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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactggaacttgttcttgattttttccttacaaataattcaataaataaataataggtgatgcaactctgctttacagtgccagtgtctctttttaatgtccaattttgttgtgccttggtaaacttgcaaagGTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGCTTAGCTCAGAAGACAGAAGGGTTTTCTGGTTCAGATATTGCTGTTTGT

Basic information

species Vitis vinifera
transcript Vv06s0080g00160.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0080g00160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g04814.3 (Oryza sativa), 3'ss of exon 5
gtactggaacttgttcttgattttttccttacaaataattcaataaataaataataggtgatgcaactctgcttt---acagtgccagtgtctctttttaatgtccaattttgttgtgccttggtaaacttgcaaagGTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGCTTAGCTCAGAAGACAGAAGGGTTTTCTGGTTCAGATATTGCTGTTTGT
                                                   |      |  | ||| || | ||    | | || ||   ||| || |||   ||      ||  |        | || ||    |||| ||||| || ||||| || |||||||| | ||||||||||||||| | ||| ||||     ||||| |||||||||||||| |||||||||||||||
--------------------------------------------------gtgcagaattgtccaattcagtttcaagaaaatgtcatgttctgttgttacaatctttggctgagggcaaacctttaatttatccagGTCCATCTCGGGGATACACCACACAACTTAAATGAAAGTGATTTTGAGAACTTGGCTCGTCGAACAGACGGGTTTTCTGGTTCGGATATTGCTGTTTGT

upper sequence: Vv06s0080g00160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g04840.1 (Oryza sativa), 3'ss of exon 5
gtactggaacttgttcttgattttttccttacaaataattcaataaataaataataggtgatgcaactctgctttacagtgccagtgtctctttttaatgtccaattttgttgtgccttggtaaacttgcaaagGTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGCTTAGCTCAGAAGACAGAAGGGTTTTCTGGTTCAGATATTGCTGTTTGT
            || |   |  |  |   ||      || |||   |  || || |  |  | |   ||||   |        | |  ||  | ||    || ||  |||  |  ||||  | || |     || | ||  |||| || || || || | ||| |||||| |||||||||  ||||| ||  |  | ||||| ||||||||||| ||||||||||||||||||
------------gtgcaaaaactaata--tatgtgcgatgcaacttaagaaaaagaatttgtacg-ttctgtcatggcaaataattaactaatctttg-atcaaagcttg--ggacctt--ttaattcatccagATCCACATTGGGGACACACCACATAGCTTAACTGAAGGTGATTTTGTGAGCTTGGCCTATCAAACAGAGGGGTTTTCTGGCTCAGATATTGCTGTTTGT

upper sequence: Vv06s0080g00160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G39410.1 (Glycine max), 3'ss of exon 6
gtactggaacttgttcttgattttttccttacaaataattcaataaataaataataggtgatgcaactctgctttacagtgccagtgtctctttttaatgtccaattttgttgtgccttggtaaacttgcaaagGTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGCTTAGCTCAGAAGACAGAAGGGTTTTCTGGTTCAGATATTGCTGTTTGT
                                                   | | ||||  |     | |||| || |   | ||    |  |||||   | |  |||| || || |||  |||| |||   |||||||||| ||||||||||| || ||||||||||||||||||||||||  ||| |||   | |||||| || |||||||||||||||||  |||| |||
-------------------------------------------------gttgacaggt--ttttgttatgctatataaacctagcaaatggttttaccatgc--tttttttctggcttactaaa-ttgagcagGTGCATCTAGGAGATACTCCCCATAACTTGACTGAAAGTGATTTTGAATACTTGGCTAGCAGGACAGAGGGTTTTTCTGGTTCAGATATATCTGTCTGT

upper sequence: Vv06s0080g00160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA12G30910.1 (Glycine max), 3'ss of exon 5
gtactggaacttgttcttgattttttccttacaaataattcaataaataaataataggtgatgcaactctgctttacagtgccagtgtctctttttaatgtccaattttgttgtgccttggtaaacttgcaaagGTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGCTTAGCTCAGAAGACAGAAGGGTTTTCTGGTTCAGATATTGCTGTTTGT
                              ||||   | |  ||   | ||| || | |  ||    | |||| || |   | || |  |  |||||   | | ||||| | |   |||  |||| |||   |||||||||| ||||||||||| || |||||||||||||| |||||||||  ||| |||   | |||||| ||||||||||||||||| ||  |||| |||
------------------------gcaaggacaatatacttgattgttgaatgatggattttgt---tgtgctatataaacctagcgaatggttttaccatgctattttctgg---cttaataaa-ttgagcagGTGCATCTAGGAGATACTCCCCATAACTTGACTGAAAGCGATTTTGAATACTTGGCTAGCAGGACAGAGGGGTTTTCTGGTTCAGACATATCTGTCTGT

upper sequence: Vv06s0080g00160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA11G19120.1 (Glycine max), 3'ss of exon 5
gtactggaacttgttcttgattttttccttacaaataattcaataaataaataataggtgatgcaactctgctttacagtgccagtgtctctttttaatgtccaattttgttgtgccttggtaaacttgcaaagGTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGCTTAGCTCAGAAGACAGAAGGGTTTTCTGGTTCAGATATTGCTGTTTGT
                              |     |||  |    || | |  |   || |   | | ||  ||      | ||    |  | ||| | |    |||| |||     || | || ||| | ||||||| || ||||||||||| || |||||| |||||||||||||||||   || ||||  |||||||| |||||||| |||||||||||  |||| |||
----------------------------gcatgggcaatatacatgatga-tgttcattggtcttattgtgtattgtgaacctagcaaatggtcttactatgtctttttcttgg---ctgatcaa-ttgaacagGTGCACCTAGGAGATACTCCCCATAACTTGGCTGAAAGTGATTTTGAACATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGT

upper sequence: Vv06s0080g00160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA12G09300.1 (Glycine max), 3'ss of exon 5
gtactggaacttgttcttgattttttccttacaaataattcaataaataaataataggtgatgcaactctgctttacagtgccagtgtctctttttaatgtccaattttgttgtgccttggtaaacttgcaaagGTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGCTTAGCTCAGAAGACAGAAGGGTTTTCTGGTTCAGATATTGCTGTTTGT
                              |     |||  |    || | |  |   || |   | | ||  ||      | ||    |    |||   |    |||| |||    ||| |||| ||| | ||||||| || ||||||||||| || |||||| ||||||||||||| |||   || ||||  |||||||| |||||||| |||||||||||  |||| |||
----------------------------gcatgggcaatatacatgatga-tgttcattggtcttattgtgtattgtgaacctagcaaatggccttacaatgtctttttcttgg---ttgataaa-ttgaacagGTGCACCTAGGAGATACTCCCCATAACTTGGCTGAAAGTGATTTCGAACATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGT

upper sequence: Vv06s0080g00160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT2G27600.1 (Arabidopsis thaliana), 3'ss of exon 5
gtactggaacttgttcttgattttttccttacaaataattcaataaataaataataggtgatgcaactctgctttacagtgccagtgtctctttttaatgtccaattttgttgtgccttggtaaacttgcaaagGTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGCTTAGCTCAGAAGACAGAAGGGTTTTCTGGTTCAGATATTGCTGTTTGT
                   ||| ||   || |    | ||    || |||| |  |    | | |          ||||  |||||     ||  |||||   |  | |||| ||      ||||  ||||  ||| ||  | |||||||| ||||| || || ||||||  ||||||||||   ||||  || ||||||||||||||||||||||||||| |  ||||||||
-----------------gtattattcatttgcttcaagtttctcaagtaaaaatcattcaagggag---------acagaaccagt-----ttactaatg---agatctgttttg------taaa--tgca--gGTCCACTTGGGAGATACACCTCATAATTTAACTGAACCTGATTTTGAATATTTAGGCCAAAAGACAGAAGGGTTTTCTGGTTCAGATGTGTCTGTTTGT

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|110374285|gb|EC938971.1|EC938971
EST:     GTATATATATTCCTCTTCCAGATCTGAAGGCTCGACAGCACATGTTCAAA                         GTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGC
genomic: GTATATATATTCCTCTTCCAGATCTGAAGGCTCGACAGCACATGTTCAAAgtactggaac ... acttgcaaagGTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGC
EST: gi|34320874|gb|CF373628.1|CF373628
EST:     CGACAGCACATGTTCAAA                         GTGCATCTGGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGC
genomic: CGACAGCACATGTTCAAAgtactggaac ... acttgcaaagGTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGC
EST: gi|71865549|gb|DT014604.1|DT014604
EST:     GTATATATATTCCTCTTCCAGATCTGAAGGCTCGACAGCACATGTTCAAA                         GTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGC
genomic: GTATATATATTCCTCTTCCAGATCTGAAGGCTCGACAGCACATGTTCAAAgtactggaac ... acttgcaaagGTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGC
EST: gi|110429534|gb|EC996029.1|EC996029
EST:     GTATATATATTCCTCTTCCAGATCTGAAGGCTCGACAGCACATGTTCAAA                         GTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGC
genomic: GTATATATATTCCTCTTCCAGATCTGAAGGCTCGACAGCACATGTTCAAAgtactggaac ... acttgcaaagGTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGC
EST: gi|77578092|gb|DV217813.1|DV217813
EST:     GATCTGAAGGCTCGACAGCACATGTTCAAA                         GTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGC
genomic: GATCTGAAGGCTCGACAGCACATGTTCAAAgtactggaac ... acttgcaaagGTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGC
EST: gi|33404951|gb|CF210578.1|CF210578
EST:     GTATATATATTCCTCTTCCAGATCTGAAGGCTCGACAGCACATGTTCAAA                         GTGCGTCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGC
genomic: GTATATATATTCCTCTTCCAGATCTGAAGGCTCGACAGCACATGTTCAAAgtactggaac ... acttgcaaagGTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGC
EST: gi|83274800|gb|DV938896.1|DV938896
EST:     AGGCTCGACAGCACATGTTCAAA                         GTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGC
genomic: AGGCTCGACAGCACATGTTCAAAgtactggaac ... acttgcaaagGTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGC
EST: gi|27582526|gb|CB005221.1|CB005221
EST:     GTATATATATTCCTCTTCCAGATCTGAAGGCTCGACAGCACATGTTCAAA                         GTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGC
genomic: GTATATATATTCCTCTTCCAGATCTGAAGGCTCGACAGCACATGTTCAAAgtactggaac ... acttgcaaagGTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGC
EST: gi|32269319|gb|CD718478.1|CD718478
EST:     GTATATATATTCCTCTTCCAGATCTGAAGGCTCGACAGCACATGTTCAAA                         GTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGC
genomic: GTATATATATTCCTCTTCCAGATCTGAAGGCTCGACAGCACATGTTCAAAgtactggaac ... acttgcaaagGTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGC
EST: gi|110703629|gb|EE080640.1|EE080640
EST:     GTATATATATTCCTCTTCCAGATCTGAAGGCTCGACAGCACATGTTCAAA                         GTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGC
genomic: GTATATATATTCCTCTTCCAGATCTGAAGGCTCGACAGCACATGTTCAAAgtactggaac ... acttgcaaagGTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGC
EST: gi|110374312|gb|EC939457.1|EC939457
EST:     GTATATTTTTTCCTCTTCCAGATCTGAAGGCTCGACAGCACATGTTCAAA                         GTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGA-TTTGAAAAG
genomic: GTATATATATTCCTCTTCCAGATCTGAAGGCTCGACAGCACATGTTCAAAgtactggaac ... acttgcaaagGTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTG-AAAG
EST: gi|32245883|gb|CD711702.1|CD711702
EST:     GTATATATATTCCTCTTCCAGATCTGAAGGCTCGACAGCACATGTTCAAA                         GTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGC
genomic: GTATATATATTCCTCTTCCAGATCTGAAGGCTCGACAGCACATGTTCAAAgtactggaac ... acttgcaaagGTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGC
EST: gi|22013056|gb|BQ798090.1|BQ798090
EST:     GGCTCGACAGCACATGTTCAAA                         GTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGC
genomic: GGCTCGACAGCACATGTTCAAAgtactggaac ... acttgcaaagGTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGC
EST: gi|110369975|gb|EC934149.1|EC934149
EST:     GTATATATATTCCTCTTCCAGATCTGAAGGCTCGACAGCACATGTTCAAA                         GTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGC
genomic: GTATATATATTCCTCTTCCAGATCTGAAGGCTCGACAGCACATGTTCAAAgtactggaac ... acttgcaaagGTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGC
EST: gi|30324099|gb|CD007361.1|CD007361
EST:     GTATATATATTCCTCTTCCAGATCTGAAGGCTCGACAGCACATGTTCAAA                         GTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGC
genomic: GTATATATATTCCTCTTCCAGATCTGAAGGCTCGACAGCACATGTTCAAAgtactggaac ... acttgcaaagGTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGC
EST: gi|110382895|gb|EC947223.1|EC947223
EST:     GTATATATATTCCTCTTCCAGATCTGAAGGCTCGACAGCACATGTTCAAA                         GTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGC
genomic: GTATATATATTCCTCTTCCAGATCTGAAGGCTCGACAGCACATGTTCAAAgtactggaac ... acttgcaaagGTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGC
EST: gi|37189302|gb|CF608651.1|CF608651
EST:     GTATATATATTCCTCTTCCAGATTTGAAGGCTCGACAGCACATGTTCAAA                         GTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGC
genomic: GTATATATATTCCTCTTCCAGATCTGAAGGCTCGACAGCACATGTTCAAAgtactggaac ... acttgcaaagGTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgccagtgtctctttttaatgtccaattttgttgtgccttggtaaacttgcaaagGTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGCTTAGCTCAGAAGACAGAAGGGTTTTCTGGTTCAGATATTGCTGTTTGT
             ttttaat  putative branch site (score: 3)
          tctttttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactggaacttgttcttgattttttccttacaaataattcaataaataaataataggtgatgcaactctgctttacagtgccagtgtctctttttaatgtccaattttgttgtgccttggtaaacttgcaaagGTGCATCTTGGAGATACTCCTCACAACTTGACTGAAAGTGATTTTGAAAGCTTAGCTCAGAAGACAGAAGGGTTTTCTGGTTCAGATATTGCTGTTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT