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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgattcttttgtattcttttttatcaatatcagttttttaaatcagattcatttatgtaccttcttacacatattgaaaactgaacgtctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTTCCATTTGTTCAAAGCTGGGGTTGAACCAAAATGGGAAGATCCTGAGTGT

Basic information

species Vitis vinifera
transcript Vv05s0049g01770.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0049g01770.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA20G21510.2 (Glycine max), 3'ss of exon 1
attgattcttttgtattcttttttatcaatatcagttttttaaatcagat-tcatttatgtaccttcttacacatattgaaaactgaacgtctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTTCCATTTGTTCAAAGCTGGGGTTGAACCAAAATGGGAAGATCCTGAGTGT
|| | || || | | ||  || |||| | ||| | |||    ||| || | |   | |  ||       | |   |||  |    | |  |  | ||  ||| ||||||||||| |||| |||||||||||||||| |  |||||| ||||| || ||||||||  ||||| |||| || |||||||||||||||||||||
atggttttttgttttttaattgttattattatta-tttggagaatgaggtgttggtaaattattggaagaaatgaatttgatgtgggaaatgctggtatagTTTGTATGATCAGGTATTCAAGCCCAGCAAGTTGCAAATCAATGCGGATTTTCACTTGTTCAAGACTGGGATTGAGCCTAAATGGGAAGATCCTGAGTGT

upper sequence: Vv05s0049g01770.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G27570.1 (Glycine max), 3'ss of exon 1
attgattcttttgtattcttttttatcaatatcagttttttaaatcagattcatttatgtaccttctt---acacatattgaaaactgaacgtctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTTCCATTTGTTCAAAGCTGGGGTTGAACCAAAATGGGAAGATCCTGAGTGT
 ||  |  |||| || |  || |||| | ||| |  |||  | ||  |     ||  |  |   |      | |   |||  |    | |  |  | ||  ||| ||||||||||| |||| |||||||||||||||| |  |||||| ||||| || ||||||||  ||||| |||| || |||||||||||||| ||||| 
-tttttgtttttttaattgttattattattatta--tttggagattgggagtgttggtaaattattggaagaaatgaatttgatgtgggaaatgctggtttagTTTGTATGATCAGGTATTCAAGCCCAGCAAGTTGCAAATCAATGCCGATTTTCACTTGTTCAAGACTGGGATTGACCCTAAATGGGAAGATCCAGAGTGC

upper sequence: Vv05s0049g01770.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G35620.1 (Arabidopsis thaliana), 3'ss of exon 1
--------------------------------------------------attgattcttttgtattct---tttttatcaa---tatcagttttttaaatca-gattcatttatgtaccttcttacacatattga----aaactgaacgtctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTTCCATTTGTTCAAAGCTGGGGTTGAACCAAAATGGGAAGATCCTGAGTGT
                                                   |||   ||| |  ||      ||| |||  |   |||   | || | ||||  |||  || | | |   | |  | |  ||  ||    ||  |    ||  ||||  ||  || | ||    |||||| || | ||||| ||| |||| ||||| ||  | || |||||||||||||| ||||| ||||| ||||||||||| ||||||
gttcgtctttctctcttctcctttgatttcaatatttgtcaatgccttgctttgtaacttctaaatctgggatttgtatagaagctatggttattgtgaatctcgatctatgtgtatggatccgaaaatctaaggatgttaattttttggttattgt-tagATTGCACGAGACTATATTTCAGACTAGCAAATTGACAGCGAATGCTGAAATTCACTTGTTCAAAGCTGGTGTTGAGCCAAAGTGGGAAGATCCAGAGTGT

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|349815714|gb|FQ400870.1|FQ400870
EST:     ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTG                         TCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
genomic: ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTGgtatctctct ... ctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
EST: gi|110381761|gb|EC935318.1|EC935318
EST:     ACCTCTCTTCGCAAGGCTTACACCTTGGAAACCGTCGAAGAATTTTGGTG                         TCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
genomic: ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTGgtatctctct ... ctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
EST: gi|110685840|gb|EE062914.1|EE062914
EST:     ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTG                         TCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
genomic: ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTGgtatctctct ... ctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
EST: gi|30133607|gb|CB918946.1|CB918946
EST:     ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTG                         TCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
genomic: ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTGgtatctctct ... ctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
EST: gi|77584480|gb|DV221309.1|DV221309
EST:     ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTG                         TCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
genomic: ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTGgtatctctct ... ctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
EST: gi|77584572|gb|DV221367.1|DV221367
EST:     ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTG                         TCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
genomic: ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTGgtatctctct ... ctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
EST: gi|110686380|gb|EE063948.1|EE063948
EST:     ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTG                         TCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
genomic: ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTGgtatctctct ... ctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
EST: gi|30129212|gb|CB914551.1|CB914551
EST:     CGAAACCGTCGAAGAATTTTGGTG                         TCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
genomic: CGAAACCGTCGAAGAATTTTGGTGgtatctctct ... ctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
EST: gi|77580010|gb|DV218885.1|DV218885
EST:     ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTG                         TCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
genomic: ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTGgtatctctct ... ctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
EST: gi|29782677|gb|CB348195.2|CB348195
EST:     ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTG                         TCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
genomic: ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTGgtatctctct ... ctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
EST: gi|110427971|gb|EC994428.1|EC994428
EST:     ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTG                         TCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
genomic: ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTGgtatctctct ... ctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
EST: gi|30135899|gb|CB921237.1|CB921237
EST:     ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTG                         TCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
genomic: ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTGgtatctctct ... ctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
EST: gi|110724989|gb|EE101297.1|EE101297
EST:     ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTG                         TCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
genomic: ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTGgtatctctct ... ctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
EST: gi|161712027|gb|FC059592.1|FC059592
EST:     ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTG                         TCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
genomic: ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTGgtatctctct ... ctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
EST: gi|110732987|gb|EE108752.1|EE108752
EST:     ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTG                         TCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
genomic: ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTGgtatctctct ... ctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
EST: gi|351040235|gb|FQ425321.1|FQ425321
EST:     ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTG                         TCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
genomic: ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTGgtatctctct ... ctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
EST: gi|30130346|gb|CB915685.1|CB915685
EST:     ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTG                         TCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
genomic: ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTGgtatctctct ... ctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
EST: gi|110731346|gb|EE105675.1|EE105675
EST:     ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTG                         TCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
genomic: ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTGgtatctctct ... ctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
EST: gi|30130329|gb|CB915668.1|CB915668
EST:     ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTG                         TCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
genomic: ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTGgtatctctct ... ctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
EST: gi|351046061|gb|FQ441444.1|FQ441444
EST:     ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTG                         TCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
genomic: ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTGgtatctctct ... ctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
EST: gi|351015262|gb|FQ445546.1|FQ445546
EST:     ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTG                         TCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
genomic: ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTGgtatctctct ... ctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
EST: gi|30131970|gb|CB917309.1|CB917309
EST:     ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTG                         TCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
genomic: ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTGgtatctctct ... ctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
EST: gi|110697840|gb|EE075280.1|EE075280
EST:     ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTG                         TCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
genomic: ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTGgtatctctct ... ctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
EST: gi|110721728|gb|EE097336.1|EE097336
EST:     ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTG                         TCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
genomic: ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTGgtatctctct ... ctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
EST: gi|110731029|gb|EE108785.1|EE108785
EST:     ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTG                         TCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
genomic: ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTGgtatctctct ... ctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
EST: gi|30132754|gb|CB918093.1|CB918093
EST:     ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTG                         TCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
genomic: ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTGgtatctctct ... ctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
EST: gi|351027640|gb|FQ446807.1|FQ446807
EST:     ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTG                         TCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
genomic: ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTGgtatctctct ... ctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
EST: gi|110375910|gb|EC940937.1|EC940937
EST:     ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTG                         TCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
genomic: ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTGgtatctctct ... ctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
EST: gi|110703148|gb|EE079739.1|EE079739
EST:     ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTG                         TCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT
genomic: ACCTCTCTTCGCAAGGCTTACACCTTCGAAACCGTCGAAGAATTTTGGTGgtatctctct ... ctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagattcatttatgtaccttcttacacatattgaaaactgaacgtctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTTCCATTTGTTCAAAGCTGGGGTTGAACCAAAATGGGAAGATCCTGAGTGT
                  ttcttac  putative branch site (score: 2)
                                          cgtcttt  putative PPT
                           atattgaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgattcttttgtattcttttttatcaatatcagttttttaaatcagattcatttatgtaccttcttacacatattgaaaactgaacgtctttgtgcagTCTGTATGATCAGATATTTAAGCCCAGCAAGTTGCCAGCCAATGCAGATTTCCATTTGTTCAAAGCTGGGGTTGAACCAAAATGGGAAGATCCTGAGTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - aatcaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acacata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgaaaa