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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTACATGTTGTGGTTACAATGTTTTCTGGCTATTTGGTTGGATATGCTGCATTCAGAGCATTGTTTAGTCACAACCCTGTCATGgtaccctttcagtgaccttgaatttatataagttctatttcttgaaaaatgttaaaacacgtttccctattcctcatgggagattattttctttgtaagtttggttctctttaattatagtgttattgaaattgatggttctctaatcctaaatttcag

Basic information

species Vitis vinifera
transcript Vv02s0012g01580.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0012g01580.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA10G35690.1 (Glycine max), 5'ss of exon 3
GTTTACATGTTGTGGTTACAATGTTTTCTGGCTATTTGGTTGGATATGCTGCATTCAGAGCATTGTTTAGTCACAACCCTGTCATGgtac--cctttcagtgaccttgaatttatataagttctatttcttgaaaaatgttaaaacacgtttccctattcctcatgggagattattttctttgtaagtttggttctctttaattatagtgttattgaaattgatggttctctaatcctaaatttcag
|||| |||||||||||||| |||||| |||||||| |  | |||||||| ||||| ||||||||||||| |||||  |||| ||||||||  |||   |      ||  |||  |||   || ||| || | ||| |  |  |   | |  |    ||| ||| | |    ||  || |||| |    |   ||  |                                                  
GTTTGCATGTTGTGGTTACCATGTTTACTGGCTATCTTCTCGGATATGCAGCATTTAGAGCATTGTTTAATCACAGTCCTGCCATGgtactacctaaaatctgtttttcattgttattcatt-tatatcctcaaatagttgtagttatgagttttcatttctcttcgt---ttccttcctttcttgtctctatttccag------------------------------------------------

upper sequence: Vv02s0012g01580.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA20G31840.3 (Glycine max), 5'ss of exon 3
GTTTACATGTTGTGGTTACAATGTTTTCTGGCTATTTGGTTGGATATGCTGCATTCAGAGCATTGTTTAGTCACAACCCTGTCATGgtaccctttcagtgaccttgaatttatataagttctatttcttgaaaaatgttaaaacacgtttccctattcctcatgggagattattttctttgtaagtttggttctctttaattatagtgttattgaaattgatggttctctaatcctaaatttcag
|||| |||||||||||||| |||||| |||||||| |  | |||||||| ||||| ||||||||||| | |||||  |||| ||||||||    | |   |  ||    ||||  |   | |||      | |  |||| |   | |    |  ||  ||         |  ||| |||  |    |   ||  |                                                  
GTTTGCATGTTGTGGTTACCATGTTTACTGGCTATCTTCTCGGATATGCAGCATTTAGAGCATTGTTCAATCACAGTCCTGCCATGgtactgcctaaaatatatttttcttattca---tttatcctcaaatagttgtttagttatgagctctcatctct---------tcgtttccttccttgtctctatttccag------------------------------------------------
















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|110423125|gb|EC989463.1|EC989463
EST:     TGGTTGGATATGCTGCATTCAGAGCATTGTTTAGTCACAACCCTGTCATG                         AATGCTGCTGGAGGAATCCTTGGATTGGTTTGTGCCATGCTTGTAGAAACC
genomic: TGGTTGGATATGCTGCATTCAGAGCATTGTTTAGTCACAACCCTGTCATGgtaccctttc ... taaatttcagAATGCTGCTGGAGGAATCCTTGGATTGGTTTGTGCCATGCTTGTAGAAACC
EST: gi|30305815|gb|CB982609.1|CB982609
EST:     TGGTTGGATATGCTGCATTCAGAGCATTGTTTAGTCACAACCCTGTCATG                         AATGCTGCTGGAGGAATCCTTGGATTGGTTTGTGCCATGCTTGTAGAAACC
genomic: TGGTTGGATATGCTGCATTCAGAGCATTGTTTAGTCACAACCCTGTCATGgtaccctttc ... taaatttcagAATGCTGCTGGAGGAATCCTTGGATTGGTTTGTGCCATGCTTGTAGAAACC
EST: gi|110366835|gb|EC930753.1|EC930753
EST:     TGGTTGGATATGCTGCATTCAGAGCATTGTTTAGTCACAACCCTGTCATG                         AATGCTGCTGGAGGAATCCTTGGATTGGTTTGTGCCATGCTTGTAGAAACC
genomic: TGGTTGGATATGCTGCATTCAGAGCATTGTTTAGTCACAACCCTGTCATGgtaccctttc ... taaatttcagAATGCTGCTGGAGGAATCCTTGGATTGGTTTGTGCCATGCTTGTAGAAACC
EST: gi|110420541|gb|EC986816.1|EC986816
EST:     TGGTTGGATATGCTGCATTCAGAGCATTGTTTAGTCACAACCCTGTCATG                         AATGCTGCTGGAGGAATCCTTGGATTGGTTTGTGCCATGCTTGTAGAAACC
genomic: TGGTTGGATATGCTGCATTCAGAGCATTGTTTAGTCACAACCCTGTCATGgtaccctttc ... taaatttcagAATGCTGCTGGAGGAATCCTTGGATTGGTTTGTGCCATGCTTGTAGAAACC
EST: gi|110401057|gb|EC967650.1|EC967650
EST:     TGGTTGGATATGCTGCATTCAGAGCATTGTTTAGTCACAACCCTGTCATG                         AATGCTGCTGGAGGAATCCTTGGATTGGTTTGTGCCATGCTTGTAGAAACC
genomic: TGGTTGGATATGCTGCATTCAGAGCATTGTTTAGTCACAACCCTGTCATGgtaccctttc ... taaatttcagAATGCTGCTGGAGGAATCCTTGGATTGGTTTGTGCCATGCTTGTAGAAACC
EST: gi|30135534|gb|CB920872.1|CB920872
EST:     GTTTAGTCACAACCCTGTCATG                         AATGCTGCTGGAGGAATCCTTGGATTGGTTTGTGCCATGCTTGTAGAAACC
genomic: GTTTAGTCACAACCCTGTCATGgtaccctttc ... taaatttcagAATGCTGCTGGAGGAATCCTTGGATTGGTTTGTGCCATGCTTGTAGAAACC
EST: gi|32457411|gb|CD798585.1|CD798585
EST:     TGGTTGGATATGCTGCATCCAGAGCATTGTTTAGTCACAACCCTGTCATG                         AATGCTGCTGGAGGAATCCTTGGATTGGTTTGTGCCATGCTTGTAGAAACC
genomic: TGGTTGGATATGCTGCATTCAGAGCATTGTTTAGTCACAACCCTGTCATGgtaccctttc ... taaatttcagAATGCTGCTGGAGGAATCCTTGGATTGGTTTGTGCCATGCTTGTAGAAACC
EST: gi|110414360|gb|EC980187.1|EC980187
EST:     TGGTTGGATATGCTGCATTCAGAGCATTGTTTAGTCACAACCCTGTCATG                         AATGCTGCTGGAGGAATCCTTGGATTGGTTTGTGCCATGCTTGTAGAAACC
genomic: TGGTTGGATATGCTGCATTCAGAGCATTGTTTAGTCACAACCCTGTCATGgtaccctttc ... taaatttcagAATGCTGCTGGAGGAATCCTTGGATTGGTTTGTGCCATGCTTGTAGAAACC
EST: gi|30305753|gb|CB982547.1|CB982547
EST:     TGATCNGATATNATGCATTCAGAGCATTGTTTAGTCACAACCCTGTCATG                         AATGCTGCTGGAGGAATCCTTGGATTGGTTTGTGCCATGCTTGTAGAAACC
genomic: TGGTTGGATATGCTGCATTCAGAGCATTGTTTAGTCACAACCCTGTCATGgtaccctttc ... taaatttcagAATGCTGCTGGAGGAATCCTTGGATTGGTTTGTGCCATGCTTGTAGAAACC
EST: gi|110393117|gb|EC958067.1|EC958067
EST:     TGGTTGGATATGCTGCATTCAGAGCATTGTTTAGTCACAACCCTGTCATG                         AATGCTGCTGGAGGAATCCTTGGATTGGTTTGTGCCATGCTTGTAGAAACC
genomic: TGGTTGGATATGCTGCATTCAGAGCATTGTTTAGTCACAACCCTGTCATGgtaccctttc ... taaatttcagAATGCTGCTGGAGGAATCCTTGGATTGGTTTGTGCCATGCTTGTAGAAACC
EST: gi|110382854|gb|EC947178.1|EC947178
EST:     TGGTTGGATATGCTGCATTCAGAGCATTGTTTAGTCACAACCCTGTCATG                         AATGCTGCTGGAGGAATCCTTGGATTGGTTTGTGCCATGCTTGTAGAAACC
genomic: TGGTTGGATATGCTGCATTCAGAGCATTGTTTAGTCACAACCCTGTCATGgtaccctttc ... taaatttcagAATGCTGCTGGAGGAATCCTTGGATTGGTTTGTGCCATGCTTGTAGAAACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTACATGTTGTGGTTACAATGTTTTCTGGCTATTTGGTTGGATATGCTGCATTCAGAGCATTGTTTAGTCACAACCCTGTCATGgtaccctttcagtgaccttgaatttatataagttctatttcttgaaaaatgttaaaacacgtttccctattcctcatgggagattattttctttgtaagtttggttctctttaattatagtgttattgaaattgatggttctctaatcctaaatttcag

- - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA