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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtactgttttaatggtttcttctcttaaccatagggataatttatctctctctgctcctctctaacactaaatattggtttgttcttccctttttgaagGTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTCTTTGTGGCAACACTGTTGCAAAGGAGGCTCATGATGATTTCAGAGAGCC

Basic information

species Vitis vinifera
transcript Vv02s0025g02420.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os03g02380.1 (Oryza sativa), 3'ss of exon 6
tgtactgttttaatggtttcttctcttaaccatagggataatttatctctctctgctcctctctaacactaaatattggtttgttcttccctttttgaagGTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTCTTTGTGGCAACACTGTTGCAAAGGAGGCTCATGATGATTTCAGAGAGCC
          |||  |    |  |||||   |     || |||    ||| |    | |  || ||     ||||    ||| ||||     ||||| |||| |||||||| || ||||||||||||||||||||||| || || ||||||||  ||||  || |  |||| ||  |||| ||| |  |||| ||    |
---------gtaagtgaaagtgttcttactgaatctcatgattctaatctgttgatttccttcaaa-----aataacatttttttctgtgaattttgcagGTGAATGCATTCCCTATCACTGTCATGTTTGGCATGTGTTCTATCTTCCTCTTCATGGCGGCAATCCTGCAGAGACGGCTAATGGTTGTTTCTGACCTAC

upper sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os10g37520.1 (Oryza sativa), 3'ss of exon 6
---------tgtactgttttaatggtttcttctcttaaccatagggata-atttatctctctctgctcct-ctctaacactaaatattggt----------ttgttcttcc------ctttttgaagGTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTCTTTGTGGCAACACTGTTGCAAAGGAGGCTCATGATGATTTCAGAGAGCC
         |  |      |  || ||| || |||| |  | |   | | |   |        |||   | |   || |  | | ||| ||          ||  || | |        || || |||| |||||||| || |||||||||||||||||||||||  | |||||||| ||  ||||| || | ||||| ||| |||| ||| |  | || ||   ||
gtaagtagctaaatccaacttctgtttttttttctttatgaaaataacacaccaacaagcaaatgcaaatgcaaaaaaaaaagacatttgtcccagtaacattaatcatacaaatgatgttctgcagGTGAATGCATTCCCCATCACTGTCATGTTTGGCATGTGTGCTATTTTCCTTTTCATGGCAGCAATCTTGCAGAGGCGGCTGATGGTTGTCTCTGATCTCC

upper sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G067638_T01 (Zea mays), 3'ss of exon 6
----tgtactgttttaatggtttcttctcttaaccatagggataatttatctctctctgctcctctctaacactaaatattggtttgttcttccctttttgaagGTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTCTTTGTGGCAACACTGTTGCAAAGGAGGCTCATGATGATTTCAGAGAGCC
      |  ||  | ||| |    | |||| || |      |||  |||   |  |||  |  |   ||  | |     ||   || |   |    |  || |||| |||||||| ||||| ||||||||||| ||||||||||| ||||||||  |  ||||| || | ||||| ||| |  | |||    | || ||    |
gaaacatg-tggataaatagaagttcctctaaatctggtatatatattaggaca-tctcattttaattattattgttcttt--cttataaatgttgtcgtgcagGTGAATGCATTCCCAATAACTGTCATGTTCGGCATGTGCTCCATTTTCCTTCTCATGGCAGCAGTCTTGCAGAGGCGCTTAATGGCTGTCTCTGATCTTC

upper sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G051189_T01 (Zea mays), 3'ss of exon 1
-----------tgtactgttttaa-tggtttcttctctt-aaccatagggataatttatctctctctgctcctctctaacactaaatattggtttgttc-ttccctttttgaagGTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTCTTTGTGGCAACACTGTTGCAAAGGAGGCTCATGATGATTTCAGAGAGCC
           |   || |   || |  | | ||||||| |    |   |  ||    | | |        |     |  | |||   || | ||||        | |||| |||| |||||||| || ||||||||||||||||| ||||| || || ||||||||  ||||| |  | ||||| ||  || | ||| |              
gtaaggagccattccctctcccaactactatgttctctttagttgtgctggcaagaattatatagaaatatcagcacacaagtaacggtttgcttgtggacatggtctttgcagGTGAATGCATTCCCTATCACTGTCATGTTTGGGATGTGTTCTATCTTCCTCTTCATGGCAGCCATCTTGCAGAGACGGTTGATGGTT-------------

upper sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G064563_T03 (Zea mays), 3'ss of exon 6
-----------tgtactgttttaa-tggtttcttctctt-aaccatagggataatttatctctctctgctcctctctaacactaaatattggtttgttc-ttccctttttgaagGTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTCTTTGTGGCAACACTGTTGCAAAGGAGGCTCATGATGATTTCAGAGAGCC
           |   || |   || |  | | ||||||| |    |   |  ||    | |          |     |  | |||   || |  |||        | |||| |||| |||||||| || ||||||||||||||||| ||||| || || ||||||||  ||||| || | ||||| ||  |||| ||| |  | || ||     
gcaaggagccattccctctcccaactactatgttctctttagttgtgctggcaagaattatacagaaatatcagcacacaagtaacgctttgcctgtggacatggtctttgcagGTGAATGCATTCCCTATCACTGTCATGTTTGGGATGTGTTCTATCTTCCTCTTCATGGCAGCAATCTTGCAGAGACGGCTGATGGTTGTCTCTGATCAAG

upper sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA04G41090.1 (Glycine max), 3'ss of exon 6
tgtactgttttaatggtttcttctcttaaccatagggataatttatctctctc-tgctcctctctaacac-taaatattggtttgtt----cttccctttttgaagGTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTCTTTGTGGCAACACTGTTGCAAAGGAGGCTCATGATGATTTCAGAGAGCC
 ||| ||||  |     | || ||   |  ||  | |  |  ||| |  | |  |  |  | ||| |  | |     |||  |  ||     ||  |||  || ||||| ||||||| || |||||||| ||||||||||||||||| |||||||| || |||||     | ||||||||| | || ||| ||||||| || |  |
-gta-tgttacacaatctactacttcaatacaatgcgcgatcttaacagtgtagtagtattttcttatgcgtgtgctttgactaattgtgtattttcttggtgcagGTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTTTTGGTGGCTTGTATCTTGCAAAGGCGACTGATGGTGATTTCGGATAAGC

upper sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA06G13760.1 (Glycine max), 3'ss of exon 6
-tgtactgttttaatggtttcttctct-taaccatagggat----aatttatctctctctgctcctctctaacactaaatattggtttgttcttccctttttgaagGTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTCTTTGTGGCAACACTGTTGCAAAGGAGGCTCATGATGATTTCAGAGAGCC
 | |  |     |     | ||||  |  ||   | | | |    |||  |    | | | ||  |||||     | | || | || | || |   ||   || ||||| ||||||| || |||||||| ||||||||||||||||| |||||||| || |||||     | ||||||||| | || ||| ||||||| || |  |
gtatgttacacaatctactacttcaatgcaatgcttgagcttaccaatgcagtagtattttcttatctctggttttgactaattgtgtatttt---ctcgatgcagGTTGATGCATTCCCTATCACTGTTATGTTTGGCATGTGCTCAATTTTCCTTTTGGTGGCTTGTATCTTGCAAAGGCGACTGATGGTGATTTCCGATAAGC

upper sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT4G27720.1 (Arabidopsis thaliana), 3'ss of exon 6
-tgtactgttttaatggtttcttctcttaaccatag-ggataatttatctctctctgctcctctctaacactaaatattggtttgttcttccctttttgaagGTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTCTTTGTGGCAACACTGTTGCAAAGGAGGCTCATGATGATTTCAGAGAGCC
 |          ||   ||  || |||  |||||||  | | |  | ||     |     |||| |         || ||  | ||| |      | ||||||| |||||||| || ||||| ||||||||||| ||||||||||| ||||||||||| ||||  ||  | |||||| ||||||||||||||   || |  |
gtaagtccccccaaca-ttctttttctgcaccatagtagctgagatttcgtgtcccatgtctctgtgttgt--ggtactgactagttttatgtgctctgaagGTAAATGCATTCCCTATCACGGTCATGTTTGGAATGTGCTCGATCTTCCTCTTTGTTGCAAGTCTCCTACAAAGGCGGCTCATGATGATTGTTGACAAAC

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|71877895|gb|DT026950.1|DT026950
EST:     CTCAATATCTTTGTGTGCATTGTGCTGTACAAT                         GTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
genomic: CTCAATATCTTTGTGTGCATTGTGCTGTACAATgtgagtaggt ... ctttttgaagGTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
EST: gi|30330382|gb|CD013644.1|CD013644
EST:     ACTTCTTCCGCATTCCTCTCAATATCTTTGTGTGCATTGTGCTGTACAAT                         GTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
genomic: ACTTCTTCCGCATTCCTCTCAATATCTTTGTGTGCATTGTGCTGTACAATgtgagtaggt ... ctttttgaagGTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
EST: gi|33409775|gb|CF215402.1|CF215402
EST:     ACTTCTTCCGCATTCCTCTCAATATCTTTGTGTGCATTGTGCTGTACAAT                         GTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
genomic: ACTTCTTCCGCATTCCTCTCAATATCTTTGTGTGCATTGTGCTGTACAATgtgagtaggt ... ctttttgaagGTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
EST: gi|110361276|gb|EC924740.1|EC924740
EST:     ACTTCTTCCGCATTCCTCTCAATATCTTTGTGTGCATTGTGCTGTACAAT                         GTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
genomic: ACTTCTTCCGCATTCCTCTCAATATCTTTGTGTGCATTGTGCTGTACAATgtgagtaggt ... ctttttgaagGTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
EST: gi|77579825|gb|DV218792.1|DV218792
EST:     ACTTCTTCCGCATTCCTCTCAATATCTTTGTGTGCATTGTGCTGTACAAT                         GTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
genomic: ACTTCTTCCGCATTCCTCTCAATATCTTTGTGTGCATTGTGCTGTACAATgtgagtaggt ... ctttttgaagGTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
EST: gi|110716274|gb|EE091110.1|EE091110
EST:     ACTTCTTCCGCATTCCTCTCAATATCTTTGTGTGCATTGTGCTGTACAAT                         GTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
genomic: ACTTCTTCCGCATTCCTCTCAATATCTTTGTGTGCATTGTGCTGTACAATgtgagtaggt ... ctttttgaagGTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
EST: gi|33410168|gb|CF215795.1|CF215795
EST:     ACTTCTTCCGCATTCCTCTCAATATCTTTGTGTGCATTGTGCTGTACAAT                         GTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
genomic: ACTTCTTCCGCATTCCTCTCAATATCTTTGTGTGCATTGTGCTGTACAATgtgagtaggt ... ctttttgaagGTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
EST: gi|22015506|gb|BQ800540.1|BQ800540
EST:     ACTTCTTCCGCATTCCTCTCAATATCTTTGTGTGCATTGTGCTGTACAAT                         GTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
genomic: ACTTCTTCCGCATTCCTCTCAATATCTTTGTGTGCATTGTGCTGTACAATgtgagtaggt ... ctttttgaagGTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
EST: gi|110702049|gb|EE080317.1|EE080317
EST:     ACTTCTTCCGCATTCCTCTCAATATCTTTGTGTGCATTGTGCTGTACAAT                         GTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
genomic: ACTTCTTCCGCATTCCTCTCAATATCTTTGTGTGCATTGTGCTGTACAATgtgagtaggt ... ctttttgaagGTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
EST: gi|254914996|gb|GR904427.1|GR904427
EST:     ATATCTTTGTGTGCATTGTGCTGTACAAT                         GTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
genomic: ATATCTTTGTGTGCATTGTGCTGTACAATgtgagtaggt ... ctttttgaagGTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
EST: gi|110360915|gb|EC924358.1|EC924358
EST:     ACTTCTTCCGCATTCCTCTCAATATCTTTGTGTGCATTGTGCTGTACAAT                         GTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
genomic: ACTTCTTCCGCATTCCTCTCAATATCTTTGTGTGCATTGTGCTGTACAATgtgagtaggt ... ctttttgaagGTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
EST: gi|34416780|gb|CF415534.1|CF415534
EST:     ACTTCTTCCGCATTCCTCTCAATATCTTTGTGTGCATTGTGCTGTACAAT                         GTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
genomic: ACTTCTTCCGCATTCCTCTCAATATCTTTGTGTGCATTGTGCTGTACAATgtgagtaggt ... ctttttgaagGTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
EST: gi|110413558|gb|EC979348.1|EC979348
EST:     ACTTCTTCCGCATTCCGCTCAATATCTTTGTGTGCATTGTGCTGTACAAT                         GTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
genomic: ACTTCTTCCGCATTCCTCTCAATATCTTTGTGTGCATTGTGCTGTACAATgtgagtaggt ... ctttttgaagGTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
EST: gi|27585660|gb|CB008355.1|CB008355
EST:     ACTTCTTCCGCATTCCTCTCAATATCTTTGTGTGCATTGTGCTGTACAAT                         GTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC
genomic: ACTTCTTCCGCATTCCTCTCAATATCTTTGTGTGCATTGTGCTGTACAATgtgagtaggt ... ctttttgaagGTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctctctgctcctctctaacactaaatattggtttgttcttccctttttgaagGTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTCTTTGTGGCAACACTGTTGCAAAGGAGGCTCATGATGATTTCAGAGAGCC
                     cactaaa  putative branch site (score: 2)
                              ttggtttgttcttccc  putative PPT
                  taacactaaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtactgttttaatggtttcttctcttaaccatagggataatttatctctctctgctcctctctaacactaaatattggtttgttcttccctttttgaagGTTAATGCATTTCCAATCACTGTCATGTTTGGCATGTGCTCGATTTTCCTCTTTGTGGCAACACTGTTGCAAAGGAGGCTCATGATGATTTCAGAGAGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - -aaccata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cactaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcttcc