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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAACATGGGTGGTCTATAAATGAATTTGGTGATCTCACAAGAGGTGCAGCAAGCACTGGTAAAGTGTTCAATCCAACAAACAAAGGAACGGATGAGGAGgtttgctctgacttatgccttttatccaaattttttatgtttctacagttttatctcaaatttgttgatagttgcaacttacaaccagtatctccttttt...

Basic information

species Vitis vinifera
transcript Vv02s0025g04830.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g04830.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os04g48410.1 (Oryza sativa), 5'ss of exon 5
---GAAACATGGGTGGTCTATAAATGAATTTGGTGATCTCACAAGAGGTGCAGCAAGCACTGGTAAAGTGTTCAATCCAACAAACAAAGGAACGGATGAGGAGgtttgctctgacttatgccttttatccaaattttttatgtttctacagtt-ttatctcaaatttgttgatagttgcaacttacaaccagtatctccttttt
    ||||| || ||||| |||||||||||||| ||| | ||||||||||||| ||| ||||| ||||| |  || ||| |  |  |  || |  || |||     |     ||   |   || |  |  |  ||    | |  |    |||   || | |   |||      | |      |||   |   | |  |     |
TGGTAAACACGGATGGTCAATAAATGAATTTGGGGATTTGACAAGAGGTGCAGAAAGTACTGGCAAAGTCTATAACCCATCGGATTATAGATCCAATAAGgtaaggtttaaggatccacatctgtcttttaccttccaaaagagtaagtagtaactagccc---tttaggatcaatcattggttatc-ctgatgttgctgcaat

upper sequence: Vv02s0025g04830.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G175728_T01 (Zea mays), 5'ss of exon 5
---GAAACATGGGTGGTCTATAAATGAATTTGGTGATCTCACAAGAGGTGCAGCAAGCACTGGTAAAGTGTTCAATCCAACAAACAAAGGAACGGATGAGGAGgtttgctctgacttatgccttttatc-caaattttttatgtttctacagtttta----tctcaaatt-tgttg-atagttgcaacttacaaccagtatctccttttt
    |||||||| ||||| |||||| | ||||| ||| | ||||||||||||| ||||||||| || || |  |||||  || |  |   | | ||| |||   | | |    ||||          ||  ||| |  |||    |  ||| ||  |      |   ||| ||||   | ||    | || |||  || ||         
TGGTAAACATGGATGGTCAATAAATCAGTTTGGGGATTTGACAAGAGGTGCAGAAAGCACTGGCAATGTCTATAATCCGCCAGATCATTTATCTGATAAGgtaatattccaacacttgaaatcacggtcataaaataattacaaatg-acaattggagaggcttgggattatgttatgttgtcttgattt-caattagcatt--------

upper sequence: Vv02s0025g04830.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA05G04170.1 (Glycine max), 5'ss of exon 5
GAAACATGGGTGGTCTATAAATGAATTTGGTGATCTCACAAGAGGTGCAGCAAGCACTGGTAAAGTGTTCAATCCAACAAACAAAGGAACGGATGAGGAGgtttgctctgacttatgccttttatccaaattttttatgtttctacagttttatctcaaatttgttgatagttgcaacttacaaccagtatctccttttt----
 || ||||| |||||||| ||||| ||||||||||| || |||||||||||||||||||||||| ||||||||||   |||  | | ||    | | |||||||||| |  |  || ||| |    |||| || |  | |    ||    |  |  || ||||  ||   |||  |     ||    ||  || |  ||     
AAAGCATGGTTGGTCTATTAATGAGTTTGGTGATCTGACTAGAGGTGCAGCAAGCACTGGTAAAATGTTCAATCCGGTAAATGAGGAAAACAGTAAAGAGgtttgcttttccacattcctat----caaacttctgttttcctgacttggtgttaacatatttcctgtaggtttaattactcatttggttcctacacttgccca

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|34547578|gb|CF515810.1|CF515810
EST:     CAAGCACTGGTAAAGTGTTCAATCCAACAACCAAAGGAACGGATGAGGAG                         CCTCTTGGTGACCTGGGAACACTGGATGTGGATGAGAATGGTGAAGCCTTC
genomic: CAAGCACTGGTAAAGTGTTCAATCCAACAAACAAAGGAACGGATGAGGAGgtttgctctg ... ttttttttagCCTCTTGGTGACCTGGGAACACTGGATGTGGATGAGAATGGTGAAGCCTTC
EST: gi|110688720|gb|EE067592.1|EE067592
EST:     CAAGCACTGGTAAAGTGTTCAATCCAACAAACAAAGGAACGGATGAGGAG                         CCTCTTGGTGACCTGNGAACACTGGATGTGGATGAGAATGGTGAAGCCTTC
genomic: CAAGCACTGGTAAAGTGTTCAATCCAACAAACAAAGGAACGGATGAGGAGgtttgctctg ... ttttttttagCCTCTTGGTGACCTGGGAACACTGGATGTGGATGAGAATGGTGAAGCCTTC
EST: gi|110363901|gb|EC927532.1|EC927532
EST:     CAAGCACTGGTAAAGTGTTCAATCCAACAAACAAAGGAACGGATGAGGAG                         CCTCTTGGTGACCTGGGAACACTGGATGTGGATGAGAATGGTGAAGCCTTC
genomic: CAAGCACTGGTAAAGTGTTCAATCCAACAAACAAAGGAACGGATGAGGAGgtttgctctg ... ttttttttagCCTCTTGGTGACCTGGGAACACTGGATGTGGATGAGAATGGTGAAGCCTTC
EST: gi|110713200|gb|EE088915.1|EE088915
EST:     AAGCACTGGGTAAGGTGTTCAATCCAACAAACAAAGGAACGGATGAGGAC                         CCTCTTGGTGACTTGGAAACACTGGATGT
genomic: AAGCACTGG-TAAAGTGTTCAATCCAACAAACAAAGGAACGGATGAGGAGgtttgctctg ... ttttttttagCCTCTTGGTGACCTGGGAACACTGGATGT
EST: gi|34548407|gb|CF516639.1|CF516639
EST:     CAAGCACTGGTAAAGTGTTCAATCCAACAAACAAAGGAACGGATGAGGAG                         CCTCTTGGTGACCTGGGAACACCGGATGTGGATGAGAATGGTGAAGCCTTT
genomic: CAAGCACTGGTAAAGTGTTCAATCCAACAAACAAAGGAACGGATGAGGAGgtttgctctg ... ttttttttagCCTCTTGGTGACCTGGGAACACTGGATGTGGATGAGAATGGTGAAGCCTTC
EST: gi|110689772|gb|EE066290.1|EE066290
EST:     AAGCACTGGTAAAGTGTTCAAATCCAACAA-CAAAGGAACGGATGAAGAG                         CCTCTTGGTGACCTGGGA-CACTGGATGTGGATGAGAATGGTGAAGCCTTC
genomic: AAGCACTGGTAAAGTGTTCAA-TCCAACAAACAAAGGAACGGATGAGGAGgtttgctctg ... ttttttttagCCTCTTGGTGACCTGGGAACACTGGATGTGGATGAGAATGGTGAAGCCTTC
EST: gi|30323907|gb|CD007169.1|CD007169
EST:     CAAGCACTGGTAAAGTGTTCAATCCAACAAACAAAGGAACGGATGAGGAG                         CCTCTTGGTGACCTGGGAACACTGGATGTGGATGA
genomic: CAAGCACTGGTAAAGTGTTCAATCCAACAAACAAAGGAACGGATGAGGAGgtttgctctg ... ttttttttagCCTCTTGGTGACCTGGGAACACTGGATGTGGATGA
EST: gi|30325689|gb|CD008951.1|CD008951
EST:     CAAGCACTGGTAAAGTGTTCAATCCAACAAACAAAGGAACGGATGAGGAG                         CCTCTTGGTGACCTGGGAACACTGGATGTGGATGAGAATGGTGAAGCCTTC
genomic: CAAGCACTGGTAAAGTGTTCAATCCAACAAACAAAGGAACGGATGAGGAGgtttgctctg ... ttttttttagCCTCTTGGTGACCTGGGAACACTGGATGTGGATGAGAATGGTGAAGCCTTC
EST: gi|254917314|gb|GR906140.1|GR906140
EST:     CAAGCACTGGTAAAGTGTTCAATCCAACAAACAAAGGAACGGATGAGGAG                         CCTCTTGGTGACCTGGGAACACTGGATGTGGATGAGAATGGTGAAGCCTTC
genomic: CAAGCACTGGTAAAGTGTTCAATCCAACAAACAAAGGAACGGATGAGGAGgtttgctctg ... ttttttttagCCTCTTGGTGACCTGGGAACACTGGATGTGGATGAGAATGGTGAAGCCTTC
EST: gi|110369057|gb|EC933200.1|EC933200
EST:     CAAGCACTGGTAAAGTGTTCAATCCAACAAACAAAGGAACGGATGAGGAG                         CCTCTTGGTGACCTGGGAACACTGGATGTGGATGAGAATGGTGAAGCCTTC
genomic: CAAGCACTGGTAAAGTGTTCAATCCAACAAACAAAGGAACGGATGAGGAGgtttgctctg ... ttttttttagCCTCTTGGTGACCTGGGAACACTGGATGTGGATGAGAATGGTGAAGCCTTC
EST: gi|110714425|gb|EE091314.1|EE091314
EST:     CAAGCACTGGTAAAGTGTTCAATCCAACAAACAAAGGAACGGATGAGGAG                         CCTCTTGGTGACCTGGGAACACTGGATGTGGATGAGAATGGTGAAGCCTTC
genomic: CAAGCACTGGTAAAGTGTTCAATCCAACAAACAAAGGAACGGATGAGGAGgtttgctctg ... ttttttttagCCTCTTGGTGACCTGGGAACACTGGATGTGGATGAGAATGGTGAAGCCTTC
EST: gi|110713270|gb|EE089042.1|EE089042
EST:     CAAGCACTGGTAAAGTGGTCAATCCAACAA-CAAAGGA-CGGATGAGGAG                         CCTCTTGGTGACCTGGGA-CACTGGATGTGGATGA
genomic: CAAGCACTGGTAAAGTGTTCAATCCAACAAACAAAGGAACGGATGAGGAGgtttgctctg ... ttttttttagCCTCTTGGTGACCTGGGAACACTGGATGTGGATGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAACATGGGTGGTCTATAAATGAATTTGGTGATCTCACAAGAGGTGCAGCAAGCACTGGTAAAGTGTTCAATCCAACAAACAAAGGAACGGATGAGGAGgtttgctctgacttatgccttttatccaaattttttatgtttctacagttttatctcaaatttgttgatagttgcaacttacaaccagtatctccttttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG