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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacaatataactctccttctggttctccttttctgtcattggaagattgataatttactcttcatttatgttacatattgttgttgctgtcttggctcagGTACTGGTGCATGGGAGAGTGCACTTACAAACACATTGTCTCCTGGAGATCGAACTGTATCATTCCTGATTGGGCAATTCAGTTTGCTGTGGATCGACCA

Basic information

species Vitis vinifera
transcript Vv06s0009g03740.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0009g03740.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA18G14740.1 (Glycine max), 3'ss of exon 1
------cacaatataactctccttctggttctccttttctgtcattggaagattgataatttactcttcatttatgttacatattgttgttgctgtcttggctcagGTACTGGTGCATGGGAGAGTGCACTTACAAACACATTGTCTCCTGGAGATCGAACTGTATCATTCCTGATTGGGCAATTCAGTTTGCTGTGGATCGACCA
            ||||       || | | ||  ||||||     |  |  | ||||  | |   |||||   |    |  || || | |||     |||| |||||||||||||| ||||||||||| || ||||||||| |||||||||| ||||||| |||||| ||||||||||| |||||||| ||||| ||||| || ||
taaggaggtttaataagaacaaatcggttactagttttcttattatcaagtaatgat--tctgtccttcaagaaaa--aagtaatgattttgta--tttggttcagGTACTGGTGCTTGGGAGAGTGCTCTCACAAACACACTGTCTCCTGGGGATCGAATTGTATCTTTCCTGATTGGCCAATTCAGCTTGCTTTGGATTGATCA

upper sequence: Vv06s0009g03740.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G41460.1 (Glycine max), 3'ss of exon 2
cacaatataactctccttctggttctccttttctgtcattggaagattgataatttact--cttcatttatgttacatattgttgttgctgt-cttggctcagGTACTGGTGCATGGGAGAGTGCACTTACAAACACATTGTCTCCTGGAGATCGAACTGTATCATTCCTGATTGGGCAATTCAGTTTGCTGTGGATCGACCA
   ||||      |  |    |  |   |  | ||| |||   |   | ||| ||||||   ||  ||  | | |  || |  || |  ||   |||| |||||||||||||| ||||||||||| || ||||||||| |||||||||| ||||||| |||||| ||||||||||| |||||||| ||||| ||||| || ||
---aataaggtagtaatataagaacaaataatttgttatttacatggttatagtttactagttttcttgttatcaggtaataatgattttgcatttggttcagGTACTGGTGCTTGGGAGAGTGCTCTCACAAACACACTGTCTCCTGGGGATCGAATTGTATCGTTCCTGATTGGCCAATTCAGCTTGCTTTGGATTGATCA

upper sequence: Vv06s0009g03740.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ08434 (Selaginella moellendorffii), 3'ss of exon 1
---cacaatataactctccttctggttctccttttctgtcattggaagattgataatttactcttcatttatgttacatattgttgttgctgtcttggctcagGTACTGGTGCATGGGAGAGTGCACTTACAAACACATTGTCTCCTGGAGATCGAACTGTATCATTCCTGATTGGGCAATTCAGTTTGCTGTGGATCGACCA
   | ||| | | ||||  ||        |  || |||| |    ||| | || |||   || ||  |||   ||               | | ||  |||||| ||||| || |||||||||||||| || |||||||| || |||||||||   | ||| || ||||   | || || || ||  |||| |||||||| ||
gtactcaaaaaatctcttttttcttgctgctcttcctgtgaagtcaagttcgaaaat--gctttttttttccttt---------------ttttttctctcagGAACTGGAGCTTGGGAGAGTGCACTGACCAACACATTATCACCTGGAGATAAGATTGTCTCGTTCCGTCTGGGACAGTTTAGCCTGCTCTGGATCGATCA

upper sequence: Vv06s0009g03740.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ15151 (Selaginella moellendorffii), 3'ss of exon 1
---cacaatataa-ctctccttctggttctccttttctgtcattggaagattgataatttactcttcatttatgttacatattgttgttgctgtcttggctcagGTACTGGTGCATGGGAGAGTGCACTTACAAACACATTGTCTCCTGGAGATCGAACTGTATCATTCCTGATTGGGCAATTCAGTTTGCTGTGGATCGACCA
   | ||  | || ||||  |||| | |   |||  |||| |    ||| | || |||   || ||  |||   ||               | |  |  |||||| ||||| || |||||||||||||| || |||||||| || |||||||||   | ||| || ||||   | || || || ||  |||| |||||||| ||
gtactcagaaaaatctctttttcttgctgctcttc-ctgtgaagtcaagttcgaaaat--gctttttttttccttt---------------ttttctctctcagGAACTGGAGCTTGGGAGAGTGCACTGACCAACACATTATCACCTGGAGATAAGATTGTCTCGTTCCGTCTGGGACAGTTTAGCCTGCTCTGGATCGATCA

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|110373386|gb|EC937617.1|EC937617
EST:     GAAGATCTTCAAGACAACTACTGGAACCCCATTTCTCATTCCCACCACAG                         GTACTGGTGCATGGGAGAGTGCACTTACAAACACATTGTCTCCTGGAGATC
genomic: GAAGATCTTCAAGACAACTACTGGAACCCCATTTCTCATTCCCACCACAGgtactgcatt ... cttggctcagGTACTGGTGCATGGGAGAGTGCACTTACAAACACATTGTCTCCTGGAGATC
EST: gi|351042988|gb|FQ434429.1|FQ434429
EST:     GAAGATCTTCAAGACAACTACTGGAACCCCATTTCTCATTCCCACCACAG                         GTACTGGTGCATGGGAGAGTGCACTTACAAACACATTGTCTCCTGGAGATC
genomic: GAAGATCTTCAAGACAACTACTGGAACCCCATTTCTCATTCCCACCACAGgtactgcatt ... cttggctcagGTACTGGTGCATGGGAGAGTGCACTTACAAACACATTGTCTCCTGGAGATC
EST: gi|110732892|gb|EE108586.1|EE108586
EST:     GAAGATCTTCAAGACAACTACTGGAACCCCATTTCTCATTCCCACCACAG                         GTACTGGTGCATGGGAGAGTGCACTTACAAACACATTGTCTCCTGGAGATC
genomic: GAAGATCTTCAAGACAACTACTGGAACCCCATTTCTCATTCCCACCACAGgtactgcatt ... cttggctcagGTACTGGTGCATGGGAGAGTGCACTTACAAACACATTGTCTCCTGGAGATC
EST: gi|161715200|gb|FC068693.1|FC068693
EST:     GAAGATCTTCAAGACAACTACCGGAACCCCATTTCTCATTCCCACCACAG                         GTACTGGTGCATGGGAAAGTGCACTTACAAACACATTGTCTCCTGGAGATC
genomic: GAAGATCTTCAAGACAACTACTGGAACCCCATTTCTCATTCCCACCACAGgtactgcatt ... cttggctcagGTACTGGTGCATGGGAGAGTGCACTTACAAACACATTGTCTCCTGGAGATC
EST: gi|110708824|gb|EE086809.1|EE086809
EST:     GAAGATCTTCAAGACAACTACTGGAACCCCATTTCTCATTCCCACCACAG                         GTACTGGTGCATGGGAGAGTGCACTTACAAACACATTGTCTCCTGGAGATC
genomic: GAAGATCTTCAAGACAACTACTGGAACCCCATTTCTCATTCCCACCACAGgtactgcatt ... cttggctcagGTACTGGTGCATGGGAGAGTGCACTTACAAACACATTGTCTCCTGGAGATC
EST: gi|18458828|gb|BM437106.1|BM437106
EST:     GAAGATCTTCAAGACAACTACCGGAACCCCATTTCTCATTCCCACCACAG                         GTACTGGTGCATGGGAAAGTGCACTTACAAACACATTGTCTCCTGGAGATC
genomic: GAAGATCTTCAAGACAACTACTGGAACCCCATTTCTCATTCCCACCACAGgtactgcatt ... cttggctcagGTACTGGTGCATGGGAGAGTGCACTTACAAACACATTGTCTCCTGGAGATC
EST: gi|156737102|gb|EV241223.1|EV241223
EST:     GAAGATCTTCAAGACAACTACCGGAACCCCATTTCTCATTCCCACCACAG                         GTACTGGTGCATGGGAAAGTGCACTTACAAACACATTGTCTCCTGGAGATC
genomic: GAAGATCTTCAAGACAACTACTGGAACCCCATTTCTCATTCCCACCACAGgtactgcatt ... cttggctcagGTACTGGTGCATGGGAGAGTGCACTTACAAACACATTGTCTCCTGGAGATC
EST: gi|71869781|gb|DT018836.1|DT018836
EST:     GAAGATCTTCAAGACAACTACCGGAACCCCATTTCTCATTCCCACCACAG                         GTACTGGTGCATGGGAAAGTGCACTTACAAACACATTGTCTCCTGGAGATC
genomic: GAAGATCTTCAAGACAACTACTGGAACCCCATTTCTCATTCCCACCACAGgtactgcatt ... cttggctcagGTACTGGTGCATGGGAGAGTGCACTTACAAACACATTGTCTCCTGGAGATC
EST: gi|71873684|gb|DT022739.1|DT022739
EST:     GAAGATCTTCAAGACAACTACTGGAACCCCATTTCTCATTCCCACCACAG                         GTACTGGTGCATGGGAGAGTGCACTTACAAACACATTGTCTCCTGGAGATC
genomic: GAAGATCTTCAAGACAACTACTGGAACCCCATTTCTCATTCCCACCACAGgtactgcatt ... cttggctcagGTACTGGTGCATGGGAGAGTGCACTTACAAACACATTGTCTCCTGGAGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgataatttactcttcatttatgttacatattgttgttgctgtcttggctcagGTACTGGTGCATGGGAGAGTGCACTTACAAACACATTGTCTCCTGGAGATCGAACTGTATCATTCCTGATTGGGCAATTCAGTTTGCTGTGGATCGACCA
 gattgat  putative branch site (score: 4)
                                         ctgtctt  putative PPT
                  atttatgttacatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacaatataactctccttctggttctccttttctgtcattggaagattgataatttactcttcatttatgttacatattgttgttgctgtcttggctcagGTACTGGTGCATGGGAGAGTGCACTTACAAACACATTGTCTCCTGGAGATCGAACTGTATCATTCCTGATTGGGCAATTCAGTTTGCTGTGGATCGACCA

cacaata
- - - - - ctctcct
- - - - - - - - - ctggttc
- - - - - - - - - - - - - - - - ctgtcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgct