 3'ss of exon 15
gtagaaactagttcatgttggtttatgcatttcataaattatgtaagccttggaggggtatggacattcttggagaattctaattttcttcatttcaattagGGTGGTATAGTCCAAATTAGATTTCAACCTCGTCATGGAAGATATCTTGCAGCAGCTGCAGAGAACGTTGTATCAATACTGGATGTGGAGACACAAGCTT
        |||   || || |   ||| || |  | | ||   |  |  ||| |     ||   || | |   | | |   || | |  | | |    |||||||||    || || || |||||||||||||| |  || || || || || |||||||||||||| ||||| || ||||| |||||||| |||||||| |
-------gtaga--attttagcacatgtatctgtttagttggttgtgtattgaatttacattt-cagtttgctaaactgacaaatcttctaact--ggttagGGTGGCGCTGTTCAGATGAGATTTCAACCTCGCCTAGGGAGGTACCTAGCTGCAGCTGCAGAGAATGTTGTTTCTATACTTGATGTGGAAACACAAGCAT
















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|161719157|gb|FC066063.1|FC066063
EST:     AGATACGATACTGGGTTATTAAGAACGCTTGCTGTGCAAGGGTATTCAAG                         GGTGGTATAGTCCAAATTAGATTTCAACCTCGTCATGGAAGATATCTTGCA
genomic: AGATACGATACTGGGTTATTAAGAACGCTTGCTGTGCAAGGGTATTCAAGgtagaaacta ... tttcaattagGGTGGTATAGTCCAAATTAGATTTCAACCTCGTCATGGAAGATATCTTGCA
EST: gi|110708875|gb|EE086916.1|EE086916
EST:     AGATACGATACTGGGTTATTAAGAACGCTTGCTGTGCAAAGGTATTCAAG                         GGTGGTATAGTCCAAATTAGATTTCAACCTCGTCATGGAAGATATCTTGCA
genomic: AGATACGATACTGGGTTATTAAGAACGCTTGCTGTGCAAGGGTATTCAAGgtagaaacta ... tttcaattagGGTGGTATAGTCCAAATTAGATTTCAACCTCGTCATGGAAGATATCTTGCA
EST: gi|110703802|gb|EE080967.1|EE080967
EST:     AGATACGATACTGGGTTATTAAGAACGCTTGCTGTGCAAGGGTATTCAAG                         GGTGGTATAGTCCAAATTAGATTTCAACCTCGTCATGGAAGATATCTTGCA
genomic: AGATACGATACTGGGTTATTAAGAACGCTTGCTGTGCAAGGGTATTCAAGgtagaaacta ... tttcaattagGGTGGTATAGTCCAAATTAGATTTCAACCTCGTCATGGAAGATATCTTGCA
EST: gi|110690242|gb|EE067180.1|EE067180
EST:     AGATACGATACTGGGTTATTAAGAACGCTTGCTGTGCAAGGGTATTCAAG                         GGTGGTATAGTCCAAATTAGATTTCAACCTCGTCATGGAAGATATCTTGCA
genomic: AGATACGATACTGGGTTATTAAGAACGCTTGCTGTGCAAGGGTATTCAAGgtagaaacta ... tttcaattagGGTGGTATAGTCCAAATTAGATTTCAACCTCGTCATGGAAGATATCTTGCA
EST: gi|34545176|gb|CF513408.1|CF513408
EST:     CTGTGCAAGGGTATTCAAG                         GGTGGTATAGTCCAAATTAGATTTCAACCTCGTCATGGAAGATATCTTGCA
genomic: CTGTGCAAGGGTATTCAAGgtagaaacta ... tttcaattagGGTGGTATAGTCCAAATTAGATTTCAACCTCGTCATGGAAGATATCTTGCA
EST: gi|110700254|gb|EE078082.1|EE078082
EST:     AGATACGATACTGGGTTATTAAGAACGCTTGCTGTGCAAGGGTATTCAAG                         GGTGGTATAGTCCAAATTAGATTTCAACCTCGTCATGGAAGATATCTTGCA
genomic: AGATACGATACTGGGTTATTAAGAACGCTTGCTGTGCAAGGGTATTCAAGgtagaaacta ... tttcaattagGGTGGTATAGTCCAAATTAGATTTCAACCTCGTCATGGAAGATATCTTGCA
EST: gi|34546171|gb|CF514403.1|CF514403
EST:     AGATACGATACTGGGTTATTAAGAACGCTTGCTGTGCAAGGGTATTCAAG                         GGTGGTATAGTCCAAATTAGATTTCAACCTCGTCATGGAAGATATCTTGCA
genomic: AGATACGATACTGGGTTATTAAGAACGCTTGCTGTGCAAGGGTATTCAAGgtagaaacta ... tttcaattagGGTGGTATAGTCCAAATTAGATTTCAACCTCGTCATGGAAGATATCTTGCA
EST: gi|110699780|gb|EE077080.1|EE077080
EST:     AGATACGATACTGGGTTATTAAGAACGCTTGCTGTGCAAGGGTATTCAAG                         GGTGGTATAGTCCAAATTAGATTTCAACCTCGTCATGGAAGATATCTTGCA
genomic: AGATACGATACTGGGTTATTAAGAACGCTTGCTGTGCAAGGGTATTCAAGgtagaaacta ... tttcaattagGGTGGTATAGTCCAAATTAGATTTCAACCTCGTCATGGAAGATATCTTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttggaggggtatggacattcttggagaattctaattttcttcatttcaattagGGTGGTATAGTCCAAATTAGATTTCAACCTCGTCATGGAAGATATCTTGCAGCAGCTGCAGAGAACGTTGTATCAATACTGGATGTGGAGACACAAGCTT
                              ttctaat  putative branch site (score: 2)
                                    ttttcttcatttc  CT-rich tract
                                 taattttcttcatttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagaaactagttcatgttggtttatgcatttcataaattatgtaagccttggaggggtatggacattcttggagaattctaattttcttcatttcaattagGGTGGTATAGTCCAAATTAGATTTCAACCTCGTCATGGAAGATATCTTGCAGCAGCTGCAGAGAACGTTGTATCAATACTGGATGTGGAGACACAAGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT