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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcagctttggttcttaacgttaatgccatctgcaattctttagcttcacaaataattaaatggtatgtcaaataagatccttaaatttattttctgcagGCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAGCTGCGGAGAGGTGGTTGCATCACATGCAACAAGCACTGGATAGTGTCAC

Basic information

species Vitis vinifera
transcript Vv04s0008g04210.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g04210.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA14G20380.1 (Glycine max), 3'ss of exon 2
agcagctttggttcttaacgttaatgccatctgcaattctttagcttcacaaataattaaatggtatgtcaaataa-----gatccttaaatttattttctgcagGCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAGCTGCGGAGAGGTGGTTGCATCACATGCAACAAGCACTGGATAGTGTCAC
    ||  || |  ||     |   |     |||  ||||||   |   | | ||| |  |  || ||  |||| |     | | | |   || |||||  ||||| ||||| || || ||||  || ||||| ||||| || ||||| || |||||||| ||||||||||| |||||||||||||| ||| | || |||   ||
---tgcactgatctttgtgtgtgtggagggttgc--ttctttgaatcatctagtaactttaaagtttgaaaaatgaaccttggttcctttcttgatttttggcagGACATCCTGCTCTAATTGCTCGACATCGACCATTTCCTGTCACGCATCAAGCTGCAGAGAGGTGGTTACATCACATGCAACATGCATTAGACAGTACTAC
















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|26258545|gb|CA809608.1|CA809608
EST:     GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAG                         GCCATCCAGCGCTGATTGGGCGTCATCGGCCATTCCCCGTCACCCACCAAG
genomic: GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAGgtaaggagca ... ttttctgcagGCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
EST: gi|110380155|gb|EC945400.1|EC945400
EST:     GTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAG                         GTCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
genomic: GTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAGgtaaggagca ... ttttctgcagGCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
EST: gi|110417416|gb|EC983468.1|EC983468
EST:     ATTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAG                         GCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
genomic: GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAGgtaaggagca ... ttttctgcagGCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
EST: gi|110370974|gb|EC934642.1|EC934642
EST:     ATTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAG                         GTCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
genomic: GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAGgtaaggagca ... ttttctgcagGCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
EST: gi|46919572|gb|CN548901.1|CN548901
EST:     GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAG                         GCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
genomic: GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAGgtaaggagca ... ttttctgcagGCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
EST: gi|32244919|gb|CD710738.1|CD710738
EST:     GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAG                         GCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
genomic: GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAGgtaaggagca ... ttttctgcagGCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
EST: gi|18458302|gb|BM436580.1|BM436580
EST:     GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAG                         GCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
genomic: GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAGgtaaggagca ... ttttctgcagGCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
EST: gi|22007494|gb|BQ792528.1|BQ792528
EST:     GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAG                         GCCATCCAGCGCTGATTGGGCGTCATCGGCCATTCCCCGTCACCCACCAAG
genomic: GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAGgtaaggagca ... ttttctgcagGCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
EST: gi|110426742|gb|EC993161.1|EC993161
EST:     ATTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAG                         GCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
genomic: GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAGgtaaggagca ... ttttctgcagGCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
EST: gi|30304131|gb|CB980925.1|CB980925
EST:     GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAG                         GCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
genomic: GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAGgtaaggagca ... ttttctgcagGCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
EST: gi|33410442|gb|CF216069.1|CF216069
EST:     ATTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAG                         GTCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
genomic: GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAGgtaaggagca ... ttttctgcagGCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
EST: gi|32457324|gb|CD798498.1|CD798498
EST:     GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAG                         GCCATCCAGCGCTGATTGGACGTCATCGGCCATCCCCCGTCACCCACCAAG
genomic: GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAGgtaaggagca ... ttttctgcagGCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
EST: gi|26261673|gb|CA812736.1|CA812736
EST:     ATTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAG                         GTCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
genomic: GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAGgtaaggagca ... ttttctgcagGCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
EST: gi|110378909|gb|EC944067.1|EC944067
EST:     GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAG                         GCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
genomic: GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAGgtaaggagca ... ttttctgcagGCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
EST: gi|27583881|gb|CB006576.1|CB006576
EST:     ATTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAG                         GTCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
genomic: GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAGgtaaggagca ... ttttctgcagGCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
EST: gi|33407799|gb|CF213426.1|CF213426
EST:     ATTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAG                         GTCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
genomic: GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAGgtaaggagca ... ttttctgcagGCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
EST: gi|110411856|gb|EC977582.1|EC977582
EST:     ATTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAG                         GCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
genomic: GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAGgtaaggagca ... ttttctgcagGCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
EST: gi|46919557|gb|CN548886.1|CN548886
EST:     GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAG                         GCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
genomic: GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAGgtaaggagca ... ttttctgcagGCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
EST: gi|26257789|gb|CA808852.1|CA808852
EST:     GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAG                         GCCATCCAGCGCTGATTGGGCGTCATCGGCCATTCCCCGTCACCCACCAAG
genomic: GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAGgtaaggagca ... ttttctgcagGCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
EST: gi|30305341|gb|CB982135.1|CB982135
EST:     GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATACCCAAAGGAAAG                         GCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
genomic: GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAGgtaaggagca ... ttttctgcagGCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
EST: gi|110717237|gb|EE092920.1|EE092920
EST:     GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAG                         GCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
genomic: GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAGgtaaggagca ... ttttctgcagGCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
EST: gi|110427333|gb|EC993768.1|EC993768
EST:     ATTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAG                         GCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
genomic: GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAGgtaaggagca ... ttttctgcagGCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
EST: gi|110385358|gb|EC949875.1|EC949875
EST:     GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAG                         GCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
genomic: GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAGgtaaggagca ... ttttctgcagGCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
EST: gi|30305413|gb|CB982207.1|CB982207
EST:     GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATACCCAAAGGAAAG                         GCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCCCCAAG
genomic: GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAGgtaaggagca ... ttttctgcagGCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
EST: gi|30304203|gb|CB980997.1|CB980997
EST:     GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAG                         GCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
genomic: GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAGgtaaggagca ... ttttctgcagGCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
EST: gi|351033864|gb|FQ447902.1|FQ447902
EST:     ATTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAG                         GTCATCCA-----GATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG
genomic: GTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAGgtaaggagca ... ttttctgcagGCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcacaaataattaaatggtatgtcaaataagatccttaaatttattttctgcagGCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAGCTGCGGAGAGGTGGTTGCATCACATGCAACAAGCACTGGATAGTGTCAC
                                         tttattttct  CT-rich tract
                         aaataagatccttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcagctttggttcttaacgttaatgccatctgcaattctttagcttcacaaataattaaatggtatgtcaaataagatccttaaatttattttctgcagGCCATCCAGCGCTGATTGGACGTCATCGGCCATTCCCCGTCACCCACCAAGCTGCGGAGAGGTGGTTGCATCACATGCAACAAGCACTGGATAGTGTCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
agcagct
- - - - - - - - - - - - -gccatct
- - - - - - - - - - - - - - - - - - - - - - - -cacaaat
- - - - - - - - - - - - - - - - - - - - - - - - -caaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - aattaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtatgt