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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGCTAGCTTATGAGGAGCCAGAAAAATCCCCAATGTTTCATCTGCTAAGCCTGGAATATCGGCAGCAAGTTGCAGATAGTTTGAACAGAGCACTTCTTGgtgtgtttccactggttcctacttgcttctgtatgctatatctggttgtaggatgttgtacacatatatgctttttatgcaaaattcattttctgattccattattctttttaataatgctctaaactgtttgattcactcttggcttgtggttcatggtgtatatcag

Basic information

species Vitis vinifera
transcript Vv18s0001g13280.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g13280.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA06G03120.1 (Glycine max), 5'ss of exon 5
CTGCTAGCTTATGAGGAGCCAGAAAAATCCCCAATGTTTCATCTGCTAAGCCTGGAATATCGGCAGCAAGTTGCAGATAGTTTGAACAGAGCACTTCTTGgtgtgtttccactggttcctacttgcttctgtatgctatatctggttgtaggatgttgtacacatatatgctttttatgcaaaattcattttctgattccattattctttttaataatgctctaaactgtttgattcactcttggcttgtggttcatggtgtatatcag
|| || |||||| |||||||||| |||||||||||||||||||| || ||| | || |||||||| || |||||||||||||||||  ||||  ||||||||  |||  |  || |  || | || |||| ||   ||||| | |||| |     |  | |   | | | || |  |||  ||||  ||     ||||   || |||   |  ||  ||   |||  ||   |                                    
CTTCTTGCTTATAAGGAGCCAGAGAAATCCCCAATGTTTCATCTCCTTAGCTTAGAGTATCGGCAACAGGTTGCAGATAGTTTGAATCGAGCTATTCTTGgttggttaac-ttgatatctgcatgtttctttaa--tatattttgttgcaaatcatgatgc---tttttcctatccatgttaaatatat-----gattttttttttcccgtggatggtggg-taatttgccag------------------------------------

upper sequence: Vv18s0001g13280.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA04G03080.1 (Glycine max), 5'ss of exon 5
CTGCTAGCTTATGAGGAGCCAGAAAAATCCCCAATGTTTCATCTGCTAAGCCTGGAATATCGGCAGCAAGTTGCAGATAGTTTGAACAGAGCACTTCTTGgtgtgtttccactggttcctacttgcttctgtatgctatatctggttgtaggatgttgtacacatatatgctttttatgcaaaattcattttctgattccattattctttttaataatgctctaaactgtttgattcactcttggcttgtggttcatggtgtatatcag
|| || |||||| |||||||||| |||||||||||||||||||| || ||| | || |||||||| || |||||||||||||||||  ||||  ||||||||  |||  |  || |  || | || |||| ||   ||||| | |||  |     |  | |   | | | || |  |||  ||||  ||     ||||   || ||| | |  ||  ||     || ||   |                                    
CTTCTTGCTTATAAGGAGCCAGAGAAATCCCCAATGTTTCATCTCCTTAGCTTAGAGTATCGGCAACAGGTTGCAGATAGTTTGAATCGAGCCATTCTTGgttggttaac-ttgatatctgcatgtttctttaa--tatattttgtttcaaatcatgatgc---ttttttctatccatgttaaatatat-----gattttttttttcctgtggatggtgggt--aattgccag------------------------------------
















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|110712193|gb|EE089538.1|EE089538
EST:     CCTGGAATATCGGCAGCAAGTTGCAGATAGTTTGGACAGAGCACTTCTTG                         CACATGCCAACCTCCCTAGCTGTTCAGCAATGGAAAGGCTGATACAACAGA
genomic: CCTGGAATATCGGCAGCAAGTTGCAGATAGTTTGAACAGAGCACTTCTTGgtgtgtttcc ... tgtatatcagCACATGCCAACCTCCCTAGCTGTTCAGCAATGGAAAGGCTGATACAACAGA
EST: gi|349813259|gb|FQ411499.1|FQ411499
EST:     CCTGGAATATCGGCAGCAAGTTGCAGATAGTTTGAACAGAGCACTTCTTG                         CACATGCCAACCTCCCTAGCTGTTCAG
genomic: CCTGGAATATCGGCAGCAAGTTGCAGATAGTTTGAACAGAGCACTTCTTGgtgtgtttcc ... tgtatatcagCACATGCCAACCTCCCTAGCTGTTCAG
EST: gi|110713521|gb|EE089516.1|EE089516
EST:     CCTGGAATATCGGCAGCAAGTTGCAGATAGTTTGAACAGAGCACTTCTTG                         CACATGCCAACCTCCCTAGCTGTTCAGCAATGGGAAGGCTGATACAACAGA
genomic: CCTGGAATATCGGCAGCAAGTTGCAGATAGTTTGAACAGAGCACTTCTTGgtgtgtttcc ... tgtatatcagCACATGCCAACCTCCCTAGCTGTTCAGCAATGGAAAGGCTGATACAACAGA
EST: gi|110718275|gb|EE094924.1|EE094924
EST:     CCTGGAATATCGGCAGCAAGTTGCAGATAGTTTGAACAGAGCACTTCTTG                         CACATGCCACCCTCCCTAGCTGTTCNAGCA-TGGAAAAGCTGATACAACAG
genomic: CCTGGAATATCGGCAGCAAGTTGCAGATAGTTTGAACAGAGCACTTCTTGgtgtgtttcc ... tgtatatcagCACATGCCAACCTCCCTAGCTGTTC-AGCAATGGAAAGGCTGATACAACAG
EST: gi|349807500|gb|FQ401493.1|FQ401493
EST:     CCTGGAATATCGGCAGCAAGTTGCAGATAGTTTGAACAGAGCACTTCTTG                         CACATGCCAACCTCCCTAGCTGTTCAGCAATGGAAAAGCTGATACAAC
genomic: CCTGGAATATCGGCAGCAAGTTGCAGATAGTTTGAACAGAGCACTTCTTGgtgtgtttcc ... tgtatatcagCACATGCCAACCTCCCTAGCTGTTCAGCAATGGAAAGGCTGATACAAC
EST: gi|110712714|gb|EE088002.1|EE088002
EST:     CCTGGAGTATCGGCAGCAAGTTGCAGATAGTTTGAACAGAGCACTTCTTG                         CACATGCCAACCTCCCTAGCTGTTCAGCAATGGGAAGGCTGATACNACAGA
genomic: CCTGGAATATCGGCAGCAAGTTGCAGATAGTTTGAACAGAGCACTTCTTGgtgtgtttcc ... tgtatatcagCACATGCCAACCTCCCTAGCTGTTCAGCAATGGAAAGGCTGATACAACAGA
EST: gi|351013733|gb|FQ433885.1|FQ433885
EST:     CCTGGGATATCGGCAGCAAGTTGCAGATAGTTTGAACAGAGCACTTCTTG                         CACATGCCAACCTCCCTAGCTGTTCAGCAATGGAAAGGCTGATACAACAGA
genomic: CCTGGAATATCGGCAGCAAGTTGCAGATAGTTTGAACAGAGCACTTCTTGgtgtgtttcc ... tgtatatcagCACATGCCAACCTCCCTAGCTGTTCAGCAATGGAAAGGCTGATACAACAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGCTAGCTTATGAGGAGCCAGAAAAATCCCCAATGTTTCATCTGCTAAGCCTGGAATATCGGCAGCAAGTTGCAGATAGTTTGAACAGAGCACTTCTTGgtgtgtttccactggttcctacttgcttctgtatgctatatctggttgtaggatgttgtacacatatatgctttttatgcaaaattcattttctgattccattattctttttaataatgctctaaactgtttgattcactcttggcttgtggttcatggtgtatatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA