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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgcaatttttatgccattccaagggctcatttctgaaagatgctttgtaccttatcttgttatgggcttgtcatagtaattatgatatcatttgttttatagGTATTGGTGCGGGTAGAGCAAGAACAAAAGTTAACTGAAGATGCTCGCAGGTTTGCTGAGCAAGATGCTGCAGCCCAGAGATATGCTGCTCAAGTGCTTC

Basic information

species Vitis vinifera
transcript Vv13s0067g03420.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0067g03420.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: LOC_Os01g61860.2 (Oryza sativa), 3'ss of exon 14
-----gttgcaatttttatgccattccaagggctcatttctgaaagatgctttgtaccttatcttgttatgggcttgtcatagtaattatgatatcatttgtttta--tagGTATTGGTGCGGGTAGAGCAAGAACAAAAGTTAACTGAAGATGCTCGCAGGTTTGCTGAGCAAGATGCTGCAGCCCAGAGATATGCTGCTCAAGTGCTTC
     || || |    ||||    ||  |     |  || | |    | | |  | ||||   ||  ||  || || || |||| || |    |  |  |  |  |  |||||  || |||| |||||||||||||| ||  | ||||| ||||| ||||  || ||||||||||||||||| || |||| ||||||||| || ||||| |
gtgtagtagctaccaatatgttgctctgaataaac-cttgtcactactacatcatgcctt---ttactactggtttatc-tagttataaactaactaggtaatgcatgtagGTCCTGATGCGTGTAGAGCAAGAACAGAAAGTCACTGAGGATGCGCGCATATTCGCTGAGCAAGATGCTGCTGCTCAGAAATATGCTGCACATGTGCTCC

upper sequence: Vv13s0067g03420.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 14
gttgcaatttttatgccattccaagggctcatttctgaaagatgctttgtaccttatcttgttatgggcttgtcatagtaattatgatatcatttgtt--ttatagGTATTGGTGCGGGTAGAGCAAGAACAAAAGTTAACTGAAGATGCTCGCAGGTTTGCTGAGCAAGATGCTGCAGCCCAGAGATATGCTGCTCAAGTGCTTC
                         | |||||||        ||  ||    ||    ||   ||  | ||    | ||  | |||  |   ||||||  | |||||| ||| ||||||| |||||||| |||||| | ||||| |||||||| |||||||||||||||||||| || || || ||||||||||| ||||| ||||
-------------------------gtctcattttgtctgtttgtattcattctcgggttaacatatgttttctcttgtg-tgatgtgagtttttgttgctgatagGTCTTGATGCGGGTGGAGCAAGAGCAAAAGGTGACTGAGGATGCTCGTAGGTTTGCTGAGCAAGATGCAGCCGCACAAAGATATGCTGCGCAAGTCCTTC

upper sequence: Vv13s0067g03420.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA10G44110.1 (Glycine max), 3'ss of exon 14
gttgcaatttttatgccattccaagggctcatttctgaaagatgctttgtaccttatcttgttatgggct-tgtcatagtaattatgatatca---tttgtt--ttatagGTATTGGTGCGGGTAGAGCAAGAACAAAAGTTAACTGAAGATGCTCGCAGGTTTGCTGAGCAAGATGCTGCAGCCCAGAGATATGCTGCTCAAGTGCTTC
                         | ||||||| ||   |    ||||||     |||||  ||    | ||   |      | ||| || |   ||||||  | |||||| ||| ||||||| |||||||| |||||| | ||||| |||||||| |||||||||||||||||||| || || || ||||||||||| ||||| ||||
-------------------------gtctcatttttgtctg----tttgtattcattcttgggataaaatatgctttctcgtatgtgacatgagtttttgttgctgatagGTCTTGATGCGGGTGGAGCAAGAGCAAAAGGTGACTGAGGATGCTCGTAGGTTTGCTGAGCAAGATGCAGCCGCACAAAGATATGCTGCGCAAGTCCTTC

upper sequence: Vv13s0067g03420.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: AT3G55020.1 (Arabidopsis thaliana), 3'ss of exon 14
gttgcaatttttatgccattccaagggctcatttctgaaagat-gctttgtaccttatcttgttatgggcttgtc--atagtaattatgatatcatttgttttata----gGTATTGGTGCGGGTAGAGCAAGAACAAAAGTTAACTGAAGATGCTCGCAGGTTTGCTGAGCAAGATGCTGCAGCCCAGAGATATGCTGCTCAAGTGCTTC
                          | |    | || | |||   | ||| | |  |||| ||  |    || |  | |   ||| ||| || | ||| | | ||    ||| ||| ||||||| ||||||||||| ||| |||| |||||||| || |  ||||||||||| ||||| | ||| ||||||||||||||||||||  | |
--------------------------gtttgcatatgcatgatcaatctgttcttcttcttttttcgtttgtgactgagaaagattctgagattaattgatatgtatgaagGTCTTGATGCGGGTGGAGCAAGAACAGAAGGTAACAGAAGATGCACGAATATTTGCTGAGCAGGATGCAGAAGCGCAGAGATATGCTGCTCAAGTCTTGC

upper sequence: Vv13s0067g03420.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: AT2G39280.1 (Arabidopsis thaliana), 3'ss of exon 14
gttgcaatttttatgccattccaagggctcatttctgaaagatgc-tttgtaccttatcttgttatgggcttgtcatagtaattatgatatcatttg----ttttatagGTATTGGTGCGGGTAGAGCAAGAACAAAAGTTAACTGAAGATGCTCGCAGGTTTGCTGAGCAAGATGCTGCAGCCCAGAGATATGCTGCTCAAGTGCTTC
                                          ||| |||| ||  | |||  |      |     |  |||||| | | | || |||    || |  |||| ||| ||||| | ||||||||||| ||  |||| |||||||| || ||  |||||||||| ||||| ||| | ||||||||||||||| |||||||||
---------------------------------------gtttgcatttgcactct-tctattggaattcaaagtaaggtaattctaagaccacttgaaatttatgaagGTCTTGATGCGGATGGAGCAAGAACATAAAGTAACAGAAGATGCACGGAGACTTGCTGAGCAGGATGCAGCAACGCAGAGATATGCTGCTGAAGTGCTTC

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|30136499|gb|CB921837.1|CB921837
EST:     TCAGGCAGGCCCTTGCTGATAAGCAGGAACAAGAGCATGCTATGCTTCAG                         GTATTGGTGCGGGTAGAGCAAGAACAAAAGTTAACTGAAGATGCTCGCAGG
genomic: TCAGGCAGGCCCTTGCTGATAAGCAGGAACAAGAGCATGCTATGCTTCAGgttgcaattt ... tgttttatagGTATTGGTGCGGGTAGAGCAAGAACAAAAGTTAACTGAAGATGCTCGCAGG
EST: gi|30135773|gb|CB921111.1|CB921111
EST:     TCAGGCAGGCCCTTGCTGATAAGCAGGAACAAGAGCATGCTATGCTTCAG                         GTATTGGTGCGGGTAGAGCAAGAACAAAAGTTAACTGAAGATGCTCGCAGG
genomic: TCAGGCAGGCCCTTGCTGATAAGCAGGAACAAGAGCATGCTATGCTTCAGgttgcaattt ... tgttttatagGTATTGGTGCGGGTAGAGCAAGAACAAAAGTTAACTGAAGATGCTCGCAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccttatcttgttatgggcttgtcatagtaattatgatatcatttgttttatagGTATTGGTGCGGGTAGAGCAAGAACAAAAGTTAACTGAAGATGCTCGCAGGTTTGCTGAGCAAGATGCTGCAGCCCAGAGATATGCTGCTCAAGTGCTTC
                                           tttgtttt  CT-rich tract
                         atagtaattatgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgcaatttttatgccattccaagggctcatttctgaaagatgctttgtaccttatcttgttatgggcttgtcatagtaattatgatatcatttgttttatagGTATTGGTGCGGGTAGAGCAAGAACAAAAGTTAACTGAAGATGCTCGCAGGTTTGCTGAGCAAGATGCTGCAGCCCAGAGATATGCTGCTCAAGTGCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT