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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaacgatttgtttatctgttttggaaatagccctttgaaggcattgatttttgttttttttcaatcttcttttgtttttatttttgagattatccacagTTGGAGCCTGCAGACCCTGATTTCTACAAGATAGGGTATGTTCGGAGTGTTCGAGCATACGGTGTTGAATTCAAGGAAGGGCCTGATGGATTTGGAGTCT

Basic information

species Vitis vinifera
transcript Vv01s0011g01080.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g01080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA09G05510.1 (Glycine max), 3'ss of exon 2
caaacgatttgtttatctgttttggaaatagccctttgaaggcattgatttttgt--tttttttcaatcttcttttgtttttatttttgagattatccacagTTGGAGCCTGCAGACCCTGATTTCTACAAGATAGGGTATGTTCGGAGTGTTCGAGCATACGGTGTTGAATTCAAGGAAGGGCCTGATGGATTTGGAGTCT
|  ||  || | | |  | ||   |   |  |  ||| || |   || || ||||  ||||| |  || |||| || | || |||| |  | |  || |  ||||||||||||||| ||||||||||||||||| || ||||| || ||  | ||||| || || ||| | || || |||||||| ||||| ||||| || |
cccacatttggatgaattcttcaaggggtttctgtttaaatgagatgtttgttgtgatttttctttattttctattttgttaatttatttgttcctcta--gTTGGAGCCTGCAGATCCTGATTTCTACAAGATTGGTTATGTCCGAAGCATGCGAGCTTATGGAGTTCATTTTAAAGAAGGGCCAGATGGTTTTGGTGTGT

upper sequence: Vv01s0011g01080.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA15G16830.1 (Glycine max), 3'ss of exon 2
caaacgatttgtttatctgttttggaaatagccctttgaaggcattgatttttgt--tttttttcaatcttcttttgtttttatttttgagattatccacagTTGGAGCCTGCAGACCCTGATTTCTACAAGATAGGGTATGTTCGGAGTGTTCGAGCATACGGTGTTGAATTCAAGGAAGGGCCTGATGGATTTGGAGTCT
| |||  || | | |  | ||   |   |  |  ||| || |   || || ||||  ||||| |  || |||| || | || |||| |  | |  || |  ||||||||| || || ||||||||||||||||| || ||||| || ||| | ||||| || || ||| | || || |||||||| ||||| |||||||| |
ccaacatttggatgaattcttcaaggggtttctgtttaaatgagatgtttattgtgatttttctttattttctattttgttaatttatttgttcctcta--gTTGGAGCCCGCTGATCCTGATTTCTACAAGATTGGTTATGTCCGAAGTATGCGAGCTTATGGAGTTCAGTTTAAAGAAGGGCCAGATGGTTTTGGAGTGT
















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|349826229|gb|FQ416034.1|FQ416034
EST:     CTTTTCCACTCTTTGAACCTCCACAAATTGAAAGTGACACACCTTCTCAG                         TTGGAGCCTGCAGACCCTGATTTCTACAAGATAGGGTATGTTCGGAGTGTT
genomic: CTTTTCCACTCTTTGAACCTCCACAAATTGAAAGTGACACACCTTCTCAGgtatgtgcca ... ttatccacagTTGGAGCCTGCAGACCCTGATTTCTACAAGATAGGGTATGTTCGGAGTGTT
EST: gi|349830971|gb|FQ418255.1|FQ418255
EST:     CTTTTCCACTCTTTGAACCTCCACAAATTGAAAGTGACACACCTTCTCAG                         TTGGAGCCTGCAGACCCTGATTTCTACAAGATAGGGTATGTTCGGAGTGTT
genomic: CTTTTCCACTCTTTGAACCTCCACAAATTGAAAGTGACACACCTTCTCAGgtatgtgcca ... ttatccacagTTGGAGCCTGCAGACCCTGATTTCTACAAGATAGGGTATGTTCGGAGTGTT
EST: gi|351025692|gb|FQ426706.1|FQ426706
EST:     CTTTTCCACTCTTTGAACCTCCACAAATTGAAAGTGACACACCTTCTCAG                         TTGGAGCCTGCAGACCCTGATTTCTACAAGATAGGGTATGTTCGGAGTGTT
genomic: CTTTTCCACTCTTTGAACCTCCACAAATTGAAAGTGACACACCTTCTCAGgtatgtgcca ... ttatccacagTTGGAGCCTGCAGACCCTGATTTCTACAAGATAGGGTATGTTCGGAGTGTT
EST: gi|349824034|gb|FQ417421.1|FQ417421
EST:     CTTTTCCACTCTTTGAACCTCCACAAATTGAAAGTGACACACCTTCTCAG                         TTGGAGCCTGCAGACCCTGATTTCTACAAGATAGGGTATGTTCGGAGTGTT
genomic: CTTTTCCACTCTTTGAACCTCCACAAATTGAAAGTGACACACCTTCTCAGgtatgtgcca ... ttatccacagTTGGAGCCTGCAGACCCTGATTTCTACAAGATAGGGTATGTTCGGAGTGTT
EST: gi|351019251|gb|FQ429411.1|FQ429411
EST:     CTTTTCCACTCTTTGAACCTCCACAAATTGAAAGTGACACACCTTCTCAG                         TTGGAGCCTGCAGACCCTGATTTCTACAAGATAGGGTATGTTCGGAGTGTT
genomic: CTTTTCCACTCTTTGAACCTCCACAAATTGAAAGTGACACACCTTCTCAGgtatgtgcca ... ttatccacagTTGGAGCCTGCAGACCCTGATTTCTACAAGATAGGGTATGTTCGGAGTGTT
EST: gi|349832506|gb|FQ421067.1|FQ421067
EST:     CTTTTCCACTCTTTGAACCTCCACAAATTGAAAGTGACACACCTTCTCAG                         TTGGAGCCTGCAGACCCTGATTTCTACAAGATAGGGTATGTTCGGAGTGTT
genomic: CTTTTCCACTCTTTGAACCTCCACAAATTGAAAGTGACACACCTTCTCAGgtatgtgcca ... ttatccacagTTGGAGCCTGCAGACCCTGATTTCTACAAGATAGGGTATGTTCGGAGTGTT
EST: gi|351048408|gb|FQ448682.1|FQ448682
EST:     CTTTTCCACTCTTTGAACCTCCACAAATTGAAAGTGACACACCTCCTCAG                         TTGGAGCCTGCAGACCCTGATTTCTACAAGATGGGGTATGTTCGGAGTGTT
genomic: CTTTTCCACTCTTTGAACCTCCACAAATTGAAAGTGACACACCTTCTCAGgtatgtgcca ... ttatccacagTTGGAGCCTGCAGACCCTGATTTCTACAAGATAGGGTATGTTCGGAGTGTT
EST: gi|349821313|gb|FQ404445.1|FQ404445
EST:     CTTTTCCACTCTTTGAACCTCCACAAATTGAAAGTGACACACCTTCTCAG                         TTGGAGCCTGCAGACCCTGATTTCTACAAGATGGGGTATGTTCGGAGTGTT
genomic: CTTTTCCACTCTTTGAACCTCCACAAATTGAAAGTGACACACCTTCTCAGgtatgtgcca ... ttatccacagTTGGAGCCTGCAGACCCTGATTTCTACAAGATAGGGTATGTTCGGAGTGTT
EST: gi|351053396|gb|FQ455732.1|FQ455732
EST:     CTTTTCCACTCTTTGAACCTCCACAAATTGAAAGTGACACACCTTCTCAG                         TTGGAGCCTGCAGACCCTGATTTCTACAAGATGGGGTATGTTCGGAGTGTT
genomic: CTTTTCCACTCTTTGAACCTCCACAAATTGAAAGTGACACACCTTCTCAGgtatgtgcca ... ttatccacagTTGGAGCCTGCAGACCCTGATTTCTACAAGATAGGGTATGTTCGGAGTGTT
EST: gi|351029274|gb|FQ436668.1|FQ436668
EST:     CTTTTCCACTCTTTGAACCTCCACAAATTGAAAGTGACACACCTTCTCAG                         TTGGAGCCTGCAGACCCTGATTTCTACAAGATAGGGTATGTTCGGAGTGTT
genomic: CTTTTCCACTCTTTGAACCTCCACAAATTGAAAGTGACACACCTTCTCAGgtatgtgcca ... ttatccacagTTGGAGCCTGCAGACCCTGATTTCTACAAGATAGGGTATGTTCGGAGTGTT
EST: gi|351028541|gb|FQ444822.1|FQ444822
EST:     CTTTTCCACTCTTTGAACCTCCACAAATTGAAAGTGACACACCTTCTCAG                         TTGGAGCCTGCAGACCCTGATTTCTACAAGATAGGGTATGTTCGGAGTGTT
genomic: CTTTTCCACTCTTTGAACCTCCACAAATTGAAAGTGACACACCTTCTCAGgtatgtgcca ... ttatccacagTTGGAGCCTGCAGACCCTGATTTCTACAAGATAGGGTATGTTCGGAGTGTT
EST: gi|351053071|gb|FQ456678.1|FQ456678
EST:     CTTTTCCACTCTTTGAACCTCCACAAATTGAAAGTGACACACCTTCTCAG                         TTGGAGCCTGCAGGCCCTGATTTCTACAAGATGGGGTATGTTCGGAGTGTT
genomic: CTTTTCCACTCTTTGAACCTCCACAAATTGAAAGTGACACACCTTCTCAGgtatgtgcca ... ttatccacagTTGGAGCCTGCAGACCCTGATTTCTACAAGATAGGGTATGTTCGGAGTGTT
EST: gi|351016333|gb|FQ446193.1|FQ446193
EST:     CTTTTCCACTCTTTGAACCTCCACAAATTGAAAGTGACACACCTTCTCAG                         TTGGAGCCTGCAGACCCTGATTTCTACAAGATAGGGTATGTTCGGAGTGTT
genomic: CTTTTCCACTCTTTGAACCTCCACAAATTGAAAGTGACACACCTTCTCAGgtatgtgcca ... ttatccacagTTGGAGCCTGCAGACCCTGATTTCTACAAGATAGGGTATGTTCGGAGTGTT
EST: gi|351013379|gb|FQ425410.1|FQ425410
EST:     CTTTTCCACTCTTTGAACCTCCACAAATTGAAAGTGACACACCTTCTCAG                         TTGGAGCCTGCAGACCCTGATTTCTACAAGATAGGGTATGTTCGGAGTGTT
genomic: CTTTTCCACTCTTTGAACCTCCACAAATTGAAAGTGACACACCTTCTCAGgtatgtgcca ... ttatccacagTTGGAGCCTGCAGACCCTGATTTCTACAAGATAGGGTATGTTCGGAGTGTT
EST: gi|351015737|gb|FQ431692.1|FQ431692
EST:     CTTTTCCACTCTTTGAACCTCCACAAATTGAAAGTGACACACCTTCTCAG                         TTGGAGCCTGCAGACCCTGATTTCTACAAGATAGGGTATGTTCGGAGTGTT
genomic: CTTTTCCACTCTTTGAACCTCCACAAATTGAAAGTGACACACCTTCTCAGgtatgtgcca ... ttatccacagTTGGAGCCTGCAGACCCTGATTTCTACAAGATAGGGTATGTTCGGAGTGTT
EST: gi|351034855|gb|FQ458212.1|FQ458212
EST:     CTTTTCCACTCTTTGAACCTCCACAAATTGAAAGTGACACACCTCCTCAG                         TTGGAGCCTGCAGACCCTGATTTCTACAAGATGGGGTATGTTCGGAGTGTT
genomic: CTTTTCCACTCTTTGAACCTCCACAAATTGAAAGTGACACACCTTCTCAGgtatgtgcca ... ttatccacagTTGGAGCCTGCAGACCCTGATTTCTACAAGATAGGGTATGTTCGGAGTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatttttgttttttttcaatcttcttttgtttttatttttgagattatccacagTTGGAGCCTGCAGACCCTGATTTCTACAAGATAGGGTATGTTCGGAGTGTTCGAGCATACGGTGTTGAATTCAAGGAAGGGCCTGATGGATTTGGAGTCT
 cattgat  putative branch site (score: 4)
     tttgttttttttcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaacgatttgtttatctgttttggaaatagccctttgaaggcattgatttttgttttttttcaatcttcttttgtttttatttttgagattatccacagTTGGAGCCTGCAGACCCTGATTTCTACAAGATAGGGTATGTTCGGAGTGTTCGAGCATACGGTGTTGAATTCAAGGAAGGGCCTGATGGATTTGGAGTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
caaacga
- - - - - - - - - - - -ggaaata
- - - - - - - - - - - - - - - gcccttt
- - - - - - - - - - - - - - - - - - -gaaggca