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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattattattattgttattattattattattattattattatcatcattttattcaggtgtacacctgaatgttaatgttaccttgaccaaagttctcagTTATATTATTGAAGGACGTGTTTGTTACTTGACAATGTGTGATCGCGCTTATCCAAAGAAACTTGCCTTCCAATACCTGGAAGATCTCAAGAATGAATTT

Basic information

species Vitis vinifera
transcript Vv09s0002g00780.t01
intron # 2
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g00780.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os08g21570.1 (Oryza sativa), 3'ss of exon 1
tattat-tattattgttattattattattattattattattatcatcattttattcaggtgtacacctgaatgttaatgttaccttgaccaaagttctcagTTATATTATTGAAGGACGTGTTTGTTACTTGACAATGTGTGATCGCGCTTATCCAAAGAAACTTGCCTTCCAATACCTGGAAGATCTCAAGAATGAATTT
     | | |||      | ||  ||  |   ||| | ||  |  |    || |  |  |        | |   |  |   |||||||   ||     |||||| || ||||| || ||||| || || |||||||||||||| | | ||||||| ||||||||||| ||||| ||| | ||||||||||| |||||||||
-gccgtatgttaagaaactaatcctttcttgaattttcatcctgtttgccttgtgaaaatcatttgtggtacacttgttgcaccttgatttaaccaaacagTTACATCATTGAGGGCCGTGTGTGCTATTTGACAATGTGTGACCACTCTTATCCGAAGAAACTTGCTTTCCAGTACTTAGAAGATCTCAAAAATGAATTT

upper sequence: Vv09s0002g00780.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g13350.2 (Oryza sativa), 3'ss of exon 2
tattattattattgttattattattattattattattattatcatcattttattcaggtgtacacctgaatgttaatgttaccttgaccaaagttctcagTTATATTATTGAAGGACGTGTTTGTTACTTGACAATGTGTGATCGCGCTTATCCAAAGAAACTTGCCTTCCAATACCTGGAAGATCTCAAGAATGAATTT
   |||  | |        || |||  |   ||| | ||  |  |    || |  |  |        | |   |  |   |||||||   ||     |||||| || || || || ||||| || || ||||||||||||||  || ||||||| ||||||||||| ||||| ||| | ||||||||||| |||||||||
ccgtatgttaagaaactaaatcatttcttgaattttcatcctgtttgccttgtgaaaatcatttgtggtacacttgttgcaccttgatttaaccaaacagTTACATCATCGAGGGCCGTGTGTGCTATTTGACAATGTGTGACTGCTCTTATCCGAAGAAACTTGCTTTCCAGTACTTAGAAGATCTCAAAAATGAATTT

upper sequence: Vv09s0002g00780.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os03g57760.1 (Oryza sativa), 3'ss of exon 2
tattatta-ttattgttattattattattattattattattatcatcattttattcaggtgtacacctgaatgttaatgtt--accttgaccaaagttctcagTTATATTATTGAAGGACGTGTTTGTTACTTGACAATGTGTGATCGCGCTTATCCAAAGAAACTTGCCTTCCAATACCTGGAAGATCTCAAGAATGAATTT
   | | |  || || |||| || | ||   | || |   |   ||   |||  |||| |  |   | | ||| |  ||||  ||||| |  ||| |   |||||| || ||||| || || || |||||  ||||||||||||| ||  ||||||||||||||||||| ||||| ||||| |||||||| || || ||||||
--ctgtcagctaatgatattcttgtaatgcattttttagcttctattggtttgctcagtt-catcgcagtatgatcttgttgaaccttaattaaaataaacagTTACATCATTGAGGGGCGAGTATGTTATCTGACAATGTGTGACCGTTCTTATCCAAAGAAACTTGCATTCCAGTACCTAGAAGATCTGAAAAACGAATTT

upper sequence: Vv09s0002g00780.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os06g09850.2 (Oryza sativa), 3'ss of exon 2
tattattattattgttattattattattattattattattatcatcattttattcaggtgtacacctgaatgttaatgttaccttgaccaaagttctcagTTATATTATTGAAGGACGTGTTTGTTACTTGACAATGTGTGATCGCGCTTATCCAAAGAAACTTGCCTTCCAATACCTGGAAGATCTCAAGAATGAATTT----------------------------------------------------------
                                                  ||||   ||||  | ||   |||| |    ||||| |   || |   |||||| || ||||| || || || || ||  |||| |||||||| ||  |||||||||||||||| || ||||| ||||| |||||||| |  ||||||||                                                           
--------------------------------------------------tattgcagtgtg-atct---tgttga----accttaattcaaataaacagttacatcattgaggggcgagtatgctatctgactatgtgtgaccgttcttatccaaagAAACTCGCATTCCAGTACCTAGAAGATCTGAGAAATGAATTCGAAAGAGTCAACGGCAGTCAAATCGAAACAGCTGCAAGGCCGTATGCGTTTATTAAGT

upper sequence: Vv09s0002g00780.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os06g09850.1 (Oryza sativa), 3'ss of exon 2
tattattattattgttattattattattattattattattatcatcattttattcaggtgtacacctgaatgttaatgtt--accttgaccaaagttctcagTTATATTATTGAAGGACGTGTTTGTTACTTGACAATGTGTGATCGCGCTTATCCAAAGAAACTTGCCTTCCAATACCTGGAAGATCTCAAGAATGAATTT
 |       || |||| || || | ||   | || |   |   ||   |||  | | || ||   | |  || |  ||||  ||||| |   || |   |||||| || ||||| || || || || ||  |||| |||||||| ||  |||||||||||||||| || ||||| ||||| |||||||| |  |||||||| 
cacc-cagctaatgttgttcttgtaatgcatgttttagcttgtattggtttgct-aagtttattgcagtgtgatcttgttgaaccttaattcaaataaacagTTACATCATTGAGGGGCGAGTATGCTATCTGACTATGTGTGACCGTTCTTATCCAAAGAAACTCGCATTCCAGTACCTAGAAGATCTGAGAAATGAATTC

upper sequence: Vv09s0002g00780.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G011636_T02 (Zea mays), 3'ss of exon 3
tattattattattgttattattattattat-tattattattatcatcattttattca--ggtgtacacctga-atgttaatgttaccttgac-caaagttctcagTTATATTATTGAAGGACGTGTTTGTTACTTGACAATGTGTGATCGCGCTTATCCAAAGAAACTTGCCTTCCAATACCTGGAAGATCTCAAGAATGAATTT
        | |  | ||| | || |    | |  ||| |  || |||||||| | ||      | |  |||      || |  |||||| |  |||      ||| || || |||||||| |||||||| || |||||  ||||||| ||  ||||||| ||||||||||| ||||| || || ||||||||||| |||||||||
-----aagtaagcgctatcactaatgacgtatggtatgaaaatgatcattttctgcactaaaatgcttctggtgctctagttgtaccttaattcaataaaaacagCTACATCATTGAAGGCCGTGTTTGCTATTTGACTTTGTGTGACCGTTCTTATCCCAAGAAACTTGCATTCCAGTATCTCGAAGATCTCAAAAATGAATTT

upper sequence: Vv09s0002g00780.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G120596_T02 (Zea mays), 3'ss of exon 2
tattattattattgttattattattatt-attattattattatcatcattttattcaggtgtacacctgaatgt-taatgttaccttgaccaaagttctcagTTATATTATTGAAGGACGTGTTTGTTACTTGACAATGTGTGATCGCGCTTATCCAAAGAAACTTGCCTTCCAATACCTGGAAGATCTCAAGAATGAATTT
 |  || |  | |      || ||  || |||  |  |    | | | || | |||   |       |||  || |  |  | ||||||   || | |  || || |||||||| ||  | || |||||  |||| |||||||| ||| ||||||| ||||||||||| ||||| ||||| |||||||| || |||||||||
aacaatcaacact-cagcaatcatgcttgattgcttgtggc-ttacccttctgttctaatcattttgtgatagtcttgttgtgccttgattcaaatgcatagCTACATTATTGAGGGCAGAGTATGTTATCTGACTATGTGTGACCGCTCTTATCCGAAGAAACTTGCATTCCAGTACCTAGAAGATCTGAAAAATGAATTT

upper sequence: Vv09s0002g00780.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA07G04740.1 (Glycine max), 3'ss of exon 2
tattattattattgttattattatt--attattattattattatcatca-ttttattcaggtgtacacctgaatgttaatgttaccttgaccaaagttctcagTTATATTATTGAAGGACGTGTTTGTTACTTGACAATGTGTGATCGCGCTTATCCAAAGAAACTTGCCTTCCAATACCTGGAAGATCTCAAGAATGAATTT
    || |||  ||| | |   |||   || |||  |  |||  ||| |  ||||||  |  |     |  |    ||| || ||||| ||  |   ||| ||||||||||| ||||||||||| ||||||||||||||||||||||| || || || |||||||| ||||| ||||| || ||||| || | |||||| |||
atccatcatttatgtgagttacatttagtttttagaaaaattggcattaactttatttggaagagtttcatagc-ctaaagtgaccttaacagag--tcttagTTATATTATAGAAGGACGTGTCTGTTACTTGACAATGTGTGATCGTGCATACCCTAAGAAACTAGCCTTTCAATATCTTGAAGAGCTGAGGAATGAGTTT

upper sequence: Vv09s0002g00780.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA16G01330.1 (Glycine max), 3'ss of exon 2
-tattat-tattattgttattattattattattatt-attattatcatcattttattcaggtgtacacctgaatgttaatgttaccttgaccaaagttctcagTTATATTATTGAAGGACGTGTTTGTTACTTGACAATGTGTGATCGCGCTTATCCAAAGAAACTTGCCTTCCAATACCTGGAAGATCTCAAGAATGAATTT
 |  ||| ||| ||   | ||| |   ||| || || |  | |    | | ||||||  |  | |       |   ||| |  ||||| ||  |    || ||||||||||| |||||||| || ||||||||||||||||||||||| || || || |||||||| ||||| ||||| || ||||| |||| ||| || |||
ttgatatgtatcatgtatgttagttacattgttttttaaaaatgcattaactttatttggaag-attttcatagcctaaagagaccttaacagag--ccttagTTATATTATAGAAGGACGGGTCTGTTACTTGACAATGTGTGATCGTGCATACCCTAAGAAACTAGCCTTTCAATATCTTGAAGAGCTCAGGAACGAGTTT

upper sequence: Vv09s0002g00780.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G11890.1 (Arabidopsis thaliana), 3'ss of exon 2
tattattattattgttattattattattattattattat-tatcatcattttattcaggtgtacacctgaatgttaatgttaccttgacca-aagttctcagTTATATTATTGAAGGACGTGTTTGTTACTTGACAATGTGTGATCGCGCTTATCCAAAGAAACTTGCCTTCCAATACCTGGAAGATCTCAAGAATGAATTT
|||  ||   ||     || | || |||| |||  || | | |||    |  | |       | ||| || | |  ||| | ||||||||| ||    | ||||| || || |||||||||||||| ||||||||||||||||| ||| |||| ||||||||||| || |||||||||||||||||||||||||||||||||
tatgtttgaaatctacgttgtcat-attagtatgcttgtatctcaaagctaaagtttaagaaagaccaga-tatgtatgcttccttgaccagaaaactttagTTACATCATAGAAGGACGTGTTTGCTACTTGACAATGTGTGACCGCTCTTACCCAAAGAAACTCGCTTTCCAATACCTGGAAGATCTCAAGAATGAATTT

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|110422751|gb|EC989081.1|EC989081
EST:     GAATGAGCCCTCAAGAATGTCAATTGAAACCGGCCCTTATATTTTTCA                         TTATATTATTGAAGGACGTGTTTGTTACTTGACAATGTGTGATCGCGCTTA
genomic: GAATGAGCCCTCAAGAATGTCAATTGAAACCGGCCCTTATATTTTTCAgtatccactt ... aagttctcagTTATATTATTGAAGGACGTGTTTGTTACTTGACAATGTGTGATCGCGCTTA
EST: gi|110385690|gb|EC950236.1|EC950236
EST:     CAGAATGAGCCCTCAAGAATGTCAATTGAAACCGGCCCTTATATTTTTCA                         TTATATTATTGAAGGACGTGTTTGTTACTTGACAATGTGTGATCGCGCTTA
genomic: CAGAATGAGCCCTCAAGAATGTCAATTGAAACCGGCCCTTATATTTTTCAgtatccactt ... aagttctcagTTATATTATTGAAGGACGTGTTTGTTACTTGACAATGTGTGATCGCGCTTA
EST: gi|110722089|gb|EE098012.1|EE098012
EST:     CAGAATGAGCCCTCAAGAATGTCAATTGAAACCGGCCCTTATATTTTTCA                         TTATATTATTGAAGGACGTGTTTGTTACTTGACAATGTGTGATCGCGCTTA
genomic: CAGAATGAGCCCTCAAGAATGTCAATTGAAACCGGCCCTTATATTTTTCAgtatccactt ... aagttctcagTTATATTATTGAAGGACGTGTTTGTTACTTGACAATGTGTGATCGCGCTTA
EST: gi|77586405|gb|DV222323.1|DV222323
EST:     CAGAATGAGCCCTCAAGAATGTCAATTGAAACCGGCCCTTATATTTTTCA                         TTATATTATTGAAGGACGTGTTTGTTACTTGACAATGTGTGATCGCGCTTA
genomic: CAGAATGAGCCCTCAAGAATGTCAATTGAAACCGGCCCTTATATTTTTCAgtatccactt ... aagttctcagTTATATTATTGAAGGACGTGTTTGTTACTTGACAATGTGTGATCGCGCTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattttattcaggtgtacacctgaatgttaatgttaccttgaccaaagttctcagTTATATTATTGAAGGACGTGTTTGTTACTTGACAATGTGTGATCGCGCTTATCCAAAGAAACTTGCCTTCCAATACCTGGAAGATCTCAAGAATGAATTT
                                  taccttgac  putative branch site 
                                                ttctc  putative PPT
                       aatgttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattattattattgttattattattattattattattattatcatcattttattcaggtgtacacctgaatgttaatgttaccttgaccaaagttctcagTTATATTATTGAAGGACGTGTTTGTTACTTGACAATGTGTGATCGCGCTTATCCAAAGAAACTTGCCTTCCAATACCTGGAAGATCTCAAGAATGAATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taccttg