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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cccggtctcgagcagtgcggcgagtcatgcgtagcgaaaccacctattttatttttactttaatacgaaatcgataatgttgggtggggtggaatgacagACGGACAAGGCTTCAATGCTGGATGAGATCATTGACTATGTCAAATTCCTGCAGCTCCAAGTGAAG

Basic information

species Vitis vinifera
transcript Vv11s0037g00040.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0037g00040.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os06g08500.1 (Oryza sativa), 3'ss of exon 3
cccggtctcgagcagtgcggcgagtcatgcgtagcgaaaccacctattttatttttactttaat-acgaaatcgataatgttgggtggggtggaatga--------------cagACGGACAAGGCTTCAATGCTGGATGAGATCATTGACTATGTCAAATTCCTGCAGCTCCAAGTGAAG
               || |   | || |||  |       || |  |||| ||   |  || || | ||||  ||     |||  ||| ||    |||              |||||||||||||| || |||||||| |||||||| ||||| ||||| ||||||||||||||||| |||
---------------tgggcgcattcgtgcccaattttgtcatcgtttttcttgacatcttgatgaagaaaatgaagtgattgaatggagttctttgatttgattttgcttgcagACGGACAAGGCGTCGATGCTGGACGAGATCATCGACTACGTCAAGTTCCTGCAGCTCCAAGTCAAG

upper sequence: Vv11s0037g00040.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os09g25040.1 (Oryza sativa), 3'ss of exon 4
---------cccggtctcgagcagtgcg---gcgagtcatgcgtagcgaaaccacctattttatttttactttaatacgaaatcgataatgttgggtggggtggaatgacagACGGACAAGGCTTCAATGCTGGATGAGATCATTGACTATGTCAAATTCCTGCAGCTCCAAGTGAAG-------------------------
         |    | |  ||     |    | || | |    |     ||   |  || | || |  | | |  |  |     |    | ||   ||| || ||    ||||||||||||||||| |||||||| |||||||| ||||| ||||| ||||| || |||||||| |||                         
cgacgctcgctttcttttcagttccccatttgagattaacctcttcgtgaattgctcatctcatctcaagtgtg-tgtgtgtgtgtgtgtctttcttggagTTGAT--GCAGACGGACAAGGCTTCCATGCTGGACGAGATCATCGACTACGTCAAGTTCCTACAACTCCAAGTCAAGGCAAGCACGTACACTAAATTACTAA

upper sequence: Vv11s0037g00040.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os02g55250.1 (Oryza sativa), 3'ss of exon 4
---------cccggtctcgagcagtgcggcgagtcatgcgt--agcgaaaccacctattttatttttactttaatacgaaatcgataatgttgggtggggtggaatgacagACGGACAAGGCTTCAATGCTGGATGAGATCATTGACTATGTCAAATTCCTGCAGCTCCAAGTGAAG
          |   |||       |  ||    ||  ||    ||   |   ||     | | | | |||       ||||| ||  |||| |  |   ||    |  ||||| |||||||| || ||||| || ||||||||||| ||||| || ||||| ||||||||||| |||
catccatcttcatatcttagctgatagggttgctccagcacaaagtagagtgacacggatcactgtcact-------gaaat-gacgatgtggaatttcgtt---ttgcagACCGACAAGGCATCGATGCTCGACGAGATCATTGATTATGTGAAGTTCCTCCAGCTCCAAGTCAAG

upper sequence: Vv11s0037g00040.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G027563_T02 (Zea mays), 3'ss of exon 3
cccggtctcgagcagtgcggcgagtcatgcgtagcgaaacc-acctattttatttt-tactttaatacgaaatcgataatgttgggtggggtggaatgacagACGGACAAGGCTTCAATGCTGGATGAGATCATTGACTATGTCAAATTCCTGCAGCTCCAAGTGAAG
   |  || |  || | |  |||||   |    |    |   | | || ||  | | |  |||   |  |  | |     | ||  || |  |      |||||||||||||| || |||||||| |||||||| ||||| ||||| ||||| |||||||||      
-ttgcgcttgctcact-caccgagtacagtactgaactattgatccatcttgctctgtgttttctcaatatcttggattggatgcctgcgccgtgcatgcagACGGACAAGGCGTCGATGCTGGACGAGATCATCGACTACGTCAAGTTCCTACAGCTCCAA------

upper sequence: Vv11s0037g00040.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G350165_T01 (Zea mays), 3'ss of exon 4
cccggtctcgagcagtgcggcga--gtcatgcgtagcgaaaccacctattttatttttactttaatacgaaatcgataatgttgggtggggtggaatgacagACGGACAAGGCTTCAATGCTGGATGAGATCATTGACTATGTCAAATTCCTGCAGCTCCAAGTGAAG
|  |   |   |  || |  |     || | | |  ||   |  |    || | ||   |    |      ||| || || |    ||   || |    |||||||||||||| || |||||||| |||||| | ||||| ||||| ||||| ||||||||||| |||
cttgtcgtaatgtcgtccaccctctatcctccttttcgtt-cttcgcgcttgacttcctcgccgacgactgatccatcatctcaa-tgtcttgtatctgcagACGGACAAGGCGTCGATGCTGGACGAGATCGTCGACTACGTCAAGTTCCTTCAGCTCCAAGTCAAG

upper sequence: Vv11s0037g00040.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G067654_T01 (Zea mays), 3'ss of exon 4
----------------------------cccggtctcgagcagtgcgg-cgagtcatgcgtagcgaaaccacc-tattttatttttactttaatacgaaatcgataatgttgggtggggtggaatgacagACGGACAAGGCTTCAATGCTGGATGAGATCATTGACTATGTCAAATTCCTGCAGCTCCAAGTGAAG
                             ||  ||||        ||  || ||| |    |   ||   ||   | |  | |       |  |  |     |     ||||  || |||    |  |||||||||||||| || |||||||| |||||||| ||||| ||||  ||| ||||||||||||| |||
gtcggcatcccccctctagctagctagctcctttctcttctctctcgctcgcgtcgtcaacaatcaacagacaacactgaaatggcgacgtggtgtgggtcggtcgtcgttgtttgtggtt---ttgcagACGGACAAGGCGTCGATGCTGGACGAGATCATCGACTACGTCAGGTTCTTGCAGCTCCAAGTCAAG

upper sequence: Vv11s0037g00040.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G316758_T01 (Zea mays), 3'ss of exon 3
cccggtctcgagcagtgcggcg--agtcatgcgtagcgaaaccacctattttatttttactttaatacgaaatcgataatgttgggtggggtggaatgacagACGGACAAGGCTTCAATGCTGGATGAGATCATTGACTATGTCAAATTCCTGCAGCTCCAAGTGAAG
  ||   | || |      ||     |    |  |   | |  ||  ||| |   |  |    |    |   |   | ||  |  |     | |  |  ||||| |||||||| || ||||| |||||||| |||||||| || || ||||| ||||||||||| |||
--cgtctttgatcgacagagcttccatggcacaaactaataagactcattgtcgctgaaaacgatcgtgccgtgtgtcatcgtatggaattttgttttgcagACCGACAAGGCATCGATGCTTGATGAGATTATTGACTACGTGAAGTTCCTCCAGCTCCAAGTCAAG

upper sequence: Vv11s0037g00040.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G14380.2 (Glycine max), 3'ss of exon 4
cccggtctcgagcagtgcggcgagtcatgcgtagcgaaaccacctattttatttttac--tttaatacgaaatcgataatgttgggtggg---gtggaatgacagACGGACAAGGCTTCAATGCTGGATGAGATCATTGACTATGTCAAATTCCTGCAGCTCCAAGTGAAG----------------------------------
     | |   |       || | |  |   |  |   |  |  | ||    || ||    | |||    ||| || ||| || | | ||   |||||||||||||| |||||||| || ||||| ||||||||||| || || || || ||||||||||||||||| |||                                  
---attataatgtttatttgcaaatattat-tgtcattattatatgttaacattatatgggtcaatcgctaattga-aatattcgtttggtttgtggaatgacagACAGACAAGGCATCCATGCTAGATGAGATCATCGATTACGTGAAGTTCCTGCAGCTCCAAGTCAAGGTGCGCATCCCGCGTTTTTCTCTTGTACTAGCAT

upper sequence: Vv11s0037g00040.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G08300.1 (Glycine max), 3'ss of exon 4
-------cccggtctcgagcagtgcggcgagtcatgcgtagcgaaaccacctattttatttttactttaatacgaaatcgataatgttgggtggggtggaatgacagACGGACAAGGCTTCAATGCTGGATGAGATCATTGACTATGTCAAATTCCTGCAGCTCCAAGTGAAG
       |    ||||    |||      | | |  |  |   | || |  | ||  ||| |||    |||| |   ||  |   ||||| | |  |||| |||||||| |||||||| || ||||||||||||||||| || ||||| || ||||| ||||||||||| |||
tcaacatctatctctcttttagtattaaaaat-acacaaacaaatacaatttcttccattgttaa---aatatgtgttcattgg-gttggctcg--tggattgacagACTGACAAGGCCTCCATGCTGGATGAGATCATCGATTATGTGAAGTTCCTACAGCTCCAAGTCAAG

upper sequence: Vv11s0037g00040.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G33020.1 (Glycine max), 3'ss of exon 4
cccggtctcgagcagtgcggcgagtcatgcgtagcga--aaccacctattttatttttac----tttaatacgaaatcgataatgttgggtggg---gtggaatgacagACGGACAAGGCTTCAATGCTGGATGAGATCATTGACTATGTCAAATTCCTGCAGCTCCAAGTGAAG
          |  | |     |  |  |  |||   |  |    |||||  ||   |||      | ||| |  ||| || ||| || | | ||   |||||||||||||| |||||||| || ||||| ||||||||||| || || || || ||||||||||||||||| |||
--------tcactattataatgtttattatgtaattattattatcctatgctaacattaaatgggtcaatccctaattga-aatattcgtttggtttgtggaatgacagACAGACAAGGCATCCATGCTAGATGAGATCATCGATTACGTGAAGTTCCTGCAGCTCCAAGTCAAG

upper sequence: Vv11s0037g00040.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G14380.1 (Glycine max), 3'ss of exon 4
cccggtctcgagcagtgcggcgagtcatgcgtagcgaaaccacctattttatttttac--tttaatacgaaatcgataatgttgggtggg---gtggaatgacagACGGACAAGGCTTCAATGCTGGATGAGATCATTGACTATGTCAAATTCCTGCAGCTCCAAGTGAAG
     | |   |       || | |  |   |  |   |  |  | ||    || ||    | |||    ||| || ||| || | | ||   |||||||||||||| |||||||| || ||||| ||||||||||| || || || || ||||||||||||||||| |||
---attataatgtttatttgcaaatattat-tgtcattattatatgttaacattatatgggtcaatcgctaattga-aatattcgtttggtttgtggaatgacagACAGACAAGGCATCCATGCTAGATGAGATCATCGATTACGTGAAGTTCCTGCAGCTCCAAGTCAAG

upper sequence: Vv11s0037g00040.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT4G30980.1 (Arabidopsis thaliana), 3'ss of exon 3
-------cccggtctcgagcagtgcggcgagtcatgcgtagcgaaaccacctattttatttttactttaatacgaaatcgataatgttgggtggggtggaatgacagACGGACAAGGCTTCAATGCTGGATGAGATCATTGACTATGTCAAATTCCTGCAGCTCCAAGTGAAG
            |||  |        |  | | || | ||   ||  ||  |     |||  ||      |      |   || ||||        |  | | |||||| ||||| || |||||||| |||||||| || || |||||||| ||| | ||||||||||| |||
tagctaattaattctaaaatttaattgataataatacttaataaa--cagatgcagaattgctaacaaggttt----tttttattgttaaaaataata-attaacagACAGACAAAGCATCAATGCTCGATGAGATTATCGATTATGTCAAGTTCTTACAGCTCCAAGTCAAG

upper sequence: Vv11s0037g00040.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT2G24260.1 (Arabidopsis thaliana), 3'ss of exon 3
cccggtctcgagcagtgcggc-gagtcatgcgtagcgaaaccacctattttatttttactttaatacgaaatcgataatgttgggtggggtggaatg-acagACGGACAAGGCTTCAATGCTGGATGAGATCATTGACTATGTCAAATTCCTGCAGCTCCAAGTGAAG
    | ||  |  | |   |   | | ||||      |||  |  ||   | |   | ||   |       |     || ||   ||      |||| |||||| |||||||| || ||||| ||||||||||| || |||||||| ||  | || |||||||| |||
--taggctacaataataaagttaactaatgcagtaataaatgagttaggatctcagttctgacagttttgtttttgtattttatttgtataataatggacagACAGACAAGGCATCGATGCTCGATGAGATCATAGATTATGTCAAGTTTTTACAACTCCAAGTCAAG

upper sequence: Vv11s0037g00040.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S209_22V6.2 (Physcomitrella patens), 3'ss of exon 3
--------------------------------------------------------------------cccggtctcgagcagtgcggcgagtcatgcgtagcgaaacc-acctattttatttttactttaat-----acgaaatcgataatgttgggt-----------ggggtggaatgacagACGGACAAGGCTTCAATGCTGGATGAGATCATTGACTATGTCAAATTCCTGCAGCTCCAAGTGAAG
                                                                    ||  ||   ||  |    || |  | | | ||| |     | ||||| ||   |    | | ||      | ||| ||  |  | ||   |           |  ||  | | |||||| || ||||| || ||||||||||| ||||| ||||||||||| |||||||| || |||||||||
gtgcggcatcgttcgaacctgcctttcacttttttgtgctctgaatcagttgtatatgtatggtttagccacgtggtgaaaacataggtgcatta-gtgtatctttctctacctacttatgtacagcatgaaagacagatgaagtctttgctatttaatcttatctcactgctgtttattaacagACTGATAAGGCGTCTATGCTGGATGAAATCATCGACTATGTCAAGTTCCTGCAACTTCAAGTGAAG

upper sequence: Vv11s0037g00040.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S173_83V6.1 (Physcomitrella patens), 3'ss of exon 3
cccggtctcgagcagtgcggcgagtcatgcgtagcgaaaccacctattttatttttactttaatacgaaatc-gataatgttgg-gtggggtggaatgacagACGGACAAGGCTTCAATGCTGGATGAGATCATTGACTATGTCAAATTCCTGCAGCTCCAAGTGAAG
       ||| | | |      |   |     |      |    | ||  | | | | |  || |    |||  ||  | ||   |  |  ||     ||||||||| ||||| || ||||||||||| ||||| || || ||||| |||||||| |||||||| |||
-gaaacttcgtgtatttttttcatctactttcacttgggct-tattttaaaatctaattagaagaaatgatccaatcctcttactgctgtctgtggatacagACGGATAAGGCGTCGATGCTGGATGAAATCATCGATTACGTCAAGTTCCTGCAACTCCAAGTAAAG

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|294964363|gb|GW838166.1|GW838166
EST:     TTGCAGAGAGAATGAAGGCACTGCAGGAACTGG-TCCCAATGCCAACAAG                         ACGGACAAGGCTTCAATGCTGGATGAGATCATCGACTATGTCAAATTCCTG
genomic: TTGCAGAGAGAATGAAGGCACTGCAGGAACTGGTTCCCAATGCCAACAAGgtaattcacc ... ggaatgacagACGGACAAGGCTTCAATGCTGGATGAGATCATTGACTATGTCAAATTCCTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttatttttactttaatacgaaatcgataatgttgggtggggtggaatgacagACGGACAAGGCTTCAATGCTGGATGAGATCATTGACTATGTCAAATTCCTGCAGCTCCAAGTGAAG
            ctttaat  putative branch site (score: 4)
     atttttactttaatac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cccggtctcgagcagtgcggcgagtcatgcgtagcgaaaccacctattttatttttactttaatacgaaatcgataatgttgggtggggtggaatgacagACGGACAAGGCTTCAATGCTGGATGAGATCATTGACTATGTCAAATTCCTGCAGCTCCAAGTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - -catgcgt
- - - - - - - - - - - - - - - - - - - -ccaccta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atacgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggtggg