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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccttattttggatatagaccatgtgaagacttctatgtgctccttctctggtgatcgttccttctgtttcttaatagttgtttttggtatgtttttgaagGTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTCTTTGTGGCATCTATCTTGCAAAGGCGGCTCATGGTGATTGCTGACAAGT

Basic information

species Vitis vinifera
transcript Vv16s0098g01290.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0098g01290.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os10g37520.1 (Oryza sativa), 3'ss of exon 6
--------------------------ccttattttggatatagaccatgtgaagacttctatgtgctccttctctggtgatcgttccttctgtttcttaatagttgtttttggtatgtt--tttgaagGTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTCTTTGTGGCATCTATCTTGCAAAGGCGGCTCATGGTGATTGCTGACAAGT
                            || || |  ||  | |  |       ||    |  |||   | |       |  |    || |      ||| | |  |  |    ||| |  | || |||| |||||||||||||||||||||||||||||||||||  | |||||||| ||  ||||| | |||||||| |||||||| |||||  |  ||||     
gtaagtagctaaatccaacttctgtttttttttctttatgaaaataacacaccaacaagcaaatgcaaatgcaaaaaaaaaagacatttgt-cccagtaacattaatcatacaaatgatgttctgcagGTGAATGCATTCCCCATCACTGTCATGTTTGGCATGTGTGCTATTTTCCTTTTCATGGCAGCAATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCC

upper sequence: Vv16s0098g01290.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os03g02380.1 (Oryza sativa), 3'ss of exon 6
ccttattttggatatagaccatgtgaagacttctatgtgctccttctctggtgatcgttccttctgtttcttaatagttgtttttggtatgtttttgaagGTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTCTTTGTGGCATCTATCTTGCAAAGGCGGCTCATGGTGATTGCTGACAAGT
        |   |  |     | | |     |||   || | ||  |||| ||||  |||||||       ||| | || ||| ||  |   ||||| |||| ||||||||||| ||||||||||||||||||||||| || || ||||||||  ||||  | ||| |||| || ||||| |||||  || |||||    
-------gtaagtgaaagtgttcttactgaatct-catgattctaatctgttgat--ttccttcaaaaa--taacatttttttctgtgaa--ttttgcagGTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATCTTCCTCTTCATGGCGGCAATCCTGCAGAGACGGCTAATGGTTGTTTCTGACCTAC

upper sequence: Vv16s0098g01290.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G064563_T03 (Zea mays), 3'ss of exon 6
ccttattttggatatagaccatgtgaagacttctatgtgctcctt-----ctctggtgatcgttcct--------tctgtttcttaatag----ttgtttttgg-tatg-tttttgaagGTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTCTTTGTGGCATCTATCTTGCAAAGGCGGCTCATGGTGATTGCTGA-CAAGT
         |||   |  || | |    ||| |||||| ||| ||       ||||  |   ||           || |      | ||     |||  | |||  ||| | |||| |||| ||||||||||| ||||||||||||||||| ||||| || || ||||||||  ||||| | |||||||| || ||||| |||||  |  |||| |||| 
-----gcaaggagccattccctctcccaactactatgttctctttagttgtgctggcaagaattatacagaaatatcagcacacaagtaacgctttgcctgtggacatggtctttgcagGTGAATGCATTCCCTATCACTGTCATGTTTGGGATGTGTTCTATCTTCCTCTTCATGGCAGCAATCTTGCAGAGACGGCTGATGGTTGTCTCTGATCAAG-

upper sequence: Vv16s0098g01290.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G051189_T01 (Zea mays), 3'ss of exon 1
ccttattttggatatagaccatgtgaagacttctatgtgctcctt-----ctctggtgatcgttcctt--------ctgtttcttaatagttgttt-----ttggtatg-tttttgaagGTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTCTTTGTGGCATCTATCTTGCAAAGGCGGCTCATGGTGATTGCTGACAAGT
      |  |||   |  || | |    ||| |||||| ||| ||       ||||  |   ||   |        | |      | ||   ||||     | |  ||| | |||| |||| ||||||||||| ||||||||||||||||| ||||| || || ||||||||  ||||| | |||||||| || ||| | |||||              
-----gtaaggagccattccctctcccaactactatgttctctttagttgtgctggcaagaattatatagaaatatcagcacacaagtaacggtttgcttgtggacatggtctttgcagGTGAATGCATTCCCTATCACTGTCATGTTTGGGATGTGTTCTATCTTCCTCTTCATGGCAGCCATCTTGCAGAGACGGTTGATGGTT-------------

upper sequence: Vv16s0098g01290.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G067638_T01 (Zea mays), 3'ss of exon 6
ccttattttggatatagaccatgtgaaga-cttct--atgtgctccttctctggtgatcgttccttctgtttcttaatagttgtttttg-gtatgtttt--tgaagGTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTCTTTGTGGCATCTATCTTGCAAAGGCGGCTCATGGTGATTGCTGACAAGT
           || | ||  |   ||||  | |||  || || |   | | |   ||    || || |  || ||| |  |  || ||    ||||| |  || |||| ||||||||||| || ||||||||||| ||||||||||| ||||||||  |  ||||| |  ||||||| |||||  | ||||   |  ||||     
------gaaacatgtggataaatagaagttcctctaaatctggtatatatattaggacatctcattttaattattattgttctttcttataaatgttgtcgtgcagGTGAATGCATTCCCAATAACTGTCATGTTCGGCATGTGCTCCATTTTCCTTCTCATGGCAGCAGTCTTGCAGAGGCGCTTAATGGCTGTCTCTGATCTTC

upper sequence: Vv16s0098g01290.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G077669_T01 (Zea mays), 3'ss of exon 6
ccttattttggatatagaccatgtgaagacttctatgtgctccttctctggtgatcgttccttctgtttcttaatagttgtttttggtatgtttttgaagGTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTCTTTGTGGCATCTATCTTGCAAAGGCGGCTCATGGTGATTGCTGACAAGT
         | |   || |  |     | |   |          |        |||    |    ||  |    |   |||    | | |  ||||| |||| || |||||||| |||||||||||||| || ||||| || || ||||||||  ||||| | |||||||| || ||||| |||||  |  | ||     
---------gtaaggagtcattccctcgtccaatggcaagaatatacagaaatatcagcacacgagtaacactttgcctgtggacgttgt-cttttgcagGTGAACGCATTCCCTATCACTGTCATGTTCGGGATGTGTTCTATCTTCCTCTTCATGGCAGCAATCTTGCAGAGACGGCTGATGGTTGTCTCGGATCTAC

upper sequence: Vv16s0098g01290.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA04G41090.1 (Glycine max), 3'ss of exon 6
ccttattttggata-tagaccatgtgaagacttctatgtgctccttc---tctggtgatcgttccttctgtttcttaatagttgtttttggtatgtttttga---agGTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTCTTTGTGGCATCTATCTTGCAAAGGCGGCTCATGGTGATTGCTGACAAGT
   ||| ||  | | |  || |  | || ||   |  | | || |     | | ||  |  || ||| ||  | |   | |     ||  |||| || |||    ||||| |||||||||| |||||||| ||||||||||||||||| |||||||| || ||||| | ||||||||||||||| || ||||||||| | || ||| 
--gtatgttacacaatctactacttcaatacaa-tgcgcgatcttaacagtgtagtagtattttcttatgcgtgtgctttgactaattgtgtattttcttggtgcagGTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTTTTGGTGGCTTGTATCTTGCAAAGGCGACTGATGGTGATTTCGGATAAGC

upper sequence: Vv16s0098g01290.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA06G13760.1 (Glycine max), 3'ss of exon 6
ccttattttggata-tagaccatgtgaagact-tctatgtgctc-cttctctggtgatcgttccttctgtttcttaatagttgtttttggtatgtttttga---agGTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTCTTTGTGGCATCTATCTTGCAAAGGCGGCTCATGGTGATTGCTGACAAGT
   ||| ||  | | |  || |  | ||  |  |   || |||  |   |   ||  |  || ||| | | |  |  |   |  || || ||| || | ||   ||||| |||||||||| |||||||| ||||||||||||||||| |||||||| || ||||| | ||||||||||||||| || ||||||||| | || ||| 
--gtatgttacacaatctactacttcaatgcaatgcttgagcttaccaatgcagtagtattttcttatctctggttttgactaattgtg-tattttctcgatgcagGTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTTTTGGTGGCTTGTATCTTGCAAAGGCGACTGATGGTGATTTCCGATAAGC

upper sequence: Vv16s0098g01290.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT4G27720.1 (Arabidopsis thaliana), 3'ss of exon 6
ccttattttggatatagaccatgtgaagacttctatgtgctccttctctggtgatcgttccttctgtttcttaatagttgtttttggtatgt-ttttgaagGTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTCTTTGTGGCATCTATCTTGCAAAGGCGGCTCATGGTGATTGCTGACAAGT
   ||  |       | |   | |     |  |   ||        | | |||  |  |   ||||| |  |  || |   |  |  |||||  | ||||||| ||||||||||| ||||| ||||||||||| ||||||||||| ||||||||||| |||  | || | ||||||||||||||| |||||| ||||||  
--gtaagtccccccaacattctttttctgcaccatagtagctgagatttcgtgtcccatgtctctgtgttgtggtactgactagttttatgtgctctgaagGTAAATGCATTCCCTATCACGGTCATGTTTGGAATGTGCTCGATCTTCCTCTTTGTTGCAAGTCTCCTACAAAGGCGGCTCATGATGATTGTTGACAAAC

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|33402137|gb|CF207764.1|CF207764
EST:     ACTTTTTCCGCATTCCCCTCAATATCTTTGTGTGCATCGTGCTATATAAT                         GTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
genomic: ACTTCTTCCGCATTCCCCTCAATATCTTTGTGTGCATCGTGCTATATAATgtatgtaacc ... gtttttgaagGTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
EST: gi|110414050|gb|EC979873.1|EC979873
EST:     ACTTCTTCCGCATTCCCCTCAATATCTTTGTGTGCATCGTGCTATATAAT                         GTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
genomic: ACTTCTTCCGCATTCCCCTCAATATCTTTGTGTGCATCGTGCTATATAATgtatgtaacc ... gtttttgaagGTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
EST: gi|254915672|gb|GR905103.1|GR905103
EST:     ACTTCTTCCGCATTCCCCTCAATATCTTTGTGTGCATCGTGCTATATAAT                         GTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTTCTCGATTTTCCTC
genomic: ACTTCTTCCGCATTCCCCTCAATATCTTTGTGTGCATCGTGCTATATAATgtatgtaacc ... gtttttgaagGTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
EST: gi|110414298|gb|EC980125.1|EC980125
EST:     ACTTCTTCCGCATTCCCCTCAATATCTTTGTGTGCATCGTGCTATATAAT                         GTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
genomic: ACTTCTTCCGCATTCCCCTCAATATCTTTGTGTGCATCGTGCTATATAATgtatgtaacc ... gtttttgaagGTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
EST: gi|110697221|gb|EE074018.1|EE074018
EST:     ACTTCTTCCGCATTCCCCTCAATATCTTTGTGTGCATCGTGCTATATAAT                         GTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
genomic: ACTTCTTCCGCATTCCCCTCAATATCTTTGTGTGCATCGTGCTATATAATgtatgtaacc ... gtttttgaagGTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
EST: gi|110372984|gb|EC937182.1|EC937182
EST:     ACTTCTTCCGCATTCCCCTCAATATCTTTGTGTGCATCGTGCTATATAAT                         GTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
genomic: ACTTCTTCCGCATTCCCCTCAATATCTTTGTGTGCATCGTGCTATATAATgtatgtaacc ... gtttttgaagGTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
EST: gi|110408163|gb|EC973786.1|EC973786
EST:     ACTTCTTCCGCATTCCCCTCAATATCTTTGTGTGCATCGTGCTATATAAT                         GTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
genomic: ACTTCTTCCGCATTCCCCTCAATATCTTTGTGTGCATCGTGCTATATAATgtatgtaacc ... gtttttgaagGTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
EST: gi|33408846|gb|CF214473.1|CF214473
EST:     ACTTCTTCCGCATTCCCCTCAATATCTTTGTGTGCATCGTGCTATATAAT                         GTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
genomic: ACTTCTTCCGCATTCCCCTCAATATCTTTGTGTGCATCGTGCTATATAATgtatgtaacc ... gtttttgaagGTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
EST: gi|110715161|gb|EE092898.1|EE092898
EST:     ACTTCTTCCGCATTCCCCTCAATATCTTTGTGTGCATCGTGCTATATAAT                         GTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
genomic: ACTTCTTCCGCATTCCCCTCAATATCTTTGTGTGCATCGTGCTATATAATgtatgtaacc ... gtttttgaagGTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
EST: gi|219554953|gb|FG984742.1|FG984742
EST:     ACTTCTTCCGCATTCCCCTCAATATCTTTGTGTGCATCGTGCTATATAAT                         GTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
genomic: ACTTCTTCCGCATTCCCCTCAATATCTTTGTGTGCATCGTGCTATATAATgtatgtaacc ... gtttttgaagGTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
EST: gi|33402350|gb|CF207977.1|CF207977
EST:     ACTTCTTCCGCATTCCCCTCAATATCTTTGTGTGCATCGTGCTATATAAT                         GTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
genomic: ACTTCTTCCGCATTCCCCTCAATATCTTTGTGTGCATCGTGCTATATAATgtatgtaacc ... gtttttgaagGTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
EST: gi|33402051|gb|CF207678.1|CF207678
EST:     ACTTCTTCCGCATTCCCCTCAATATCTTTGTGTGCATCGTGCTATATAAT                         GTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
genomic: ACTTCTTCCGCATTCCCCTCAATATCTTTGTGTGCATCGTGCTATATAATgtatgtaacc ... gtttttgaagGTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
EST: gi|56409197|gb|CX017449.1|CX017449
EST:     ACTTCTTCCGCATTCCCCTCAATATCTTTGTGTGCATCGTGCTATATAAT                         GTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
genomic: ACTTCTTCCGCATTCCCCTCAATATCTTTGTGTGCATCGTGCTATATAATgtatgtaacc ... gtttttgaagGTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
EST: gi|110387970|gb|EC952680.1|EC952680
EST:     ACTTCTTCCGCATTCCCCTCAATATCTTTGTGTGCATCGTGCTATATAAT                         GTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
genomic: ACTTCTTCCGCATTCCCCTCAATATCTTTGTGTGCATCGTGCTATATAATgtatgtaacc ... gtttttgaagGTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
EST: gi|110722212|gb|EE098246.1|EE098246
EST:     ACTTCTTCCGCATTCCCCTCAATATCTTTGTGTGCATCGTGCTATATAAT                         GTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
genomic: ACTTCTTCCGCATTCCCCTCAATATCTTTGTGTGCATCGTGCTATATAATgtatgtaacc ... gtttttgaagGTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctggtgatcgttccttctgtttcttaatagttgtttttggtatgtttttgaagGTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTCTTTGTGGCATCTATCTTGCAAAGGCGGCTCATGGTGATTGCTGACAAGT
                       tcttaat  putative branch site (score: 3)
                                            tgttttt  putative PPT
                         ttaatagttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccttattttggatatagaccatgtgaagacttctatgtgctccttctctggtgatcgttccttctgtttcttaatagttgtttttggtatgtttttgaagGTTAATGCATTCCCCATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTCTTTGTGGCATCTATCTTGCAAAGGCGGCTCATGGTGATTGCTGACAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - -catgtga
- - - - - - - - - - - - - - - - -tatgtgc
- - - - - - - - - - - - - - - - - - - - -ccttctc