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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGTTGGTAGAGTTGCAAATAGAATCAAAGATGGGAAGTTTACTCTCAATGGGATTGAATACCAATTGCCCATCAACAAGCCCCCAAACAGTCTCCACGgtatggaatttgtctgttctcttatattctaatgattttctcaattgccttagggttttgtttggatctcaggaaaattgaggaaaggaaagggaaatac...

Basic information

species Vitis vinifera
transcript Vv17s0000g02260.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g02260.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G132036_T01 (Zea mays), 5'ss of exon 1
ATTGTTGGTAGAGTTGCAAATAGAATCAAAGATGGGAAGTTTACTCTCAATGGGATTGAATACCAATTGCCCATCAACAAGCCCCCAAACAGTCTCCACGgtatg--gaatt--tgtctgttctcttatattctaatgattttctcaattgccttagggttttgtttgg-atctcaggaaaattgaggaaaggaaagggaaatac
||||||||| ||||||||||||||||||| ||||| ||||| ||||| |||||| |  | ||| |  ||   |||||||| || || |||| ||| || |||| |   |||   | |||  |    |||| ||   |||| |     ||| ||       ||  ||||| || ||        | |||||     ||        
ATTGTTGGTCGAGTTGCAAATAGAATCAAGGATGGAAAGTTCACTCTAAATGGGGTGCAGTACAATCTGAGTATCAACAACCCACCTAACACTCTTCATGgtaagccaaatcagtatctactgaactatagtcagttgatgtatgttattaccaagtctcttaatttggtatatctatttgtattaggaacacctagcat-----
















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|161714271|gb|FC063529.1|FC063529
EST:     TGGGATTGAATACCAATTGCCCATCAACAAGCCCCCAAACAGTCTCCACG                         GTGGGCACAAGGGCTTTAGTAAGAAGGTCTGGGAGGTGGTTGAAAGGAAAG
genomic: TGGGATTGAATACCAATTGCCCATCAACAAGCCCCCAAACAGTCTCCACGgtatggaatt ... ttgtctttagGTGGGCACAAGGGCTTTAGCAAGAAGGTCTGGGAGGTGGCTGAAAGGAAAG
EST: gi|110711155|gb|EE087370.1|EE087370
EST:     TGGGATTGAATACCAATTGCCCATCAACAAGCCCCCAAACAGTCTCCACG                         GTGGGCACAAGGGCTTTAGTAAGAAGGTCTGGGAGGTGGTTGAAAGGAAAG
genomic: TGGGATTGAATACCAATTGCCCATCAACAAGCCCCCAAACAGTCTCCACGgtatggaatt ... ttgtctttagGTGGGCACAAGGGCTTTAGCAAGAAGGTCTGGGAGGTGGCTGAAAGGAAAG
EST: gi|110685468|gb|EE062213.1|EE062213
EST:     TGGGATTGAATACCAATTGCCCATCAACAAGCCCCCAAACAGTCTCCACG                         GTGGGCACAAGGGCTTTAGTAAGAAGGTCTGGGAGGTGGCTGAAAGGAAAG
genomic: TGGGATTGAATACCAATTGCCCATCAACAAGCCCCCAAACAGTCTCCACGgtatggaatt ... ttgtctttagGTGGGCACAAGGGCTTTAGCAAGAAGGTCTGGGAGGTGGCTGAAAGGAAAG
EST: gi|161707206|gb|FC057321.1|FC057321
EST:     TGGGATTGAATACCAATTGCCCATCAACAAGCCCCCAAACAGTCTCCACG                         GTGGGCACAAGGGCTTTAGTAAGAAGGTCTGGGAGGTGGCTGAAAGGAAAG
genomic: TGGGATTGAATACCAATTGCCCATCAACAAGCCCCCAAACAGTCTCCACGgtatggaatt ... ttgtctttagGTGGGCACAAGGGCTTTAGCAAGAAGGTCTGGGAGGTGGCTGAAAGGAAAG
EST: gi|33407393|gb|CF213020.1|CF213020
EST:     TGGGATTGAATACCAATTGCCCATCAACAAGCCCCCAAACAGTCTCCACG                         GTGGGCACAAGGGCTTTAGTAAGAAGGTCTGGGAGGTGGTTGAAAGGAAAG
genomic: TGGGATTGAATACCAATTGCCCATCAACAAGCCCCCAAACAGTCTCCACGgtatggaatt ... ttgtctttagGTGGGCACAAGGGCTTTAGCAAGAAGGTCTGGGAGGTGGCTGAAAGGAAAG
EST: gi|110712305|gb|EE089778.1|EE089778
EST:     TGGGATTGAATACCAATTGCCCATCAACAAGCCCCCAAACAGTCTCCACG                         GTGGGCACAAGGGCTTTAGTAAGAAGGTCTGGGAGGTGGTTGAAAGGAAAG
genomic: TGGGATTGAATACCAATTGCCCATCAACAAGCCCCCAAACAGTCTCCACGgtatggaatt ... ttgtctttagGTGGGCACAAGGGCTTTAGCAAGAAGGTCTGGGAGGTGGCTGAAAGGAAAG
EST: gi|161714524|gb|FC062974.1|FC062974
EST:     TGGGATTGAATACCAATTGCCCATCAACAAGCCCCCAAACAGTCTCCACG                         GTGGGCACAAGGGCTTTAGTAAGAAGGTCTGGGAGGTGGTTGAAAGGAAAG
genomic: TGGGATTGAATACCAATTGCCCATCAACAAGCCCCCAAACAGTCTCCACGgtatggaatt ... ttgtctttagGTGGGCACAAGGGCTTTAGCAAGAAGGTCTGGGAGGTGGCTGAAAGGAAAG
EST: gi|30134841|gb|CB920179.1|CB920179
EST:     AAACAGTCTCCACG                         GTGGGCACAAGGGCTTTAGTAAGAAGGTCTGGGAGGTGGCTGAAAGGAAAG
genomic: AAACAGTCTCCACGgtatggaatt ... ttgtctttagGTGGGCACAAGGGCTTTAGCAAGAAGGTCTGGGAGGTGGCTGAAAGGAAAG
EST: gi|110720115|gb|EE095756.1|EE095756
EST:     TGGGATTGAATACCAATTGCCCATCAACAAGCCCCCAAACAGTCTCCACG                         GTGGGCACAAGGGCTTTAGTAAGAAGGTCTGGGAGGTGGTTGAAAGGAAAG
genomic: TGGGATTGAATACCAATTGCCCATCAACAAGCCCCCAAACAGTCTCCACGgtatggaatt ... ttgtctttagGTGGGCACAAGGGCTTTAGCAAGAAGGTCTGGGAGGTGGCTGAAAGGAAAG
EST: gi|110719295|gb|EE097104.1|EE097104
EST:     TGGGATTGAATACCAATTGCCCATCAACAAGCCCCCAAACAGTCTCCACG                         GTGGGCACAAGGGCTTTAGTAAGAAGGTCTGGGAGGTGGTTGAAAGGAAAG
genomic: TGGGATTGAATACCAATTGCCCATCAACAAGCCCCCAAACAGTCTCCACGgtatggaatt ... ttgtctttagGTGGGCACAAGGGCTTTAGCAAGAAGGTCTGGGAGGTGGCTGAAAGGAAAG
EST: gi|161715455|gb|FC069043.1|FC069043
EST:     TGGGATTGAATACCAATTGCCCATCAACAAGCCCCCAAACAGTCTCCACG                         GTGGGCACAAGGGCTTTAGTAAGAAGGTCTGGGAGGTGGTTGAAAGGAAAG
genomic: TGGGATTGAATACCAATTGCCCATCAACAAGCCCCCAAACAGTCTCCACGgtatggaatt ... ttgtctttagGTGGGCACAAGGGCTTTAGCAAGAAGGTCTGGGAGGTGGCTGAAAGGAAAG
EST: gi|30125066|gb|CB910405.1|CB910405
EST:     AAACAGTCTCCACG                         GTGGGCACAAGGGCTTTAGTAGGAAGGTCTGGGAGGTGGCTGAAAGGAAAG
genomic: AAACAGTCTCCACGgtatggaatt ... ttgtctttagGTGGGCACAAGGGCTTTAGCAAGAAGGTCTGGGAGGTGGCTGAAAGGAAAG
EST: gi|294965333|gb|GW837048.1|GW837048
EST:     TGGGATTGAATACCAATTGCCCATCAACAAGCCCCCAAACAGTCTCCACG                         GTGGGCACAAGGGCTTTAGTAAGAAGGTCTGGGAGGTGGCTGAAAGGAAAG
genomic: TGGGATTGAATACCAATTGCCCATCAACAAGCCCCCAAACAGTCTCCACGgtatggaatt ... ttgtctttagGTGGGCACAAGGGCTTTAGCAAGAAGGTCTGGGAGGTGGCTGAAAGGAAAG
EST: gi|110396622|gb|EC962314.1|EC962314
EST:     TGGGATTGAATACCAATTGCCCATCAACAAGCCCCCAAACAGTCTCCACG                         GTGGGCACAAGGGCTTTAGTAAGAAGGTCTGGGAGGTGGCTGAAAGGAAAG
genomic: TGGGATTGAATACCAATTGCCCATCAACAAGCCCCCAAACAGTCTCCACGgtatggaatt ... ttgtctttagGTGGGCACAAGGGCTTTAGCAAGAAGGTCTGGGAGGTGGCTGAAAGGAAAG
EST: gi|110724807|gb|EE100960.1|EE100960
EST:     TGGGATTGAATACCAATTGCCCATCAACAAGCCCCCAAACAGTCTCCACG                         GTGGGCACAAGGGCTTTAGTAAGAAGGTCTGGGAGGTGGTTGAAAGGAAAG
genomic: TGGGATTGAATACCAATTGCCCATCAACAAGCCCCCAAACAGTCTCCACGgtatggaatt ... ttgtctttagGTGGGCACAAGGGCTTTAGCAAGAAGGTCTGGGAGGTGGCTGAAAGGAAAG
EST: gi|30301902|gb|CB978696.1|CB978696
EST:     TGGGATTGAATACCAATTGCCCATCAACAAGCCCCCAAACAGTCTCCACG                         GTGGGCACAAGGGCTTTAGTAAGAAGGTCTGGGAGGTGGTTGAAAGGAAAG
genomic: TGGGATTGAATACCAATTGCCCATCAACAAGCCCCCAAACAGTCTCCACGgtatggaatt ... ttgtctttagGTGGGCACAAGGGCTTTAGCAAGAAGGTCTGGGAGGTGGCTGAAAGGAAAG
EST: gi|110712306|gb|EE089779.1|EE089779
EST:     TGGGATTGAATACCAATTGCCCATCAACAAGCCCCCAAACAGTCTCCACG                         GTGGGCACAAGGGCTTTAGTAAGAAGGTCTGGGAGGTGGTTGAAAGGAAAG
genomic: TGGGATTGAATACCAATTGCCCATCAACAAGCCCCCAAACAGTCTCCACGgtatggaatt ... ttgtctttagGTGGGCACAAGGGCTTTAGCAAGAAGGTCTGGGAGGTGGCTGAAAGGAAAG
EST: gi|33402576|gb|CF208203.1|CF208203
EST:     TGGGATTGAATACCAATTGCCCATCAACAAGCCCCCAAACAGTCTCCACG                         GTGGGCACAAGGGCTTTAGTAAGAAGGTCTGGGAGGTGGTTGAAAGGAAAG
genomic: TGGGATTGAATACCAATTGCCCATCAACAAGCCCCCAAACAGTCTCCACGgtatggaatt ... ttgtctttagGTGGGCACAAGGGCTTTAGCAAGAAGGTCTGGGAGGTGGCTGAAAGGAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGTTGGTAGAGTTGCAAATAGAATCAAAGATGGGAAGTTTACTCTCAATGGGATTGAATACCAATTGCCCATCAACAAGCCCCCAAACAGTCTCCACGgtatggaatttgtctgttctcttatattctaatgattttctcaattgccttagggttttgtttggatctcaggaaaattgaggaaaggaaagggaaatac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agggaaa