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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgtatatatatatagatagatatatagatattgcaagggatttttatcactttatgcttcagaattcaagttaaagttggtgccttattaattatcagGTCCGAGAATGAAATTCAACCTATTACTGAGAAAGCTAACCGTGAAGTACGGCGAGCACCAAGCTTTAGTGGTCCATTGATGCTTCCGAATCGAGCTTCA

Basic information

species Vitis vinifera
transcript Vv02s0025g02480.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g02480.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA20G35970.2 (Glycine max), 3'ss of exon 9
tatgtatatatatatagatagatatatagatattgcaagggatttttatcactttatgcttcagaattca--agttaaagttggt---gccttattaattatcagGTCCGAGAATGAAATTCAACCTATTACTGAGAAAGCTAACCGTGAAGTACGGCGAGCACCAAGCTTTAGTGGTCCATTGATGCTTCCGAATCGAGCTTCA
| ||  | |  || |  || | |   | |  ||||  |||  || || | |      || | |   ||     |||||| || ||   || |||||| || | ||||  ||||||||||  ||         |||||||  ||| |||||  |||| ||||| |||||||||||||||||||| |||||||| || |||||||||
tctggttctg-atctttat-gctgcttggtgattg--aggttttcttgttatcaccagcataatcttttgcttgttaaaatttgtaatgctttattactt-ttagGTTTGAGAATGAAAACCAGTTAGCGGGTGAGAAAAGTAATCGTGATATACGACGAGCTCCAAGCTTTAGTGGTCCATTAATGCTTCCAAACCGAGCTTCA

upper sequence: Vv02s0025g02480.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA10G31630.1 (Glycine max), 3'ss of exon 9
tatgtatatatatatagatagatatatagatattgcaagggatttttatcactttatgcttcagaattcaa--gttaaagtt---ggtgccttattaattatcagGTCCGAGAATGAAATTCAACCTATTACTGAGAAAGCTAACCGTGAAGTACGGCGAGCACCAAGCTTTAGTGGTCCATTGATGCTTCCGAATCGAGCTTCA
    |   | | |       | |   | |  ||||  |||  || || | |      || | |  |||     |||||| ||     ||| |||||| || | ||||  |||||||||| |||     |   |||||||  ||| |||||  |||| ||||| |||||||||||||||||||| |||||||| || |||||||||
---ctggttttgtcctttatgctgcctggtgattg--aggttttcttgttatcaccagcataaccatttgcttgttaaaatttgtaatgctttattactttttagGTTTGAGAATGAAAATCAGTTATTGGGTGAGAAAAGTAATCGTGATATACGACGAGCTCCAAGCTTTAGTGGTCCATTAATGCTTCCAAACCGAGCTTCA

upper sequence: Vv02s0025g02480.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA20G16510.2 (Glycine max), 3'ss of exon 10
tatgtatatatatatagatagatatatagatattgcaagggattt-ttatc-actttatgcttcagaattcaagttaa-agttggtgccttattaattatcagGTCCGAGAATGAAATTCAACCTATTACTGAGAAAGCTAACCGTGAAGTACGGCGAGCACCAAGCTTTAGTGGTCCATTGATGCTTCCGAATCGAGCTTCA
|||  || | | ||  ||| | |  |  |  ||||      | || || || |  | ||  |       || |   || | ||  ||| || ||| || | |||   ||||||| || |||     |    ||||||  |||||||||||  || | | | ||||| |||||||||||||||||||||||||  |||||||||
tatccatttct-tactgat-gcttcagtgtgattgttgtttacttcttgtcgatatcatcatattttgctcgataaaacatttaatgctttgttattt-ttagGCTTGAGAATGGAAATCAGTTATTGGGCGAGAAAAATAACCGTGAAGCGCGACAACCTCCAAGTTTTAGTGGTCCATTGATGCTTCCGACGCGAGCTTCA

upper sequence: Vv02s0025g02480.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA13G10450.2 (Glycine max), 3'ss of exon 10
-tatgtatatatat-atagatagatatatagatattgcaagggattttt--atcactttatgcttcagaattcaagttaaagttggtgccttattaattatcagGTCCGAGAATGAAATTCAACCTATTACTGAGAAAGCTAACCGTGAAGTACGGCGAGCACCAAGCTTTAGTGGTCCATTGATGCTTCCGAATCGAGCTTCA
 | | |  || | | |  ||| | |  |  |  ||||      | || |  ||  | | ||  || |   || |    | | ||  ||| |||||| || | |||   ||||||| || |||     |   |||||||  ||||| |||||  || ||||| ||||| ||||||||||||||||||||||| |  |||||||||
ttctttccatttcttactgat-gcttcagtgtgattgttgtttacttgtcaatatcatcatattttac--ttgataaaacatttaatgctttattattt-ttagGCTTGAGAATGGAAATCAGTTACTGGGTGAGAAAAATAACCATGAAGCGCGACGAGCGCCAAGTTTTAGTGGTCCATTGATGCTTCCAATGCGAGCTTCA

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|110418566|gb|EC984726.1|EC984726
EST:     GGTGTTGTGCTTAGTCATTCATTGTCAGACAGGGGGCGCTCCTTTGAAAG                         GTCCGAGAATGAAATTCAACCAATTACTGAGAAAGCTAACCGTGAAGTACG
genomic: GGTGTTGTGCTTAGTCATTCATTGTCAGACAGGGGGCGCTCCTTTGAAAGgttcataatg ... taattatcagGTCCGAGAATGAAATTCAACCTATTACTGAGAAAGCTAACCGTGAAGTACG
EST: gi|161710935|gb|FC058203.1|FC058203
EST:     GGTGTTGTGCTTAGTCATTCATTGTCAGACAGGGGGCGCTCCTTTGAAAG                         GTCCGAGAATGAAATTCAACCTATTACTGAGAAAGCTAACCGTGAAGTACG
genomic: GGTGTTGTGCTTAGTCATTCATTGTCAGACAGGGGGCGCTCCTTTGAAAGgttcataatg ... taattatcagGTCCGAGAATGAAATTCAACCTATTACTGAGAAAGCTAACCGTGAAGTACG
EST: gi|352764110|gb|FQ467680.1|FQ467680
EST:     GGTGTTGTGCTTAGTCATTCATTGTCAGACAGGGGGCGCTCCTTTGAAAG                         GTCCGAGAATGAAATTCAACCTATTACTGAGAAAGCTAACCGTGAAGTACG
genomic: GGTGTTGTGCTTAGTCATTCATTGTCAGACAGGGGGCGCTCCTTTGAAAGgttcataatg ... taattatcagGTCCGAGAATGAAATTCAACCTATTACTGAGAAAGCTAACCGTGAAGTACG
EST: gi|30132243|gb|CB917582.1|CB917582
EST:     GGTGTTGTGCTTAGTCATTCATTGTCAGACAGGGGGCGCTCCTTTGAAAG                         GTCCGAGAATGAAATTCAACCAATTACTGAGAAAGCTAACCGTGAAGTACG
genomic: GGTGTTGTGCTTAGTCATTCATTGTCAGACAGGGGGCGCTCCTTTGAAAGgttcataatg ... taattatcagGTCCGAGAATGAAATTCAACCTATTACTGAGAAAGCTAACCGTGAAGTACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatcactttatgcttcagaattcaagttaaagttggtgccttattaattatcagGTCCGAGAATGAAATTCAACCTATTACTGAGAAAGCTAACCGTGAAGTACGGCGAGCACCAAGCTTTAGTGGTCCATTGATGCTTCCGAATCGAGCTTCA
                                          tattaat  putative branch site (score: 2)
                                       ccttatt  CT-rich tract
                                         ttattaattatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgtatatatatatagatagatatatagatattgcaagggatttttatcactttatgcttcagaattcaagttaaagttggtgccttattaattatcagGTCCGAGAATGAAATTCAACCTATTACTGAGAAAGCTAACCGTGAAGTACGGCGAGCACCAAGCTTTAGTGGTCCATTGATGCTTCCGAATCGAGCTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcctta