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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttattattatttttttgtaaagaaaaaatttaacctttattgcactgaggtgatgtgctgaccttctgtacctatgggcattaattattgcgatacaagAGCTGCATGTCATAGATGGGATTCCACAGCTTATTTTTGTTCGTGCAAACTATACTATTGAG

Basic information

species Vitis vinifera
transcript Vv19s0015g01950.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0015g01950.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA04G12890.1 (Glycine max), 3'ss of exon 3
------tttattattatttttttgtaaagaaaaaatttaacc-tttattgcactgaggtgatgtgctgaccttctgtacctatgggcattaattattgcgatacaagAGCTGCATGTCATAGATGGGATTCCACAGCTTATTTTTGTTCGTGCAAACTATACTATTGAG
       |    |  | ||| || |   |      |||  |   ||| || ||| |||  ||    ||      |||   |   ||   |   |||| | ||||| || |||||||||||||||||||||||||| ||||| ||||||||  ||| |||||||||||||
ttcacaatagccaacactttattttttggtgttgttttgtctgcttactgtactaaggaaattaattg------tgttattgctggtgctggctattacaataca-gAACTGCATGTCATAGATGGGATTCCACAACTTATCTTTGTTCGCTCAAGCTATACTATTGAG

upper sequence: Vv19s0015g01950.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G47850.1 (Glycine max), 3'ss of exon 3
------tttattattatttttttgtaaagaaaaaatttaacc-tttattgcactgaggtgatgtgctgaccttctgtacctatgggcattaattattgcgatacaagAGCTGCATGTCATAGATGGGATTCCACAGCTTATTTTTGTTCGTGCAAACTATACTATTGAG
       |    |  | ||     |   |      |||  |   ||| || |||||||  ||    ||      |||  ||   ||   |   |||| | ||||| || |||||||||||||||||||||||||| ||||| ||||||||  |||  ||||||||||||
ttcacaatagccaacacttcaccttttggtgttgttttgtctgcttactgtactgaggaaattaattg------tgtttctgctggtgctggctattacaataca-gAACTGCATGTCATAGATGGGATTCCACAACTTATCTTTGTTCGCTCAAGTTATACTATTGAG
















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|110713432|gb|EE089350.1|EE089350
EST:     GTCAATCAATCATGCACAAAAGGATCTCCCTGTGACTATCTATGAAAGTG                         AGCTGCATGTCATAGATGGGATTCCACAGCTTATTTTTGTTCGTGCAAACT
genomic: GTCAATCAATCATGCACAAAAGGATCTCCCTGTGACTATCTATGAAAGTGgtatgtaacc ... gcgatacaagAGCTGCATGTCATAGATGGGATTCCACAGCTTATTTTTGTTCGTGCAAACT
EST: gi|71855098|gb|DT004153.1|DT004153
EST:     GTCAATCAATCATGCACAAAAGGATCTCCCTGTGACTATCTATGAAAGTG                         AGCTGCATGTCATAGATGGGATTCCACAGCTTATTTTTGT
genomic: GTCAATCAATCATGCACAAAAGGATCTCCCTGTGACTATCTATGAAAGTGgtatgtaacc ... gcgatacaagAGCTGCATGTCATAGATGGGATTCCACAGCTTATTTTTGT
EST: gi|26261888|gb|CA812951.1|CA812951
EST:     GTCAATCAATCATGCACAAAAGGATCTCCCTGTGACTATCTATGAAAGTG                         AGCTGCATGTCATAGATGGGATTCCACAGCTTAT
genomic: GTCAATCAATCATGCACAAAAGGATCTCCCTGTGACTATCTATGAAAGTGgtatgtaacc ... gcgatacaagAGCTGCATGTCATAGATGGGATTCCACAGCTTAT
EST: gi|71856758|gb|DT005813.1|DT005813
EST:     GTCAATCAATCATGCACAAAAGGATCTCCCTGTGACTATCTATGAAAGTG                         AGCTGCATGTCATAGATGGGATTCCACAGCTTATTTTTGTTCGTGCAAACT
genomic: GTCAATCAATCATGCACAAAAGGATCTCCCTGTGACTATCTATGAAAGTGgtatgtaacc ... gcgatacaagAGCTGCATGTCATAGATGGGATTCCACAGCTTATTTTTGTTCGTGCAAACT
EST: gi|110363635|gb|EC927237.1|EC927237
EST:     GTCAATCAATCATGCACAAAAGGATCTCCCTGTGACTATCTATGAAAGTG                         AGCTGCATGTCATAGATGGGATTCCACAGCTTATTTTTGTTCGTGCAAACT
genomic: GTCAATCAATCATGCACAAAAGGATCTCCCTGTGACTATCTATGAAAGTGgtatgtaacc ... gcgatacaagAGCTGCATGTCATAGATGGGATTCCACAGCTTATTTTTGTTCGTGCAAACT
EST: gi|110368023|gb|EC931983.1|EC931983
EST:     GTCAATCAATCATGCACAAAAGGATCTCCCTGTGACTATCTATGAAAGTG                         AGCTGCATGTCATAGATGGGATTCCACAGCTTATTTTTGTTCGTGCAAACT
genomic: GTCAATCAATCATGCACAAAAGGATCTCCCTGTGACTATCTATGAAAGTGgtatgtaacc ... gcgatacaagAGCTGCATGTCATAGATGGGATTCCACAGCTTATTTTTGTTCGTGCAAACT
EST: gi|110404227|gb|EC968960.1|EC968960
EST:     GTCAATCAATCATGCACAAAAAGATCTCCCTGTGACTATCTATGAAAGTG                         AGCTGCATGTC
genomic: GTCAATCAATCATGCACAAAAGGATCTCCCTGTGACTATCTATGAAAGTGgtatgtaacc ... gcgatacaagAGCTGCATGTC
EST: gi|349818410|gb|FQ409185.1|FQ409185
EST:     GTCAATCAATCATGCACAAAAGGATCTCCCTGTGACTATCTATGAAAGTG                         AGCTGCATGTCATAGATGGGATTCCCCAGCTTATTTTTGTTCGTGCAAACT
genomic: GTCAATCAATCATGCACAAAAGGATCTCCCTGTGACTATCTATGAAAGTGgtatgtaacc ... gcgatacaagAGCTGCATGTCATAGATGGGATTCCACAGCTTATTTTTGTTCGTGCAAACT
EST: gi|110684768|gb|EE062427.1|EE062427
EST:     GTCAATCAATCATGCACAAAAGGATCTCCCTGTGACTATCTATGAAAGTG                         AGCTGCATGTCATAGATGGGATTCCACAGCTTATTTTTGTTCGTGCAAACT
genomic: GTCAATCAATCATGCACAAAAGGATCTCCCTGTGACTATCTATGAAAGTGgtatgtaacc ... gcgatacaagAGCTGCATGTCATAGATGGGATTCCACAGCTTATTTTTGTTCGTGCAAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgaggtgatgtgctgaccttctgtacctatgggcattaattattgcgatacaagAGCTGCATGTCATAGATGGGATTCCACAGCTTATTTTTGTTCGTGCAAACTATACTATTGAG
                                   attaattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttattattatttttttgtaaagaaaaaatttaacctttattgcactgaggtgatgtgctgaccttctgtacctatgggcattaattattgcgatacaagAGCTGCATGTCATAGATGGGATTCCACAGCTTATTTTTGTTCGTGCAAACTATACTATTGAG

- - - - - - - - - - - -aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - -ggtgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggcatta