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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtgcgtaaccaaggggaactacgatcagaatggttgtgatttctaaatgtttgtgatgcaggttacttatcaaaaaaaaaaaaaatgtttgtgatgcagGTTGTGAAGAGCTTCTCTTCTGGTAAAAGAGAAGGTGGAGATTTTGTTGCAGCCTGTGTCTCACCCAAAGGAGAATGGATTTATTGTGTTGGTGAAGACA

Basic information

species Vitis vinifera
transcript Vv17s0000g08930.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os01g21940.1 (Oryza sativa), 3'ss of exon 12
-ggtgcgtaaccaaggggaactacgatcagaatggttgtgatttctaaatgtttgtgatgcaggttacttatcaaaaaaaaaaaaaatgtttgtgatgcagGTTGTGAAGAGCTTCTCTTCTGGTAAAAGAGAAGGTGGAGATTTTGTTGCAGCCTGTGTCTCACCCAAAGGAGAATGGATTTATTGTGTTGGTGAAGACA
      ||  | |  | | |      |   | || || |    | |  ||| || |     |  |   ||||    |      |         || | |||||||| || || || || ||||||||| | ||||| ||||||||  ||||||| |  || ||||| |||||||||||||| |||||||||||||||||||
cataaagtggctattgagcatcgaagt-gcattgcttttttcattttgatggttatttatgaattctattatggttattcttgactggaaacttgttacagGTTGTAAAAAGTTTTTCATCTGGTAAACGGGAAGGGGGAGATTTCCTTGCAGCTTCCGTTTCACCAAAAGGAGAATGGATATATTGTGTTGGTGAAGACA

upper sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G037683_T01 (Zea mays), 3'ss of exon 12
-----ggtgcgtaaccaaggggaactacgatcagaatggttgtgatttctaaatgtttgtgatgcaggttacttatcaaaaaaaaaaaaaatgtttgtgatgcagGTTGTGAAGAGCTTCTCTTCTGGTAAAAGAGAAGGTGGAGATTTTGTTGCAGCCTGTGTCTCACCCAAAGGAGAATGGATTTATTGTGTTGGTGAAGACA
          |      | |  ||  | |   || ||   |  |   | ||| ||||  |  |   | ||  |||| |        ||||   |||||  | |||||||||||||| ||||| || |||||  ||||||| ||||||||||||||||| |  || ||||| |||||||||||||| |||||||||||||||||||
tttaacaaaggctgtagaagataagcaaggcgaggatatctcagccatttaactgttatttctagtgcttggttatgattgccttgaaaa---tttgt--ttcagGTTGTGAAGAGTTTCTCATCAGGTAAGCGAGAAGGGGGAGATTTTGTTGCAGCTTCAGTTTCACCAAAAGGAGAATGGATATATTGTGTTGGTGAAGACA

upper sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA05G30430.2 (Glycine max), 3'ss of exon 13
----------ggtgcgtaaccaaggggaactacgatcagaatggttgtgatttctaaatgtttgtgatgcaggttacttatcaaaaaaaaaaaaaatgtttgtgatgcagGTTGTGAAGAGCTTCTCTTCTGGTAAAAGAGAAGGTGGAGATTTTGTTGCAGCCTGTGTCTCACCCAAAGGAGAATGGATTTATTGTGTTGGTGAAGACA
            |    ||  ||| |      |     |   || | | ||| |  || || || ||     |||  | ||||        | || || |        ||||||||||||||||||| ||||||||||||||||| ||||| ||||||||||||||||| ||||| ||||||||||||||||| ||||||||||||||||
ttttcatctttttttacaatgaagtgttgtagcagcatgttaggatctaattgc--aaggtatgagaattgagttcatcatcatttctctgacaattgat--------agGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAAGGCGGAGACTTTGTTGCAGCCTGTGTTTCACCTAAAGGAGAATGGATTTACTGTGTTGGTGAAGACA

upper sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA08G13560.2 (Glycine max), 3'ss of exon 13
ggtgcgtaaccaaggggaactacgatcaga-atggttgtgatttctaaatgtttgtgatgcaggttacttatcaaaaaaaaaaaaaatgtttgtgat---gcagGTTGTGAAGAGCTTCTCTTCTGGTAAAAGAGAAGGTGGAGATTTTGTTGCAGCCTGTGTCTCACCCAAAGGAGAATGGATTTATTGTGTTGGTGAAGACA
      |   |    |    ||| || | |  | ||       | | |   | ||   |||| | ||     |   |    |  |  ||| ||| |      ||||||||||||||||||| ||||||||||||||||| ||||| ||||||||||||||||| ||||| ||||||||||||||||| |||||||||||||| |
---ttcttttcttttgttcttacaatgaaatgttgtaacagcatgttaggatctg-attgcaaggtatgagacttgagttcattatttgtctgtcaattgatagGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAAGGCGGAGACTTTGTTGCAGCCTGTGTTTCACCTAAAGGAGAATGGATTTACTGTGTTGGTGAAGATA

upper sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA02G18000.1 (Glycine max), 3'ss of exon 9
----------------------------------------------------------------------------ggtgcgtaaccaaggggaactacgatcaga-atggttgtgatttctaaatgtttgtgatgcaggttacttatcaaaaaaaaaaaaaatgtttgtga---tgcagGTTGTGAAGAGCTTCTCTTCTGGTAAAAGAGAAGGTGGAGATTTTGTTGCAGCCTGTGTCTCACCCAAAGGAGAATGGATTTATTGTGTTGGTGAAGACA
                                                                              |   |   |         ||| || | |  | ||    |  | | |   | |    |||| | ||     |   |    |  |  ||| | | |      ||||||||||||||||||| ||||||||||||||  ||| ||| ||||||||  |||| || ||||||||||||||||||||||||| ||||||||||||||
gtaactcatattcatgctagccaaaggtggaaatttacttacatgtggattggagaccttgggttatactttttctcatttcttttcttttattcttacaatgaaatgttgtaacaacatgttaggatcta-attgcaaggtatgagacttgagttcattatttgtctatcagttgatagGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAGAGTGAAGACTTTGTTGCCACCTGCGTTTCACCCAAAGGAGAATGGATTTATTTTGTTGGTGAAGACA

upper sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT1G73720.1 (Arabidopsis thaliana), 3'ss of exon 13
---ggtgcgtaaccaaggggaactacga-tcagaatggttgtgatttctaaatgtttgtgatgcaggttacttatcaaaaaaaaaaaaaatgtttgtgatgcagGTTGTGAAGAGCTTCTCTTCTGGTAAAAGAGAAGGTGGAGATTTTGTTGCAGCCTGTGTCTCACCCAAAGGAGAATGGATTTATTGTGTTGGTGAAGACA
     |    | | | ||    || | | ||||  |  |||| ||  | |||      | |    | | || |      | |    ||    ||||     |||||||||||||| ||||| || ||||| || ||||| ||||||||||| ||||| ||||| ||  | |||||||| ||||| || ||  | || |||||||
gtaaatttccagcaacggtctcctgcaaatcagtgtcattgtcatgccaaaac-----taagattgttcacatgcttctatattggaatccttttg-----cagGTTGTGAAGAGTTTCTCATCCGGTAATAGGGAAGGAGGAGATTTTGTAGCAGCATGTGTATCTACAAAAGGAGATTGGATATACTGCATCGGCGAAGACA

upper sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: EFJ30597 (Selaginella moellendorffii), 3'ss of exon 11
ggtgcgtaaccaaggggaactacgatcagaatggttgtgatttctaaatgtttgtgatgcaggttacttatcaaaaaaaaaaaaaatgtttgtgatg-cagGTTGTGAAGAGCTTCTCTTCTGGTAAAAGAGAAGGTGGAGATTTTGTTGCAGCCTGTGTCTCACCCAAAGGAGAATGGATTTATTGTGTTGGTGAAGACA
                                    |||  ||     | |   |  |||  | |  ||  |                ||||   || |||||||| ||||||||||| ||||| |||||||| ||||| ||||| || || ||||| ||||| || |||||||| ||||||||||| ||||| |||||||
------------------------------------gtgcatttctcctttcctttgtgcctgatttttcccttccgg---------ctttgcattggcagGTTGTCAAGAGCTTCTCGTCTGGCAAAAGAGAGGGTGGCGATTTCGTCGCGGCCTGCGTCTCGCCAAAAGGAGACTGGATTTATTGCGTTGGAGAAGACA

upper sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: EFJ15973 (Selaginella moellendorffii), 3'ss of exon 11
ggtgcgtaaccaaggggaactacgatcagaatggttgtgatttctaaatgtttgtgatgcaggttacttatcaaaaaaaaaaaaaatgtttgtgatg-cagGTTGTGAAGAGCTTCTCTTCTGGTAAAAGAGAAGGTGGAGATTTTGTTGCAGCCTGTGTCTCACCCAAAGGAGAATGGATTTATTGTGTTGGTGAAGACA
                                    |||  ||     | ||  |  |||  | |  ||  |                ||||   || |||||||| ||||||||||| ||||| |||||||| ||||| ||||| || || ||||| ||||| || |||||||| ||||||||||| ||||| |||||||
------------------------------------gtgcatttctccttttctttgtgcctgatttttcccttccgg---------ctttgcattggcagGTTGTCAAGAGCTTCTCGTCTGGCAAAAGAGAGGGTGGCGATTTCGTCGCGGCCTGCGTCTCGCCAAAAGGAGACTGGATTTATTGCGTTGGAGAAGACA

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|351014184|gb|FQ434773.1|FQ434773
EST:     TTGTGTGTAACAGGACATCATCAATATACCTTATGACACTTCAAGGACAG                         GTTGTGAAGAGCTTCTCTTCTGGTAAAAGAGAAGGTGGAGATTTTGTTGCA
genomic: TTGTGTGTAACAGGACATCATCAATATACCTTATGACACTTCAAGGACAGgtacttattc ... tgtgatgcagGTTGTGAAGAGCTTCTCTTCTGGTAAAAGAGAAGGTGGAGATTTTGTTGCA
EST: gi|33403518|gb|CF209145.1|CF209145
EST:     TTGTGTGTAACAGGACATCATCAATATACCTTATGACACTTCAAGGACAG                         GTTGTGAAGAGCTTCTCTTCTGGTAAAAGAGAAGGTGGAGATTTTGTTGCA
genomic: TTGTGTGTAACAGGACATCATCAATATACCTTATGACACTTCAAGGACAGgtacttattc ... tgtgatgcagGTTGTGAAGAGCTTCTCTTCTGGTAAAAGAGAAGGTGGAGATTTTGTTGCA
EST: gi|110430180|gb|EC996718.1|EC996718
EST:     TTGTGTGTAACAGGACATCATCAATATACCTTATGACACTTCAAGGACAG                         GTTGTGAAGAGCTTCTCTTCTGGTAAAAGAGAAGGTGGAGATTTTGTTGCA
genomic: TTGTGTGTAACAGGACATCATCAATATACCTTATGACACTTCAAGGACAGgtacttattc ... tgtgatgcagGTTGTGAAGAGCTTCTCTTCTGGTAAAAGAGAAGGTGGAGATTTTGTTGCA
EST: gi|110686642|gb|EE064514.1|EE064514
EST:     TTGTGTGTAACAGGACATCATCAATATACCTTATGACACTTCAAGGACAG                         GTTGTGAAGAGCTTCTCTTCTGGTAAAAGAGAAGGTGGAGATTTTGTTGCA
genomic: TTGTGTGTAACAGGACATCATCAATATACCTTATGACACTTCAAGGACAGgtacttattc ... tgtgatgcagGTTGTGAAGAGCTTCTCTTCTGGTAAAAGAGAAGGTGGAGATTTTGTTGCA
EST: gi|110387409|gb|EC952071.1|EC952071
EST:     TTGTGTGTAACAGGACATCATCAATATACCTTATGACACTTCAAGGACAG                         GTTGTGAAGAGCTTCTCTTCTGGTAAAAGAGAAGGTGGAGATTTTGTTGCA
genomic: TTGTGTGTAACAGGACATCATCAATATACCTTATGACACTTCAAGGACAGgtacttattc ... tgtgatgcagGTTGTGAAGAGCTTCTCTTCTGGTAAAAGAGAAGGTGGAGATTTTGTTGCA
EST: gi|110687493|gb|EE064965.1|EE064965
EST:     TTGTGTGTAACAGGACATCATCAATATACCTTATGACACTTCAAGGACAG                         GTTGTGAAGAGCTTCTCTTCTGGTAAAAGAGAAGGTGGAGATTTTGTTGCA
genomic: TTGTGTGTAACAGGACATCATCAATATACCTTATGACACTTCAAGGACAGgtacttattc ... tgtgatgcagGTTGTGAAGAGCTTCTCTTCTGGTAAAAGAGAAGGTGGAGATTTTGTTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatgtttgtgatgcaggttacttatcaaaaaaaaaaaaaatgtttgtgatgcagGTTGTGAAGAGCTTCTCTTCTGGTAAAAGAGAAGGTGGAGATTTTGTTGCAGCCTGTGTCTCACCCAAAGGAGAATGGATTTATTGTGTTGGTGAAGACA
 ttctaaa  putative branch site (score: 2)
                  ttacttatcaaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtgcgtaaccaaggggaactacgatcagaatggttgtgatttctaaatgtttgtgatgcaggttacttatcaaaaaaaaaaaaaatgtttgtgatgcagGTTGTGAAGAGCTTCTCTTCTGGTAAAAGAGAAGGTGGAGATTTTGTTGCAGCCTGTGTCTCACCCAAAGGAGAATGGATTTATTGTGTTGGTGAAGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - taaccaa
- - - - - - - - - - - - - cagaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa