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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttatcaaaaaataattaattttttgatgggttcttataaaaaatatattttatttcttctgtggtgggttttattacatgtttcacatcttactgcagGTAGATGGTATGGATGTTCTTGCTGTGAAACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATT

Basic information

species Vitis vinifera
transcript Vv09s0018g01940.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0018g01940.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g50620.1 (Oryza sativa), 3'ss of exon 2
--tcttatcaaaaaataattaattttttgatgggttcttataaaaaatatattttatttcttctgtggtgggttttatt-acatgtttca--catcttactgcagGTAGATGGTATGGATGTTCTTGCTGTGAAACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATT
  || |||    || ||  |       |||    || | ||      ||| ||| | |||| || |  |   |   | | ||||  |  |      ||  || |||| ||||| |||||||||||||||||||| |||||||||| ||| || || ||||||||| |   |||||| || |||
tttcctattttgaattatattgacaactgaaatcttttcattt----tatgtttaagttctact-taatatctgccactgacatcatctaattgctttggtgtagGTTGATGGAATGGATGTTCTTGCTGTGAAGCAGGCATGCAAATTCGCAAAAGAGCATGCTATTGCAAATGGCCCAATT

upper sequence: Vv09s0018g01940.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os06g13720.1 (Oryza sativa), 3'ss of exon 2
----tcttatcaaaaaataattaattttttgatgggttcttataaaaaatatattttatttcttctgtggtgggttttattacatgtttcacatcttactgcagGTAGATGGTATGGATGTTCTTGCTGTGAAACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATT
         | |       ||  |    | || | |  | | |      | |  ||| | || | |||| ||    ||||   |  ||       ||  ||||||| |||||||||||||||||||| || ||||| || || | |||||| ||| | |||||| |  |||||||||| |||
tgcaagaagttatggggatatgcaggcatggaggtggccgtgttggtgctcttgtttgtatcgt-tgtgatgatggttatggtaccttgtgt---ttggtgcagGTCGATGGTATGGATGTTCTTGCAGTCAAACAAGCTTGTAAATTTGCCAAGCAACATGCTCTTGAAAATGGACCGATT

upper sequence: Vv09s0018g01940.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G361693_T01 (Zea mays), 3'ss of exon 2
tcttatcaaaaaataattaattttttgatgggttcttataaaaaat-atattt-tatttcttctgtggtgggttttat-tacatgtttcacatcttactgcagGTAGATGGTATGGATGTTCTTGCTGTGAAACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATT
     || | |  | | |  |     ||| ||||    |   |  | || ||   ||| ||| |   |||      |  ||  |   |   || ||  ||||||| ||||| |||||||||||||||||||| || || |||| |||||| || || |||||| |   |||||| || |||
--aactctagatttgacttttaaggggataggttaagcttggacttcatgttggcattacttttagtgtgccacaaacataactaaattgtattttg-tgcagGTTGATGGAATGGATGTTCTTGCTGTGAAGCAAGCGTGCAAATTTGCAAAAGATCATGCTGTCGCAAATGGCCCAATT

upper sequence: Vv09s0018g01940.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G140150_T01 (Zea mays), 3'ss of exon 2
-------tcttatcaaaaaataattaattttttgatgggttcttataaaaaatatattttatttcttctgtggtgggttttattacatgtttcacatcttactgcagGTAGATGGTATGGATGTTCTTGCTGTGAAACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATT
       | | |     ||   | ||  ||   | | || ||| ||        || |||   | || ||         | | || ||       |  | | ||||||| ||||| |||||||||||||||||||| || || |||| |||||| || || |||||| |   |||||| || |||
tcttgactttgactgttaagggaatagcttaa-gcttggatctcatgttggcattacttttagtgtt-tgctacacacataactaaat----tgtaattca-tgcagGTTGATGGAATGGATGTTCTTGCTGTGAAGCAAGCGTGCAAATTTGCAAAAGATCATGCTGTTGCAAATGGCCCAATT

upper sequence: Vv09s0018g01940.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G027627_T01 (Zea mays), 3'ss of exon 2
--tcttatcaaaaaataattaattttttgatgggttcttataaaaaatatattttatttcttctgtggtgggttttattaca-tgtttcacatcttactgcagGTAGATGGTATGGATGTTCTTGCTGTGAAACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATT
      | |||||  |   ||||    || ||   | ||       || | |   || |       | | ||   |   |   |   |    | ||  || |||| ||||| |||||||||||||||||||| || || |||| |||||| || || |||||  |  ||||||| || |||
tggtccagcaaaatctgcataataggatgctga--ttttggtctccatgtctgcaatctagctaacgcttggcactgaaatggtaccttgtgttttg-tgtagGTCGATGGAATGGATGTTCTTGCTGTGAAGCAAGCTTGCAAATTTGCCAAAGAACATGCCCTTGAAAATGGGCCAATT

upper sequence: Vv09s0018g01940.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G03080.1 (Glycine max), 3'ss of exon 2
-tcttatcaaaaaataattaattttttgatgggttcttataaaaaatatattttatttcttctgtggtgggttttattacatgtttcacatcttactgcagGTAGATGGTATGGATGTTCTTGCTGTGAAACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATT
    |    |   |||   |  ||  | |    | | ||  ||  |    ||||      ||| |  |   ||| |    |   || | |  ||  | ||||| ||||||||||||||||||||||| ||||| || |||| |||||| ||||| |||||||| || ||||||||| ||
tgtctgcatatctatacacaggttaattaaatatacatagtaagtagtctttttgaacaatcttttttaattttcaaatgaatatttatactttg-tacagGTTGATGGTATGGATGTTCTTGCTGTTAAACAAGCTTGCAAATTTGCAAAGGAACATGCTTTGAAGAATGGACCCCTT

upper sequence: Vv09s0018g01940.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA18G17240.1 (Glycine max), 3'ss of exon 2
tcttatcaaaaaataattaattttttgatgggttcttataaaaaatatattttatttcttctgtggtgggttttattacatgt-----ttcacatcttactgcagGTAGATGGTATGGATGTTCTTGCTGTGAAACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATT
     | ||| |   ||  |    |      | |   ||      | |  |  ||| ||  | || | | | || ||  | ||     || | |  ||  ||||||||||||| ||||||| ||||||||||||||| || || | |||||| ||||||  ||||||||| ||||| ||||||
----ctgaaacacctatatacagctaagaaagcttaaattttttctttcctgcattgctgttttgattgttgtttttggaagtaaatatttatactttg-tgcagGTAGATGGCATGGATGCTCTTGCTGTGAAACAAGCTTGTAAATTTGCAAAGGAGTTTGCTTTAAAGAATGGTCCCATT

upper sequence: Vv09s0018g01940.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G40380.1 (Glycine max), 3'ss of exon 2
--------tcttatcaaaaaataatt-aattttttgatgggttcttataaaaaatatattttatttcttctgtggtgggttttattacatgtttcacatcttactgcagGTAGATGGTATGGATGTTCTTGCTGTGAAACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATT
        | |   ||     | ||| ||| | |||  |  || |  | ||  | || ||||     || | |||  |       || || ||| | |  ||  ||||||||||||| ||||||| ||||||||||||||| || || | |||||| ||||||  |||||| || ||||| ||||||
agctatgatatatacatgtgctgattgaatgtgttgtagtcttttcgtgaactacattttttgaaatttttttggaag-------taaatattt-atactttg-tgcagGTAGATGGCATGGATGCTCTTGCTGTGAAACAAGCTTGTAAATTTGCAAAGGAGTTTGCTTTGAAGAATGGTCCCATT

upper sequence: Vv09s0018g01940.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G24180.1 (Arabidopsis thaliana), 3'ss of exon 2
-------tcttatcaaaaaataattaattttttgatgggttcttataaaaaatatattttatttcttctgtggtgggttttattacatgtttcacatcttactgcagGTAGATGGTATGGATGTTCTTGCTGTGAAACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATT
         ||| | || |  | |  ||   ||| |   |||| ||     | |  | | |  |      |   |  |  |     || |||  | |  |  |  |||| |||||||||||||  || |||||||||||||| ||||  ||||| |||||||||||| | || ||||| || |||
tttattactttacccaatagaattgtatccgttgttt--ttctgattggtgaga-gtgtgaacttaaagctaacgaatgat----tatcttttgctttgttttctagGTGGATGGTATGGATGCACTGGCTGTGAAACAGGCGTGCAAGTTTGCCAAGGAGCATGCTCTCAAGAATGGTCCTATT

upper sequence: Vv09s0018g01940.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G59900.1 (Arabidopsis thaliana), 3'ss of exon 2
tcttatcaaaaaataattaattttttgatgggttcttataaaaaatat-attttatttcttctgtggtgggttttattacatgt---ttcacatcttactgcagGTAGATGGTATGGATGTTCTTGCTGTGAAACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATT
     |  |  | ||  |  || ||    || ||||| |||     || |  |||     | | |  || |||| |     ||    ||   ||       |||||||||||||||||||   ||||||| ||||| || |||| |||||||||| ||||||| ||  | || || || || 
----gtgcatcattaccttgttcttattaggtttcttgtaacctgcatcaagttagcaactttcttttgagtttgaccggttgctggtttgtatggataaacagGTAGATGGTATGGATGCATTTGCTGTCAAACAAGCTTGCAAATTTGCTAAGCAGCATGCGTTGGAGAAGGGGCCAATA

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|30252075|gb|CB968714.1|CB968714
EST:     CCAAGAGTCCAGCATATTACAAGCGTGGGGACTATGTGCCTGGGTTGAAG                         GTAGATGGTATGGATGTTCTTGCTGTGAAACAGGCATGCAGATTTGCTAAG
genomic: CCAAGAGTCCAGCATATTACAAGCGTGGGGACTATGTGCCTGGGTTGAAGgtaattttta ... cttactgcagGTAGATGGTATGGATGTTCTTGCTGTGAAACAGGCATGCAGATTTGCTAAG
EST: gi|110697825|gb|EE075244.1|EE075244
EST:     CCAAGAGTCCAGCATATTACAAGCGTGGGGACTATGTGCCTGGGTTGAAG                         GTAGATGGTATGGATGTTCTTGCTGTGAAACAGGCATGCAGATTTGCTAAG
genomic: CCAAGAGTCCAGCATATTACAAGCGTGGGGACTATGTGCCTGGGTTGAAGgtaattttta ... cttactgcagGTAGATGGTATGGATGTTCTTGCTGTGAAACAGGCATGCAGATTTGCTAAG
EST: gi|110361744|gb|EC925240.1|EC925240
EST:     CCAAGAGTCCAGCATATTACAAGCGTGGGGACTATGTGCCTGGGTTGAAG                         GTAGATGGTATGGATGTTCTTGCTGTGAAACAGGCATGCAGATTTGCTAAG
genomic: CCAAGAGTCCAGCATATTACAAGCGTGGGGACTATGTGCCTGGGTTGAAGgtaattttta ... cttactgcagGTAGATGGTATGGATGTTCTTGCTGTGAAACAGGCATGCAGATTTGCTAAG
EST: gi|29783684|gb|CB350018.2|CB350018
EST:     CCAAGAGTCCAGCATATTACAAGCGTGGGGACTATGTGCCTGGGTTGAAG                         GTAGATGGTATGGATGTTCTTGCTGTGAAACAGGCATGCAGATTTGCTAAG
genomic: CCAAGAGTCCAGCATATTACAAGCGTGGGGACTATGTGCCTGGGTTGAAGgtaattttta ... cttactgcagGTAGATGGTATGGATGTTCTTGCTGTGAAACAGGCATGCAGATTTGCTAAG
EST: gi|30127098|gb|CB912437.1|CB912437
EST:     CCAAGAGTCCAGCATATTACAAGCGTGGGGACTATGTGCCTGGGTTGAAG                         GTAGATGGTATGGATGTTCTTGCTGTGAAACAGGCATGCAGATTTGCTAAG
genomic: CCAAGAGTCCAGCATATTACAAGCGTGGGGACTATGTGCCTGGGTTGAAGgtaattttta ... cttactgcagGTAGATGGTATGGATGTTCTTGCTGTGAAACAGGCATGCAGATTTGCTAAG
EST: gi|71888581|gb|DT037636.1|DT037636
EST:     CCAAGAGTCCAGCATATTACAAGCGTGGGGACTATGTGCCTGGGTTGAAG                         GTAGATGGTATGGATGTTCTTGCTGTGAAACAGGCATGCAGATTTGCTAAG
genomic: CCAAGAGTCCAGCATATTACAAGCGTGGGGACTATGTGCCTGGGTTGAAGgtaattttta ... cttactgcagGTAGATGGTATGGATGTTCTTGCTGTGAAACAGGCATGCAGATTTGCTAAG
EST: gi|161719074|gb|FC065701.1|FC065701
EST:     CCAAGAGTCCAGCATATTACAAGCGTGGGGACTATGTGCCTGGGTTGAAG                         GTAGATGGTATGGATGTTCTTGCTGTGAAACAGGCATGCAGATTTGCTAAG
genomic: CCAAGAGTCCAGCATATTACAAGCGTGGGGACTATGTGCCTGGGTTGAAGgtaattttta ... cttactgcagGTAGATGGTATGGATGTTCTTGCTGTGAAACAGGCATGCAGATTTGCTAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatattttatttcttctgtggtgggttttattacatgtttcacatcttactgcagGTAGATGGTATGGATGTTCTTGCTGTGAAACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATT
                                           atcttac  putative branch site (score: 3)
                                            tcttact  CT-rich tract
                         ttttattacatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttatcaaaaaataattaattttttgatgggttcttataaaaaatatattttatttcttctgtggtgggttttattacatgtttcacatcttactgcagGTAGATGGTATGGATGTTCTTGCTGTGAAACAGGCATGCAGATTTGCTAAGGAGCATGCTTTAAAAAATGGACCCATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - -aaaaaat
- - - - - - - - - - - - -tgatggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatgtt