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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatctcattctttgatttcccttaaaagttagtgatatggttgtgattgaataacaaactgtgagttggctagtaatccctgaaccaatgtatggacagATTTGGGATGCTTACAATGTAAAGGCACAGACCTTTAAGACAGCCATTGAAGCTGCTTGCATGCTGCTTAGGATCGATGACATAGTGAGCGGGATCAAGA

Basic information

species Vitis vinifera
transcript Vv07s0130g00410.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0130g00410.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 13
--tgatctcattctttgatttcccttaaaagttagtgatatggttgtgattgaataacaaactgtgagttggctagtaatccctgaaccaatgtatggacagATTTGGGATGCTTACAATGTAAAGGCACAGACCTTTAAGACAGCCATTGAAGCTGCTTGCATGCTGCTTAGGATCGATGACATAGTGAGCGGGATCAAGA
  ||  ||  ||||     | | ||      |   |    || || || |||  || || | |   |      ||||| | |||   |           ||||| |||||| |||||| ||| |||||||| || || |||||||| || || || ||||||||||| ||||||||||| ||||| || ||||| |||||||
gttggcctttttctccatgtgcactgctgcat--atatcctgcttttg-ttgtgta-cacattaaaacacca-tagtattgccttgtc----------gcagATCTGGGATTCTTACAGTGTCAAGGCACAAACGTTCAAGACAGCTATCGAGGCAGCTTGCATGCTTCTTAGGATCGACGACATCGTCAGCGGTATCAAGA

upper sequence: Vv07s0130g00410.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os02g14929.1 (Oryza sativa), 3'ss of exon 13
tgatctcattctttgatttcccttaaaagttagtgatatggttgtgattgaataacaaactgtgagttggctagtaatccctgaaccaatgtatggacagATTTGGGATGCTTACAATGTAAAGGCACAGACCTTTAAGACAGCCATTGAAGCTGCTTGCATGCTGCTTAGGATCGATGACATAGTGAGCGGGATCAAGA
                | || ||       | ||| |     |||| ||   |  |    |   | |   || | || | |   | | ||   |   ||||| |||||  | |||| ||| ||||| ||||| || |||||||| ||||| ||||| |||||||| || ||||||||||| || || || || |||||||
---------------gtctctctccccccctcgtgct-----tgtgctt---ttgcgtgtttgcattcatcttgaaacctcattatctatcctttt-cagATCTGGGACTCGTACAGTGTCAAGGCGCAGACATTCAAGACAGCTATTGAGGCTGCCTGCATGCTCCTGAGGATCGATGATATTGTCAGTGGCATCAAGA

upper sequence: Vv07s0130g00410.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G069765_T05 (Zea mays), 3'ss of exon 13
tgatctcattctttgatttcccttaaaagttagtgatatggttgtgattgaataacaaactgtgagttggctagtaatccctgaaccaatgtatggacagATTTGGGATGCTTACAATGTAAAGGCACAGACCTTTAAGACAGCCATTGAAGCTGCTTGCATGCTGCTTAGGATCGATGACATAGTGAGCGGGATCAAGA
               |||||  || |    |    | |      ||  |||  ||       |    || |||   |         | || |      |||| |||||| | |||| ||| || ||||| || || |||||||| ||||| ||||||||||||||  | || ||||||||||| || ||||| |||||||
-------------gtatttcttttta----tgtgcacaaaagcatgcctgaccaatgtttgtttgcatgtctaaccacaatgttgtccattt-----tagATCTGGGATTCCTACAGTGTTAAAGCACAAACGTTCAAGACAGCAATTGAGGCTGCTTGCATGCTTTTGAGAATCGATGACATTGTCAGCGGTATCAAGA

upper sequence: Vv07s0130g00410.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G175510_T01 (Zea mays), 3'ss of exon 13
tgatctcattctttgatttcccttaaaagttagtgatatggttgtgattgaataacaaactgtgagttggctagtaatccctgaaccaatgtatggacagATTTGGGATGCTTACAATGTAAAGGCACAGACCTTTAAGACAGCCATTGAAGCTGCTTGCATGCTGCTTAGGATCGATGACATAGTGAGCGGGATCAAGA
              |  ||||||| |     |   ||     | |||   | |       ||   ||   |||     | |    || || |      |||| |||||| | ||||  || || || ||||| || |||||||| ||||| ||||||||||||||  | || || |||||||| || ||||| |||||||
--------------gtattcccttcatctgcacaaatgcaagtttgacc-attgtttgtttgcatgt---ctaaatgccacaatgcccattt-----tagATCTGGGATTCCTACAGCGTTAAAGCGCAGACGTTCAAGACAGCGATTGAGGCTGCTTGCATGCTTTTGAGAATAGATGACATTGTCAGCGGTATCAAGA

upper sequence: Vv07s0130g00410.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT5G26360.1 (Arabidopsis thaliana), 3'ss of exon 12
----tgatctcattctttgatttcccttaaaagttagtgatatggttgtgattgaataacaaactgtgagttggctagtaatccctgaaccaatgtatggacagATTTGGGATGCTTACAATGTAAAGGCACAGACCTTTAAGACAGCCATTGAAGCTGCTTGCATGCTGCTTAGGATCGATGACATAGTGAGCGGGATCAAGA
     |||   ||    | |  |   || |   | |   | |||      |   |||   |  | | |||||| |||  |     | |  |||| |     ||||| |||||| | |||||||| ||||| || || || ||||| || || ||||| || || ||||| || ||||||||||| |||||||| || |||||||
gtaaggattaaatcacataaccttggttgattctca-caacatga-----aaccaatgtgactcagagagttgactaaaagcttttaa--caattttc---cagATATGGGATTCGTACAATGTGAAGGCGCAAACTTTCAAGACGGCTATAGAAGCAGCGTGTATGCTTCTAAGGATCGATGATATAGTGAGTGGAATCAAGA

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|349808330|gb|FQ405474.1|FQ405474
EST:     TGGGCATAGATGGGAACACGGGTGCAATCACTGATATGAAAGAGCGCAAG                         ATTTGGGATGCTTACAATGTAAAGGCACAGACCTTTAAGACAGCCCTTGAA
genomic: TGGGCATAGATGGGAACACGGGTGCAATCACTGATATGAAAGAGCGCAAGgtaagagctt ... gtatggacagATTTGGGATGCTTACAATGTAAAGGCACAGACCTTTAAGACAGCCATTGAA
EST: gi|349823591|gb|FQ415001.1|FQ415001
EST:     TGGGCATAGATGGGAACACGGGTGCAATCACTGATATGAAAGAGCGCAAG                         ATTTGGGATGCTTACAATGTAAAGGCACAGACCTTTAAGACAGCCATCGAA
genomic: TGGGCATAGATGGGAACACGGGTGCAATCACTGATATGAAAGAGCGCAAGgtaagagctt ... gtatggacagATTTGGGATGCTTACAATGTAAAGGCACAGACCTTTAAGACAGCCATTGAA
EST: gi|351034297|gb|FQ448094.1|FQ448094
EST:     TGGGCATAGATGGGAACACGGGTGCAATCACTGATATGAAAGAGCGCAAG                         ATTTGGGATGCTTACAATGTAAAGGCACAGACCTTTAAGACAGCCATTGAA
genomic: TGGGCATAGATGGGAACACGGGTGCAATCACTGATATGAAAGAGCGCAAGgtaagagctt ... gtatggacagATTTGGGATGCTTACAATGTAAAGGCACAGACCTTTAAGACAGCCATTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattgaataacaaactgtgagttggctagtaatccctgaaccaatgtatggacagATTTGGGATGCTTACAATGTAAAGGCACAGACCTTTAAGACAGCCATTGAAGCTGCTTGCATGCTGCTTAGGATCGATGACATAGTGAGCGGGATCAAGA
    gaataac  putative branch site (score: 2)
     aataacaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatctcattctttgatttcccttaaaagttagtgatatggttgtgattgaataacaaactgtgagttggctagtaatccctgaaccaatgtatggacagATTTGGGATGCTTACAATGTAAAGGCACAGACCTTTAAGACAGCCATTGAAGCTGCTTGCATGCTGCTTAGGATCGATGACATAGTGAGCGGGATCAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - ctcattc
- - - - - - - - - -cccttaa
- - - - - - - - - - - - - - - - - - - -ggttgtg
- - - - - - - - - - - - - - - - - - - - - - - - -gaataac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaccaa