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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctaaagttacatctttataaggtgtggtttcagagacacagtgggttccccatgttaattattcatcttctcattgcttttttcttttctctgtaatcagGATGTAACACTTCATGACCTGGATGCTGCAAATGCACGGCCTCAAGGTGGACAAGATATATTGTCCCTAATGGGTCAGATGATGAAGCCCAGGAAAACAG

Basic information

species Vitis vinifera
transcript Vv06s0004g02910.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os07g08170.1 (Oryza sativa), 3'ss of exon 5
-----ctaaagttacatctttataaggtgtggtttcagagacacagtgggttccccatgttaattattcatcttctcattgcttttttcttttctctgtaatcagGATGTAACACTTCATGACCTGGATGCTGCAAATGCACGGCCTCAAGGTGGACAAGATATATTGTCCCTAATGGGTCAGATGATGAAGCCCAGGAAAACAG
     |   |||    | | || | | | |   || |          |   |    |||||| |||   | ||     ||   || |   |||   ||||  |||||||| || ||||||||||| |||||||||||||| |  || ||||| || |||||||| |||||||| ||||| ||||||||||||||  ||||||| |
tacagcattagtgtgttatatacaggctctctgtttatgattctcaagttatatggatgttagttaaagagctgaaacttcagttatcaattt---tgta--cagGATGTTACGCTTCATGACCTTGATGCTGCAAATGCTCAACCACAAGGAGGCCAAGATATTTTGTCCCTTATGGGACAGATGATGAAGCCACGGAAAACTG

upper sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g62040.1 (Oryza sativa), 3'ss of exon 5
-ctaaagttacatctttataaggtgtggtttcagagacacagtgggttccccatgttaattattcatcttctcattgcttttttcttttctctgtaatcagGATGTAACACTTCATGACCTGGATGCTGCAAATGCACGGCCTCAAGGTGGACAAGATATATTGTCCCTAATGGGTCAGATGATGAAGCCCAGGAAAACAG
 |  | |     |   |  |     |  ||      |               |||  | ||| | |   |   |   ||| |  || |  | | |   |||||||| |||||||||||||| || ||||||||||| |  || ||||| || |||||||| |||||||| ||||| || |||||||||||  | || || |
tcatatgcagtgttagtgcattcaatctttctgcttatggctcttaagttatatggaagttaatgaatataggaaaacttctc-ctgtcatttatgtacagGATGTTACACTTCATGACCTTGACGCTGCAAATGCTCAACCACAAGGAGGCCAAGATATTTTGTCCCTTATGGGGCAAATGATGAAGCCACGAAAGACTG

upper sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G018697_T03 (Zea mays), 3'ss of exon 6
ctaaagttacatctttataaggtgtggtttcagagacaca--gtgggttccccatgttaattattcatcttctcattgcttttttcttttctctgtaatcagGATGTAACACTTCATGACCTGGATGCTGCAAATGCACGGCCTCAAGGTGGACAAGATATATTGTCCCTAATGGGTCAGATGATGAAGCCCAGGAAAACAG
   |  ||  ||    || |    | || |  | | | ||   |||   |  |||||    |  |  |        |    | ||||   |  ||||  |||||||| |||||||||||||| ||||| |||||||| | ||| |||||||| |||||||| |||||||| ||||| ||||||||||| ||  | || || |
--gatttttaataagaattaatgcttgtatttgcgtctcaacatggaggcttcatgtgctcttgttctgaagaggatctaatcttctcaccgatgtatgcagGATGTCACACTTCATGACCTTGATGCAGCAAATGCTCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAACCACGAAAGACTG

upper sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G032267_T02 (Zea mays), 3'ss of exon 5
ctaaagttacatctttataag-gtgtggtttcagagacacagtgggttccccatgttaattattcatcttctcattgcttttttcttttctctgtaatcagGATGTAACACTTCATGACCTGGATGCTGCAAATGCACGGCCTCAAGGTGGACAAGATATATTGTCCCTAATGGGTCAGATGATGAAGCCCAGGAAAACAG
 |||   |  ||  || ||   |  |     ||  ||  |     ||   | ||| |  |  |          | |    |  || |   | | |   |||||||| ||||| |||||||| ||||| |||||||| | ||| |||||||| |||||||| |||||||| ||||| ||||||||||||||  |||| || |
-taagaattaattcttgtatttgcatctcaacatggaggcctcctgtattctatgctcttgttctgaagaggaaataacctcctcatcattttttttgcagGATGTCACACTCCATGACCTTGATGCAGCAAATGCCCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAGCCACGGAAGACTG

upper sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G21830.1 (Glycine max), 3'ss of exon 5
ctaaagttacatctttataaggtgtggtttcagagacacagtgggttccccatgttaattattc--atcttctcattgcttttttcttttctctgtaatcagGATGTAACACTTCATGACCTGGATGCTGCAAATGCACGGCCTCAAGGTGGACAAGATATATTGTCCCTAATGGGTCAGATGATGAAGCCCAGGAAAACAG
  | ||     |  |  |    | || ||  |      |      ||  | || |||  ||||      |||| ||||   |||   ||  | |      ||||||| || || ||||| ||||||||||| |||||||| |||||||| |||||||||||  |||| || |||||||||||||||||||||||||||||||
--agaggcttgtactggtgtactctgtttgaatgtgttctagacattgactatattatatatttcagatttcttattgtgatttgtattgttgttcttaaagGATGTTACCCTACATGATCTGGATGCTGCCAATGCACGACCTCAAGGGGGACAAGATATTCTGTCTCTGATGGGTCAGATGATGAAGCCCAGGAAAACAG

upper sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA07G02170.1 (Glycine max), 3'ss of exon 5
ctaaagttacatctttataaggtgtggtttcagag-acacagtgggttccccatgttaattattcat--cttctcattgcttttttcttttctctgtaatcagGATGTAACACTTCATGACCTGGATGCTGCAAATGCACGGCCTCAAGGTGGACAAGATATATTGTCCCTAATGGGTCAGATGATGAAGCCCAGGAAAACAG
    |||  | | |   ||  ||    | | |||        | |       || ||   ||||  |   |||| ||||   |||   ||  | |      |||||||||| || ||||| || |||||||| |||||||| |||||||| |||||||||||  |||| || |||||||||||||||||||| ||||||||||
--tgagtggcttgtac-tagtgtactctgtaagaatgtgttctagacattgaatattgtatatttctgatttcttattgtgatttggattgttgttcttaaagGATGTAACCCTACATGATCTTGATGCTGCCAATGCACGACCTCAAGGGGGACAAGATATTCTGTCTCTTATGGGTCAGATGATGAAGCCTAGGAAAACAG

upper sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 5
-------------------------------------------------ctaaagttacatctttataaggtgtggtttcagagacacagtg-----ggttccccatgttaattattcatcttctcatt--gcttttttcttttctctgtaat--cagGATGTAACACTTCATGACCTGGATGCTGCAAATGCACGGCCTCAAGGTGGACAAGATATATTGTCCCTAATGGGTCAGATGATGAAGCCCAGGAAAACAG
                                                  |  | |||  | | | | | || |   ||   |     | |       |||||  |  ||| | |  |  ||| | | |   ||      | | || |  | |   ||||||| ||||| || || |||||||| |||||||| || ||||||||||| || |||||| | ||  | ||||| || |||||||| ||  |||| || |
gtttaccttctttgacctctcccttctgtgtagagtaattattttctttgttgatttat-tatctgttatgtattagtttgtatgtgtattaaccttagttcctaagtttattaagactacttgttactcaactagaccatatacttttgactgatagGATGTCACACTCCAAGATCTGGATGCAGCAAATGCTCGACCTCAAGGTGGCCAGGATATACTTTCTTTGATGGGCCAAATGATGAAACCGCGGAAGACTG

upper sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S4_73V6.1 (Physcomitrella patens), 3'ss of exon 6
-------ctaaagttaca----tctttataaggtgtggtttcagag-----acacagtgggttccccatgttaattattcatcttctcattgcttttttcttttctctgtaat---cagGATGTAACACTTCATGACCTGGATGCTGCAAATGCACGGCCTCAAGGTGGACAAGATATATTGTCCCTAATGGGTCAGATGATGAAGCCCAGGAAAACAG
       |||   |||      || ||  |  ||     |   ||      | |||||    |    || ||   |  |  |  ||| || ||   ||||| |    | |  |    ||||||| || || ||||| || |||||||||||||| || |||||||| || ||||||||||||||| | ||||| ||||||||||| ||  | || || |
gttagtgctatgattattatgctcgttgcagtgtagccctcttgattctttatacagtatcctttgtatattttatgcttgtaatcttat-gcccatttctatgtgttatggtacatagGATGTCACGCTCCATGATCTAGATGCTGCAAATGCTCGCCCTCAAGGAGGCCAAGATATATTGTCCATGATGGGCCAGATGATGAAACCTCGTAAGACTG

upper sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ27201 (Selaginella moellendorffii), 3'ss of exon 5
ctaaagttacatctttataaggtgtggtttcagagacacagtgggttccccatgttaattattcatcttctcattgcttttttcttttctctgtaatcagGATGTAACACTTCATGACCTGGATGCTGCAAATGCACGGCCTCAAGGTGGACAAGATATATTGTCCCTAATGGGTCAGATGATGAAGCCCAGGAAAACAG
                                        ||     |        ||   | ||  ||||| |  |        | |   ||||   |||| || ||||| ||||| || |||||||||||||| || ||||||||||||||||||||  | ||| | ||||| |||||||||||||| |  || || |
----------------------------------------gtactaactgtgaagaaagggtccagtttctcttcacacagcaagtgtgggtgtatgtagGACGTCACACTGCATGATCTAGATGCTGCAAATGCGCGTCCTCAAGGTGGACAAGATATTCTTTCCATGATGGGACAGATGATGAAGCCGAAAAAGACTG

upper sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ33466 (Selaginella moellendorffii), 3'ss of exon 5
ctaaagttacatctttataaggtgtggtttcagagacacagtgggttccccatgtt--aattattcatcttctcattgcttttttcttttctctgtaatcagGATGTAACACTTCATGACCTGGATGCTGCAAATGCACGGCCTCAAGGTGGACAAGATATATTGTCCCTAATGGGTCAGATGATGAAGCCCAGGAAAACAG
                                          |   |  |  || |  ||   | ||  ||||| |  |      |   |   |||| |||||| || ||||| ||||| || |||||||||||||| || ||||||||||||||||||||  | ||| | ||||| |||||||||||||| |  || || |
------------------------------------------gtactaactgtgatgaaagggtccagtttctcttcacacag--caagtgggtgtattcagGACGTCACACTGCATGATCTAGATGCTGCAAATGCGCGTCCTCAAGGTGGACAAGATATTCTTTCCATGATGGGACAGATGATGAAGCCGAAAAAGACTG

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|110689388|gb|EE065570.1|EE065570
EST:     GAGATAGTTCAG                         GATGTAACACTTCATGACCTGGATGCTGCAAATGCACGGCCTCAAGGTGGA
genomic: GAGATAGTTCAGgtttgttttt ... ctgtaatcagGATGTAACACTTCATGACCTGGATGCTGCAAATGCACGGCCTCAAGGTGGA
EST: gi|71863654|gb|DT012709.1|DT012709
EST:     ATGTTCCACTTCCTAAAGGAGAGGTTCACAAAAAGAAGGAGATAGTTCAG                         GATGTAACACTTCATGACCTGGATGCTGCAAATGCGCGGCCTCAAGGTGGA
genomic: ATGTTCCACTTCCTAAAGGAGAGGTTCACAAAAAGAAGGAGATAGTTCAGgtttgttttt ... ctgtaatcagGATGTAACACTTCATGACCTGGATGCTGCAAATGCACGGCCTCAAGGTGGA
EST: gi|71865178|gb|DT014233.1|DT014233
EST:     ATGTTCCACTTCCTAAAGGAGAGGTTCACAAAAAGAAGGAGATAGTTCAG                         GATGTAACACTTCATGACCTGGATGCTGCAAATGCGCGGCCTCAAGGTGGA
genomic: ATGTTCCACTTCCTAAAGGAGAGGTTCACAAAAAGAAGGAGATAGTTCAGgtttgttttt ... ctgtaatcagGATGTAACACTTCATGACCTGGATGCTGCAAATGCACGGCCTCAAGGTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccccatgttaattattcatcttctcattgcttttttcttttctctgtaatcagGATGTAACACTTCATGACCTGGATGCTGCAAATGCACGGCCTCAAGGTGGACAAGATATATTGTCCCTAATGGGTCAGATGATGAAGCCCAGGAAAACAG
       tgttaat  putative branch site (score: 3)
             ttattcatcttctcat  CT-rich tract
      atgttaattattcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctaaagttacatctttataaggtgtggtttcagagacacagtgggttccccatgttaattattcatcttctcattgcttttttcttttctctgtaatcagGATGTAACACTTCATGACCTGGATGCTGCAAATGCACGGCCTCAAGGTGGACAAGATATATTGTCCCTAATGGGTCAGATGATGAAGCCCAGGAAAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - ggtgtgg
- - - - - - - - - - - - - - - - -agacaca
- - - - - - - - - - - - - - - - - - - - - - -ttcccca