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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctgaattgatcctatactctttccactattttttttttttttccctgtttgtgaaactaatttatgacaatctttttctttatgaaaattagGTGATAAAAGAAAGAAGCTTGAGGAAGAGAAGGGCATCATAGTTCGCTTTGTAATAGGTCACAG

Basic information

species Vitis vinifera
transcript Vv19s0090g00560.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0090g00560.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 5
-------------------------------------------------------------------gttctgaat--tgatcctatactctttccactattttttttttttttccctgt-ttgtgaaactaatttatgacaatctttttctttatgaaaattagGTGATAAAAGAAAGAAGCTTGAGGAAGAGAAGGGCATCATAGTTCGCTTTGTAATAGGTCACAG
                                                                   ||   | |   |  |  | | | | | |    |             | | | | | ||   | |    |    | ||    |     |  ||||  |||||| ||||| ||||||||||| ||||||||||| |||||  |||| || || || || |||||
gttgttgacattaaaatctggaatatgtgtttcattaagaaaaatctgtttattccatcgcaaaaaagtgaaggacagtacttttgttcccctgctgaaaagaaaaggaacagtacttctatagttttattggcatgactcgataaactaacagacaaaaaacagGTGAAAAAAGGAAGAAGCTTGAAGAAGAGAAGGGGATCATCATTCGTTTCGTCATTGGCCACAG
















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|110724992|gb|EE101306.1|EE101306
EST:     TAGTAGTAGAAAGCGGAGAGATTCAGTTCGCGCTACTTGGATGCCACAAG                         GTGATAAAAGAAAGAAGCTTGAGGAAGAGAAGGGCATCATAGTTCGCTTTG
genomic: TAGTAGTAGAAAGCGGAGAGATTCAGTTCGCGCTACTTGGATGCCACAAGgttctgaatt ... tgaaaattagGTGATAAAAGAAAGAAGCTTGAGGAAGAGAAGGGCATCATAGTTCGCTTTG
EST: gi|110688432|gb|EE066976.1|EE066976
EST:     TAGTAGTAGAAAGCGGAGAGATTCAGTTCGCGCTACTTGGATGCCACAAG                         GTGATAAAAGAAAGAAGCTTGANGAAGAGAAAGGCATCATAGTTCGCTTTG
genomic: TAGTAGTAGAAAGCGGAGAGATTCAGTTCGCGCTACTTGGATGCCACAAGgttctgaatt ... tgaaaattagGTGATAAAAGAAAGAAGCTTGAGGAAGAGAAGGGCATCATAGTTCGCTTTG
EST: gi|71875910|gb|DT024965.1|DT024965
EST:     GATTCAGTTCGCGCTACTTGGATGCCACAAG                         GTGATAAAAGAAAGAAGCTTGAGGAAGAGAAGGGCATCATAGTTCGCTTTG
genomic: GATTCAGTTCGCGCTACTTGGATGCCACAAGgttctgaatt ... tgaaaattagGTGATAAAAGAAAGAAGCTTGAGGAAGAGAAGGGCATCATAGTTCGCTTTG
EST: gi|77583730|gb|DV220900.1|DV220900
EST:     GATTCAGTTCGCGCTACTTGGATGCCACAAG                         GTGATAAAAGAAAGAAGCTTGAGGAAGAGAAGGGCATCATAGTTCGCTTTG
genomic: GATTCAGTTCGCGCTACTTGGATGCCACAAGgttctgaatt ... tgaaaattagGTGATAAAAGAAAGAAGCTTGAGGAAGAGAAGGGCATCATAGTTCGCTTTG
EST: gi|71875911|gb|DT024966.1|DT024966
EST:     GATTCAGTTCGCGCTACTTGGATGCCACAAG                         GTGATAAAAGAAAGAAGCTTGAGGAAGAGAAGGGCATCATAGTTCGCTTTG
genomic: GATTCAGTTCGCGCTACTTGGATGCCACAAGgttctgaatt ... tgaaaattagGTGATAAAAGAAAGAAGCTTGAGGAAGAGAAGGGCATCATAGTTCGCTTTG
EST: gi|37184436|gb|CF603790.1|CF603790
EST:     TAGTAGTAGAAAGCGGAGAGATTCAGTTCGCGCTACTTGGATGCCACAAG                         GTGATAAAAGAAAGAAGCTTGAGGAAGAGAAGGGCATCATAGT
genomic: TAGTAGTAGAAAGCGGAGAGATTCAGTTCGCGCTACTTGGATGCCACAAGgttctgaatt ... tgaaaattagGTGATAAAAGAAAGAAGCTTGAGGAAGAGAAGGGCATCATAGT
EST: gi|110712361|gb|EE089898.1|EE089898
EST:     GGAGAGATTCAGTTCGCGCTACTTGGATGCCACAAG                         GTGATAAAAGAAAGAAGCTTGAGGAAGAGAAGGGCATCATAGTTCGCTTTG
genomic: GGAGAGATTCAGTTCGCGCTACTTGGATGCCACAAGgttctgaatt ... tgaaaattagGTGATAAAAGAAAGAAGCTTGAGGAAGAGAAGGGCATCATAGTTCGCTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttccctgtttgtgaaactaatttatgacaatctttttctttatgaaaattagGTGATAAAAGAAAGAAGCTTGAGGAAGAGAAGGGCATCATAGTTCGCTTTGTAATAGGTCACAG
                 aactaat  putative branch site (score: 2)
                                 tctttttctttat  putative PPT
                    taatttatgacaatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctgaattgatcctatactctttccactattttttttttttttccctgtttgtgaaactaatttatgacaatctttttctttatgaaaattagGTGATAAAAGAAAGAAGCTTGAGGAAGAGAAGGGCATCATAGTTCGCTTTGTAATAGGTCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA