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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggatatcatgttgttcatttttgtatccttctctctgaaaatctgagtttattgtgaactcacatcattgtatttctcatttctatattgtgtcaatagAACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCCAAAAGGTATTTGGAGGATGTTCTGGTCCACAAGCAAGCCATACCTTTCA

Basic information

species Vitis vinifera
transcript Vv01s0010g03380.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0010g03380.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G10910.2 (Glycine max), 3'ss of exon 3
tggatatcatgttgttcatttttgtatccttctct----ctgaaaatctgagtttattgtgaactcacatcattgtatttctcatttctatattgtgtcaatagAACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCCAAAAGGTATTTGGAGGATGTTCTGGTCCACAAGCAAGCCATACCTTTCA
    |    | |  || ||  | | |   | || |     | |   | |    ||||       ||  |   ||       |  ||| || ||||       ||||||||||||| |||||   ||| || ||||||||||| |||| |||||| |||||||| ||||| |||||||| | ||||||||| || || || ||||
----tgctgtttcattgatgctggaacaatactatggggtttattttattgagttataccattttcctagacttaagacattgctttttaaattgcaatttcagAACACAAGGGAAACTGCCTTTGCAATCAGGAAGTTGCCCTTGGTCAAGGCTAAAAGGTACTTGGAAGATGTTCTTGCCCACAAGCAGGCAATTCCATTCA

upper sequence: Vv01s0010g03380.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G37160.1 (Glycine max), 3'ss of exon 3
tggatatcatgttgttcatttttgtatccttctctctgaaaatctgagtttattgtgaact-cacatcattgtatttctcatttctatattgtgtcaatagAACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCCAAAAGGTATTTGGAGGATGTTCTGGTCCACAAGCAAGCCATACCTTTCA
 || ||  ||||| | || || |||    ||   | | | ||     |||  | || |           |   ||   |  ||| | | |    |  | ||||||| |||||||||||   |||||| |||||||||||  |||  || || ||||| ||  ||||||||||| ||| |||||| || ||||| |||||| 
-ggttaatatgttttccacttatgttgatttaagtttcataaggatggttattggtcagtgatgagctttcaaataatttgtttgtctgtccacttcacagAACACTAGGGAGACTGCCTTTGCCATCAGGAAGTTGCCCCTGGTTAAAGCTAAAAGATACCTGGAGGATGTTTTGGCCCACAAACAGGCCATCCCTTTCC
















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|351013781|gb|FQ433933.1|FQ433933
EST:     CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAG                         AACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
genomic: CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAGgtatttttat ... gtgtcaatagAACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
EST: gi|110385986|gb|EC950553.1|EC950553
EST:     CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAG                         AACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGTCAAGGCC
genomic: CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAGgtatttttat ... gtgtcaatagAACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
EST: gi|110378218|gb|EC943338.1|EC943338
EST:     CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAG                         AACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
genomic: CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAGgtatttttat ... gtgtcaatagAACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
EST: gi|110688549|gb|EE067229.1|EE067229
EST:     CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAG                         AACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGTCAAGGCC
genomic: CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAGgtatttttat ... gtgtcaatagAACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
EST: gi|71869773|gb|DT018828.1|DT018828
EST:     CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAG                         AACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
genomic: CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAGgtatttttat ... gtgtcaatagAACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
EST: gi|110689920|gb|EE066564.1|EE066564
EST:     CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAG                         AACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGTCAAGGCC
genomic: CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAGgtatttttat ... gtgtcaatagAACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
EST: gi|110715617|gb|EE093874.1|EE093874
EST:     CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAG                         AACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
genomic: CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAGgtatttttat ... gtgtcaatagAACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
EST: gi|110419782|gb|EC986031.1|EC986031
EST:     CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAG                         AACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
genomic: CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAGgtatttttat ... gtgtcaatagAACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
EST: gi|34416764|gb|CF415518.1|CF415518
EST:     GCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAG                         AACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
genomic: GCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAGgtatttttat ... gtgtcaatagAACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
EST: gi|110717067|gb|EE092597.1|EE092597
EST:     CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAG                         AACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
genomic: CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAGgtatttttat ... gtgtcaatagAACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
EST: gi|351024796|gb|FQ430621.1|FQ430621
EST:     CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAG                         AACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
genomic: CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAGgtatttttat ... gtgtcaatagAACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
EST: gi|110374693|gb|EC939616.1|EC939616
EST:     CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAG                         AACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
genomic: CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAGgtatttttat ... gtgtcaatagAACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
EST: gi|110387423|gb|EC952086.1|EC952086
EST:     CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAG                         AACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
genomic: CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAGgtatttttat ... gtgtcaatagAACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
EST: gi|352787033|gb|FQ476066.1|FQ476066
EST:     CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAG                         AACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
genomic: CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAGgtatttttat ... gtgtcaatagAACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
EST: gi|110372343|gb|EC936500.1|EC936500
EST:     CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAG                         AACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGTCAAGGCC
genomic: CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAGgtatttttat ... gtgtcaatagAACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
EST: gi|110694415|gb|EE071499.1|EE071499
EST:     CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAG                         AACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGTCAAGGCC
genomic: CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAGgtatttttat ... gtgtcaatagAACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
EST: gi|110705483|gb|EE082385.1|EE082385
EST:     CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAG                         AACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
genomic: CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAGgtatttttat ... gtgtcaatagAACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
EST: gi|77588447|gb|DV223435.1|DV223435
EST:     CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAG                         AACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
genomic: CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAGgtatttttat ... gtgtcaatagAACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
EST: gi|77579783|gb|DV218769.1|DV218769
EST:     CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAG                         AACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGTCAAGGCC
genomic: CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAGgtatttttat ... gtgtcaatagAACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
EST: gi|110375254|gb|EC940222.1|EC940222
EST:     CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAG                         AACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGTCAAGGCC
genomic: CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAGgtatttttat ... gtgtcaatagAACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
EST: gi|110715297|gb|EE093186.1|EE093186
EST:     CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAG                         AACACAAGGGGGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
genomic: CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAGgtatttttat ... gtgtcaatagAACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
EST: gi|351013783|gb|FQ433935.1|FQ433935
EST:     CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAG                         AACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
genomic: CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAGgtatttttat ... gtgtcaatagAACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
EST: gi|110716791|gb|EE092082.1|EE092082
EST:     CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAG                         AACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
genomic: CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAGgtatttttat ... gtgtcaatagAACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
EST: gi|110696430|gb|EE072550.1|EE072550
EST:     CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAG                         AACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGTCAAGGCC
genomic: CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAGgtatttttat ... gtgtcaatagAACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
EST: gi|110701152|gb|EE078432.1|EE078432
EST:     CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAG                         AACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
genomic: CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAGgtatttttat ... gtgtcaatagAACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
EST: gi|110725494|gb|EE102063.1|EE102063
EST:     CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAG                         AACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC
genomic: CTTGCAAGGCCAGGGGGTCAGATCTCAGAGTTCATTTCAAGgtatttttat ... gtgtcaatagAACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtttattgtgaactcacatcattgtatttctcatttctatattgtgtcaatagAACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCCAAAAGGTATTTGGAGGATGTTCTGGTCCACAAGCAAGCCATACCTTTCA
            aactcac  putative branch site (score: 2)
                                  atttctatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggatatcatgttgttcatttttgtatccttctctctgaaaatctgagtttattgtgaactcacatcattgtatttctcatttctatattgtgtcaatagAACACAAGGGAGACTGCTCATGCCATTAGGAAGTTGCCTTTGGCCAAGGCCAAAAGGTATTTGGAGGATGTTCTGGTCCACAAGCAAGCCATACCTTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - tcatgtt
- - - - - - - - - - - - - -ccttctc
- - - - - - - - - - - - - - - - - - -gaaaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcacat