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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatagatttctgttgcatatttctgtgtaaccaagcatgtcaacccttgatgtgttgccaatcatttcactgtaagttggtgctattcgcttgtggacagTGATGGTGCGGCTGCATTAGTGCTAGTGAGTGGTAAGAAGGCAGTTGAGCTTAGACTCCAAGTGATTGCTAAGATTGCAGGATATGGTGATGCTGCTCAG

Basic information

species Vitis vinifera
transcript Vv00s0531g00050.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0531g00050.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA07G39870.1 (Glycine max), 3'ss of exon 9
gatagatttctgttgcat--atttctgtgtaaccaagcatgtcaacccttgatgtgt-tgccaatcatttcactgtaagttggtgctattcgcttgtggacagTGATGGTGCGGCTGCATTAGTGCTAGTGAGTGGTAAGAAGGCAGTTGAGCTTAGACTCCAAGTGATTGCTAAGATTGCAGGATATGGTGATGCTGCTCAG
  ||| || ||  |  ||  ||     ||    | |  |  |       | |  ||  ||||  ||   | |   |   |||||  |||| |||||     ||||||||||| ||||||||||||||||||||||   ||||||||  ||||||| || | || || ||||| |||||   ||||||||| ||||| ||| ||
agtagtttgctaataaattaatactcatgccttccaatacttatggttctaaactgcatgccgttctgctgataatggattggt-ttattggcttg--actagTGATGGTGCTGCTGCATTAGTGCTAGTGAGTGAAGAGAAGGCACGTGAGCTTGGATTGCATGTAATTGCAAAGATAAAAGGATATGGGGATGCAGCTAAG

upper sequence: Vv00s0531g00050.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA17G00910.1 (Glycine max), 3'ss of exon 9
gatagatttctgttgcat--atttctgtgtaac-caagcatgtcaacccttgatgtgttgccaatcatttcactgtaagttggtgctattcgcttgtggacagTGATGGTGCGGCTGCATTAGTGCTAGTGAGTGGTAAGAAGGCAGTTGAGCTTAGACTCCAAGTGATTGCTAAGATTGCAGGATATGGTGATGCTGCTCAG
   || || ||  |  ||  ||   | ||     |||   |       ||  |     |||   ||   | |   |   |||||  |||| |||||     ||||||||||| |||||||||||||||||||| |   ||||||||  ||||||| || | || || ||||| |||||   ||||||||| ||||| ||| ||
agaagtttgctaataaattaatacttatgccttgcaatagttatggttctaaactgcatgctcttctgctgataatggattggt-ttattggcttg--actagTGATGGTGCTGCTGCATTAGTGCTAGTGAGCGAAGAGAAGGCACGTGAGCTTGGATTGCATGTAATTGCAAAGATAAAAGGATATGGGGATGCAGCTAAG
















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|30301836|gb|CB978630.1|CB978630
EST:     AGTTTCAAGGATGGGGGTTCAGTTACTGCAGGGAATGCTTCTAGCATAAG                         TGATGGTGCGGCTGCATTAGTGCTAGTGAGTGGTAAGAAGGCAGTTGAGCT
genomic: AGTTTCAAGGATGGGGGTTCAGTTACTGCAGGGAATGCTTCTAGCATAAGgtatgtgtgt ... ttgtggacagTGATGGTGCGGCTGCATTAGTGCTAGTGAGTGGTAAGAAGGCAGTTGAGCT
EST: gi|77584049|gb|DV221063.1|DV221063
EST:     AGTTTCAAGGATGGGGGTTCAGTTACTGCAGGGAATGCTTCTAGCATAAG                         TGATGGTGCGGCTGCATTAGTGCTAG
genomic: AGTTTCAAGGATGGGGGTTCAGTTACTGCAGGGAATGCTTCTAGCATAAGgtatgtgtgt ... ttgtggacagTGATGGTGCGGCTGCATTAGTGCTAG
EST: gi|30301768|gb|CB978562.1|CB978562
EST:     AGTTTCAAGGATGGGGGTTCAGTTACTGCAGGGAATGCTTCTAGCATAAG                         TGATGGTGCGGCTGCATTAGTGCTAGTGAGTGGTAAGAAGGCAGTTGAGCT
genomic: AGTTTCAAGGATGGGGGTTCAGTTACTGCAGGGAATGCTTCTAGCATAAGgtatgtgtgt ... ttgtggacagTGATGGTGCGGCTGCATTAGTGCTAGTGAGTGGTAAGAAGGCAGTTGAGCT
EST: gi|34362568|gb|CF404153.1|CF404153
EST:     TGGGGGTTCAGTTACTGCAGGGAATGCTTCTAGCATAAG                         TGATGGTGCGGCTGCATTAGTGCTAGTGAGTGGTAAGAAGGCAGTTGAGCT
genomic: TGGGGGTTCAGTTACTGCAGGGAATGCTTCTAGCATAAGgtatgtgtgt ... ttgtggacagTGATGGTGCGGCTGCATTAGTGCTAGTGAGTGGTAAGAAGGCAGTTGAGCT
EST: gi|77586184|gb|DV222186.1|DV222186
EST:     AGTTTCAAGGATGGGGGTTCAGTTACTGCAGGGAATGCTTCTAGCATAAG                         TGATGGTGCGGCTGCATTAGTGCTAGTGAGTGGTAAGAAGGCAGTTGAGCT
genomic: AGTTTCAAGGATGGGGGTTCAGTTACTGCAGGGAATGCTTCTAGCATAAGgtatgtgtgt ... ttgtggacagTGATGGTGCGGCTGCATTAGTGCTAGTGAGTGGTAAGAAGGCAGTTGAGCT
EST: gi|37190107|gb|CF609456.1|CF609456
EST:     AGAAACAAGGATGGGGGTTCAGTTACTGCAGGGAATGCTTCTAGCATAAG                         TGATGGTGCGGCTGCATTAGTGCTAGTGAGTGGTAAGAAGGCAGTTGAGCT
genomic: AGTTTCAAGGATGGGGGTTCAGTTACTGCAGGGAATGCTTCTAGCATAAGgtatgtgtgt ... ttgtggacagTGATGGTGCGGCTGCATTAGTGCTAGTGAGTGGTAAGAAGGCAGTTGAGCT
EST: gi|110358833|gb|EC923335.1|EC923335
EST:     AGTTTCAAGGATGGGGGTTCAGTTACTGCAGGGAATGCTTCTAGCATAAG                         TGATGGTGCGGCTGCATTAGTGCTAGTGAGTGGTAAGAAGGCAGTTGAGCT
genomic: AGTTTCAAGGATGGGGGTTCAGTTACTGCAGGGAATGCTTCTAGCATAAGgtatgtgtgt ... ttgtggacagTGATGGTGCGGCTGCATTAGTGCTAGTGAGTGGTAAGAAGGCAGTTGAGCT
EST: gi|110381509|gb|EC934651.1|EC934651
EST:     AGTTTCAAGGATGGGGGTTCAGTTACTGCAGGGAATGCTTCTAGCATAAG                         TGATGGTGCGGCTGCATTAGTGCTAGTGAGTGGTAAGAAGGCAGTTGAGCT
genomic: AGTTTCAAGGATGGGGGTTCAGTTACTGCAGGGAATGCTTCTAGCATAAGgtatgtgtgt ... ttgtggacagTGATGGTGCGGCTGCATTAGTGCTAGTGAGTGGTAAGAAGGCAGTTGAGCT
EST: gi|30298600|gb|CB975394.1|CB975394
EST:     AGTTTCAAGGATGGGGGTTCAGTTACTGCAGGGAATGCTTCTAGCATAAG                         TGATGGTGCGGCTGCATTAGTGCTAGTGAGTGGTAAGAAGGCAGTTGAGCT
genomic: AGTTTCAAGGATGGGGGTTCAGTTACTGCAGGGAATGCTTCTAGCATAAGgtatgtgtgt ... ttgtggacagTGATGGTGCGGCTGCATTAGTGCTAGTGAGTGGTAAGAAGGCAGTTGAGCT
EST: gi|110376548|gb|EC941608.1|EC941608
EST:     AGTTTCAAGGATGGGGGTTCAGTTACTGCAGGGAATGCTTCTAGCATAAG                         TGATGGTGCGGCTGCATTAGTGCTAGTGAGTGGTAAGAAGGCAGTTGAGCT
genomic: AGTTTCAAGGATGGGGGTTCAGTTACTGCAGGGAATGCTTCTAGCATAAGgtatgtgtgt ... ttgtggacagTGATGGTGCGGCTGCATTAGTGCTAGTGAGTGGTAAGAAGGCAGTTGAGCT
EST: gi|110378421|gb|EC943552.1|EC943552
EST:     AGTTTCAAGGATGGGGGTTCAGTTACTGCAGGGAATGCTTCTAGCATAAG                         TGATGGTGCGGCTGCATTAGTGCTAGTGAGTGGTAAGAAGGCAGTTGAGCT
genomic: AGTTTCAAGGATGGGGGTTCAGTTACTGCAGGGAATGCTTCTAGCATAAGgtatgtgtgt ... ttgtggacagTGATGGTGCGGCTGCATTAGTGCTAGTGAGTGGTAAGAAGGCAGTTGAGCT
EST: gi|110395476|gb|EC961142.1|EC961142
EST:     AGTTTCAAGGATGGGGGTTCAGTTACTGCAGGGAATGCTTCTAGCATAAG                         TGATGGTGCGGCTGCATTAGTGCTAGTGAGTGGTAAGAAGGCAGTTGAGCT
genomic: AGTTTCAAGGATGGGGGTTCAGTTACTGCAGGGAATGCTTCTAGCATAAGgtatgtgtgt ... ttgtggacagTGATGGTGCGGCTGCATTAGTGCTAGTGAGTGGTAAGAAGGCAGTTGAGCT
EST: gi|110361851|gb|EC925352.1|EC925352
EST:     AGTTTCAAGGATGGGGGTTCAGTTACTGCAGGGAATGCTTCTAGCATAAG                         TGATGGTGCGGCTGCATTAGTGCTAGTGAGTGGTAAGAAGGCAGTTGAGCT
genomic: AGTTTCAAGGATGGGGGTTCAGTTACTGCAGGGAATGCTTCTAGCATAAGgtatgtgtgt ... ttgtggacagTGATGGTGCGGCTGCATTAGTGCTAGTGAGTGGTAAGAAGGCAGTTGAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgatgtgttgccaatcatttcactgtaagttggtgctattcgcttgtggacagTGATGGTGCGGCTGCATTAGTGCTAGTGAGTGGTAAGAAGGCAGTTGAGCTTAGACTCCAAGTGATTGCTAAGATTGCAGGATATGGTGATGCTGCTCAG
 ccttgat  putative branch site (score: 5)
                                        ttcgctt  putative PPT
              aatcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatagatttctgttgcatatttctgtgtaaccaagcatgtcaacccttgatgtgttgccaatcatttcactgtaagttggtgctattcgcttgtggacagTGATGGTGCGGCTGCATTAGTGCTAGTGAGTGGTAAGAAGGCAGTTGAGCTTAGACTCCAAGTGATTGCTAAGATTGCAGGATATGGTGATGCTGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - tgttgca
- - - - - - - - - - - - - -taaccaa
- - - - - - - - - - - - - - - - - - - - caaccct
- - - - - - - - - - - - - - - - - - - - - - - -tgatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - ttgccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttggtg