Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtacactgttaatttcagatgtagttgacttgccttcgcttttcatcatttccaagtcctgttatttaggcttttatctaaccatcttctggtacagCCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG

Basic information

species Vitis vinifera
transcript Vv12s0035g01060.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G138676_T02 (Zea mays), 3'ss of exon 8
gtagtacactgttaatttcagatgtagttgacttgccttcgcttttcatcatttccaagtcctgttatttaggcttttatctaaccatcttctggtacagCCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG
                            || | ||  |||  ||| | ||   ||    || |    ||| |  | || |   | |||       |  || || |||||||||||||||| ||||| || |||||||||||||||||||||
-------------------------gtctggcatg--ttcagtttccctc-cctctggttcttacctttttgcttcttctgatatcattcatccatgtagGCTCTGTTTCCTGGAGAAAGTGGAGTCGACCAACTAGTTGAGATCATCAAG

upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 7
----gtagtacactgttaatttcagatgtagttgacttgccttcgcttttcatcatttccaagtcctgttatttaggcttttatctaacc-atcttctggtacagCCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG
     | || ||     ||  |  ||   | ||  ||    |   | |||| |  ||| |  ||| | || || |   |||  |  |    |  ||    | ||||| |||||||||||||| || ||||||||||| |||||||| |||||||||
gtatttggtgcaagaaaaaaatgtgacaaatttttctcatttcatcatttctttgttttct-gtcttctttttca--ttttcctgaagttgaagttgatttgcagCCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG

upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 8
gtagtacactgttaatttcagatgtagttgacttgccttcgcttttcatcatttccaagtcctgt---tatttaggcttttatctaa---ccatcttctggtacagCCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG
||| |    | || |    | ||||     | ||   ||| | ||||||||||||   ||  | |   |  ||  || |||  || |    ||  ||    | ||||| |||||||||||||| || ||||||||||| |||||||| |||||||||
gtatttggttctttaaaa-aaatgtgacaaattt---ttctcatttcatcatttctctgttttctgtcttcttttgcattttcctgaagttcaagttgatttgcagCCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAG

upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT1G09840.1 (Arabidopsis thaliana), 3'ss of exon 8
---gtagtacactgttaatttcagatgtagttgacttgccttcgcttttcatcatttccaagtcctgttatttaggcttttatctaaccatcttctggtacagCCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG
     || |   | ||    | || | ||  |   |   ||   | ||   |   ||||  ||| |  ||||| |     |  ||||     || | ||||||||| |||||||||| || |||||||||||||| || ||||| ||||| |||
gttaaagcatgatttttgcattagctatatgttgtt---ctattcattcagtttattccttgtcttactattttgtgcccttgctaat----ttgtcgtacagCCTCTGTTTCCTGGTGAGAGCGGAGTTGATCAGCTTGTTGAAATCATTAAG

upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 6
-gtagtacactgtta-atttcagatgtagttgacttgccttcgcttttcatcatttccaagtcctgttatttaggcttttatctaaccatcttctgg--tacagCCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG
     ||   || |      ||  |||||  |  |||   | |   |     |  |  | ||   || || | || ||| |     |  |     ||  | |||||||||||||||||||| || ||||| |||||| | || || |||||||||
gacgatatgttgctgtggcgcaagtgtaga-ggtttgaagttgaggtgagggagctttatgt---gtaatctgggttttgacgacgcttttgatgggattgcagCCTTTGTTTCCTGGAGAGAGTGGAGTGGATCAATTGGTGGAAATCATCAAG

upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 6
gtagtacactgttaatttcagatgtagttgacttgccttcgcttttcatcattt-ccaagtcctgttatttaggcttttatctaaccatctt----ctggtacagCCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG
 |||   |  |||  | | || || |   || |||  |   ||||  |   ||      ||    || | |||  | | |    |   |||      |||| ||||||||||| ||||||||||| ||||| |||||| | || || |||||||||
-tagatga--gtttgtgtgagctggaagcgagttg--tgaactttatagtgttggtttggtgagattttatagattctgactggatagtctggatgttggtgcagCCTTTGTTCCCTGGAGAAAGTGGAGTCGATCAATTGGTGGAAATCATCAAG

upper sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 7
----------------------------------------------------------------------------gtagtacactgt--taatt----tcagatgtagttgacttgccttcgcttttcatcatttccaagtcctgttatttaggcttttatctaaccatcttc-----tggtacagCCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG
                                                                             |||  || |||  | |||    | |||||||  ||  | |  |    |  ||||  ||          | |  |  |  || | |||   ||  |||     |||| ||||||||||| |||||||||||||||||||||||| | || ||||||||||||
gtacttatgtagttcctggtagatggtgaattcatggagattctattactcctgagtactatggttcggaatggagatagatcattgtgttgattgtaatgagatgtaagtggttgg--tgaagtgatcattgttggtttagttagatgatatgaattctgtctggacaatttcgatgttggtgcagCCTTTGTTCCCTGGAGAAAGCGGAGTTGATCAATTGGTGGAGATCATCAAG

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|30126156|gb|CB911495.1|CB911495
EST:     TAGATATTTGGTCTACTGGCTGTGTGATGGCTGAATTGCTTCTGGGACAG                         CCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG
genomic: TAGATATTTGGTCTACTGGCTGTGTGATGGCTGAATTGCTTCTGGGACAGgtagtacact ... tctggtacagCCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG
EST: gi|110726124|gb|EE101641.1|EE101641
EST:     TAGATATTTGGTCTACTGGCTGTGTGATGGCTGAATTGCTTCTGGGACAG                         CCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG
genomic: TAGATATTTGGTCTACTGGCTGTGTGATGGCTGAATTGCTTCTGGGACAGgtagtacact ... tctggtacagCCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG
EST: gi|27580396|gb|CB003091.1|CB003091
EST:     TAGATATTTGGTCTACTGGCTGTGTGATGGCTGAATTGCTTCTGGGACAG                         CCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG
genomic: TAGATATTTGGTCTACTGGCTGTGTGATGGCTGAATTGCTTCTGGGACAGgtagtacact ... tctggtacagCCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG
EST: gi|161715603|gb|FC067769.1|FC067769
EST:     TAGATATTTGGTCTACTGGCTGTGTGATGGCTGAATTGCTTCTGGGACAG                         CCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG
genomic: TAGATATTTGGTCTACTGGCTGTGTGATGGCTGAATTGCTTCTGGGACAGgtagtacact ... tctggtacagCCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG
EST: gi|27579322|gb|CB002017.1|CB002017
EST:     TAGATATTTGGTCTACTGGCTGTGTGATGGCTGAATTGCTTCTGGGACAG                         CCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG
genomic: TAGATATTTGGTCTACTGGCTGTGTGATGGCTGAATTGCTTCTGGGACAGgtagtacact ... tctggtacagCCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG
EST: gi|156736132|gb|EV240253.1|EV240253
EST:     TAGATATTTGGTCTACTGGCTGTGTGATGGCTGAATTGCTTCTGGGACAG                         CCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG
genomic: TAGATATTTGGTCTACTGGCTGTGTGATGGCTGAATTGCTTCTGGGACAGgtagtacact ... tctggtacagCCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG
EST: gi|27581595|gb|CB004290.1|CB004290
EST:     TAGATATTTGGTCTACTGGCTGTGTGATGGCTGAATTGCTTCTGGGACAG                         CCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG
genomic: TAGATATTTGGTCTACTGGCTGTGTGATGGCTGAATTGCTTCTGGGACAGgtagtacact ... tctggtacagCCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG
EST: gi|27581007|gb|CB003702.1|CB003702
EST:     TAGATATTTGGTCTACTGGCTGTGTGATGGCTGAATTGCTTCTGGGACAG                         CCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG
genomic: TAGATATTTGGTCTACTGGCTGTGTGATGGCTGAATTGCTTCTGGGACAGgtagtacact ... tctggtacagCCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG
EST: gi|30130728|gb|CB916067.1|CB916067
EST:     TAGATATTTGGTCTACTGGCTGTGTGATGGCTGAATTGCTTCTGGGACAG                         CCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG
genomic: TAGATATTTGGTCTACTGGCTGTGTGATGGCTGAATTGCTTCTGGGACAGgtagtacact ... tctggtacagCCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG
EST: gi|27579129|gb|CB001824.1|CB001824
EST:     TAGATATTTGGTCTACTGGCTGTGTGATGGCTGAATTGCTTCTGGGACAG                         CCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG
genomic: TAGATATTTGGTCTACTGGCTGTGTGATGGCTGAATTGCTTCTGGGACAGgtagtacact ... tctggtacagCCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatcatttccaagtcctgttatttaggcttttatctaaccatcttctggtacagCCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG
                                 atctaac  putative branch site (score: 2)
                                       ccatcttct  CT-rich tract
                             ttttatctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtacactgttaatttcagatgtagttgacttgccttcgcttttcatcatttccaagtcctgttatttaggcttttatctaaccatcttctggtacagCCTTTGTTTCCTGGAGAAAGCGGAGTTGATCAACTAGTTGAGATCATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA