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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcctgtttcacattttattagattcttttgtgcgtcatataccacagctatgagaggcatacatttgttattgactgttcaatgccagGTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTG

Basic information

species Vitis vinifera
transcript Vv01s0011g05370.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 12
gtatcctgtttcacattttattagattcttttgt-gcgtcatataccacagctatgagaggcatacatttgttattgactgttcaatgccagGTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTG
              |  | |||||   | |  ||  | | || | | | |    ||   | ||  ||| |  ||| ||       ||  ||||| || ||||| |||||||||||||| ||||| |||||||||||| | || |||||||||||||||||||| ||||| ||||
------------gtaagt-attaggaccgtcagtcacatgattttcaaaa----tgccggacaagcatatcatat-gaaaaccatatttcagGTGCCTACTGGGTGGAAATTTTTTGGGAACTTGATGGATGCTGGAATGTGCTCAATTTGTGGTGAAGAAAGCTTTGGCACTG

upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 12
gtatcctgtttcacattttattagattcttttgtgcgtcatataccacagctatga-gaggcatacatttgttattgactgttcaatgccagGTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTG
                     || | | ||  |  | |  | | | | |  |   | |    ||| || |   ||  |        |  ||||| || ||||| |||||||||||||| || || |||||||||||| | || ||||| |||||||||||||| ||||| ||||
--------------------gtaaagtattaagaccttggtttgcaagattttgaatgctagataaatctaacataaaaaacatgtt-tcagGTGCCTACTGGGTGGAAATTTTTTGGGAATTTGATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTG

upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G109383_T02 (Zea mays), 3'ss of exon 12
gtatcctgtttcacattttattagattcttttgtgcgtcatataccacagctatgagaggcataca--tttgttattgactgttca-atgccagGTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTG
                     || | | ||     | |  | | | | |  | |||  | |||| |  | ||  ||  |     ||  |  ||||| || ||||| ||||| |||||||| || || |||||||||||| | || ||||| |||||||||||||| ||||| ||||
--------------------gtaaaatattaaaatcttggtttgcaagatttttgaatgtcatataaatctgacataaaaaaaccatgtttcagGTGCCTACTGGATGGAAGTTTTTTGGGAATTTGATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTG

upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA05G34790.1 (Glycine max), 3'ss of exon 12
gtatcctgtttcaca-ttttattagattcttttgtgcgtcatataccacagctatgagaggcatacatttg--ttattgactgttcaatgccagGTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTG
|||| ||| |   || | || |||          | | | ||   | ||   || || | | |   ||||   ||| | | | |||||  ||||||||| || || ||||| || |||||||| |||||||||||||||||||||||| | |||||||||||||||||||| ||||
gtatactgctattcaatatttttaagcatgaaaatacttgatg-gcgactttta-gacatgtaattatttaatttaattattattcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG

upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA08G04890.1 (Glycine max), 3'ss of exon 12
--gtatcctgtttcacattttattagattcttttgtgcgtcatataccacagctatgagaggca--tacatttgttattgactgttcaatgccagGTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTG
   |||     ||||   | | |||  |       | | |  |  |   |   || || | |||  ||  ||  ||| |   | |||||  ||||||||| || || ||||| || |||||||| |||||||||||||||||||||||| | |||||||||||||||||||| ||||
gtatattgctcttcaatgtcttttaagtatgaaaatac-ttgttgatggctttta-gacatgcaattattttatttaattgttattcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG

upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA03G05150.1 (Glycine max), 3'ss of exon 6
gtatcctgtttcacattttattagattcttttgtgcgtcatataccacagctatgagaggcatacatttgttattgactgttcaatgccagGTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTG
                                                              ||  ||  ||  |   | |||||  ||||||||| || || ||||| || |||||||| |||||||||||| ||||||||||| | |||||||||||||||||||| ||||
---------------------------------------------------------gtaattattttatttgattgttattcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTAGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG

upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 12
gtatcctgtttcacattttattagattcttttgtgcgtcatataccacagctatgagaggcatacatttgttattgactgttca-atgccagGTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTG
      |   |  ||   |   |  |||| |   || || | |  |  | |||    |   |      | |   |      ||| ||  ||||| ||||| |||||||| |||||||||||  | |||||||||||  | |||||  ||||||| |||||||||||||||||||
-----gtacatgtcaccgtgc-aacttctatccagcttcttttctcctaactacataatttaatttcatatctctattaaatcacatatcagGTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTG

upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: EFJ09195 (Selaginella moellendorffii), 3'ss of exon 11
gtatcctgtttcacattttattagatt-cttttgtgcgtcatataccacagctatgagaggcatacatttgttattgactgttcaatgccagGTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTG
                 | ||  |||| || |||| | |  | | | |||        | || ||||| |    |||            |||||||| ||||| ||||| |||||||| ||||| |||||||||||  | ||||| || ||||||||||||||||| ||||| |
----------------gtgataggattgctcttgttcttgctttcctacac-------acgcgtacatgttgcgttg------------cagGTCCCTACTGGATGGAAGTTTTTTGGAAACTTGATGGATGCTGGCATGTGTTCCATCTGTGGTGAAGAAAGTTTCGGAACCG

upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: EFJ05270 (Selaginella moellendorffii), 3'ss of exon 11
gtatcctgtttcacattttattagatt-cttttgtgcgtcatataccacagctatgagaggcatacatttgttattgactgttcaatgccagGTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTG
                 | ||  |||| || |||| | |  | | | |||        | || ||||| |    |||            |||||||| ||||| ||||| |||||||| ||||| |||||||||||  | ||||| || ||||||||||||||||| ||||| |
----------------gtgataggatttctcttgttcttgctttcctacac-------acgcgtacatgttgcgttg------------cagGTCCCTACTGGATGGAAGTTTTTTGGAAACTTGATGGATGCTGGCATGTGTTCCATCTGTGGTGAAGAAAGTTTCGGAACCG

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|30129214|gb|CB914553.1|CB914553
EST:     CTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCTGAAATTCTTTGAG                         GTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGT
genomic: CTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCTGAAATTCTTTGAGgtatcctgtt ... tcaatgccagGTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGT
EST: gi|110388407|gb|EC953157.1|EC953157
EST:     CTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCTGAAATTCTTTGAG                         GTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGT
genomic: CTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCTGAAATTCTTTGAGgtatcctgtt ... tcaatgccagGTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGT
EST: gi|30133454|gb|CB918793.1|CB918793
EST:     CTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCTGAAATTCTTTGAG                         GTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGT
genomic: CTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCTGAAATTCTTTGAGgtatcctgtt ... tcaatgccagGTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGT
EST: gi|30305224|gb|CB982018.1|CB982018
EST:     CTGCTGCTCTTGACGTTGTAGCCAAACATTTAAATCTGAAATTCTTTGAG                         GTCCCAACTGGCTGG
genomic: CTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCTGAAATTCTTTGAGgtatcctgtt ... tcaatgccagGTCCCAACTGGCTGG
EST: gi|37188896|gb|CF608245.1|CF608245
EST:     CTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCTGAAATTCTTTGAG                         GTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGT
genomic: CTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCTGAAATTCTTTGAGgtatcctgtt ... tcaatgccagGTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGT
EST: gi|32270099|gb|CD719258.1|CD719258
EST:     CTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCTGAAATTCTTTGAG                         GTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGT
genomic: CTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCTGAAATTCTTTGAGgtatcctgtt ... tcaatgccagGTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGT
EST: gi|30137874|gb|CB923212.1|CB923212
EST:     CTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCTGAAATTCTTTGAG                         GTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGT
genomic: CTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCTGAAATTCTTTGAGgtatcctgtt ... tcaatgccagGTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGT
EST: gi|37183515|gb|CF602869.1|CF602869
EST:     CTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCTGAAATTCTTTGAG                         GTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGT
genomic: CTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCTGAAATTCTTTGAGgtatcctgtt ... tcaatgccagGTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGT
EST: gi|30305289|gb|CB982083.1|CB982083
EST:     CTGCTGCTCTTGACGTTGTAGCCAAACATTTAAATCTGAAATTCTTTGAG                         GTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGAATGCTGGATTATGT
genomic: CTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCTGAAATTCTTTGAGgtatcctgtt ... tcaatgccagGTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGT
EST: gi|161715091|gb|FC063627.1|FC063627
EST:     CTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCTGAAATTCTTTGAG                         GTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGT
genomic: CTGCTGCTCTTGATGTTGTAGCCAAACATTTAAATCTGAAATTCTTTGAGgtatcctgtt ... tcaatgccagGTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcatataccacagctatgagaggcatacatttgttattgactgttcaatgccagGTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTG
                                   tattgac  putative branch site (score: 2)
                         atacatttgttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcctgtttcacattttattagattcttttgtgcgtcatataccacagctatgagaggcatacatttgttattgactgttcaatgccagGTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA