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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgtcatactatttgtctgaatgcttcagcttttcctatgtattcacaaaatgtgctttaacacgtgtttattttattcttgaagGATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAG

Basic information

species Vitis vinifera
transcript Vv13s0019g04680.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04680.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os03g05740.1 (Oryza sativa), 3'ss of exon 6
gtgagtgtcatactatttgtctgaatgcttcagcttttcctatgtattcacaaaatgtgctttaacacgtgtttattttattcttgaagGATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAG
|| ||  || |       ||   | |        | |  | || |  |  |||||| || ||| ||   | |       ||||| |||||| |     || |||||||||||||||  |||| | || || || ||||| ||||||||||||||||| ||||||||  | ||||||
gtcag-atcttgtgtgaagttgtagtaaacatagtatcacaatatgct-gcaaaat-tgttttgacg-atatggtgcacattct-gaagGAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCAGCAAAGACAGCTGATAATATAAACCAAGTATTTGAG

upper sequence: Vv13s0019g04680.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G362088_T02 (Zea mays), 3'ss of exon 7
gtgagtgt-catactatttgtc---tgaatgcttcagcttttcctatgtattcacaaaatgtgctttaacacgtgtttattttattctt---gaagGATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAG
|| || ||  || || |||| |   |||  | |   |   ||  |   |  | || | |||  ||| | ||  ||  |||  | | |||   | ||||||     || || |||||||||||   |||||| || ||||| || || || |||||||||||||| |||||||| |||||||||
gtaagagtatatgctctttgccaactgatagatattgtagttaatggctgct-actatatgatcttgaccatatggatatggtgtacttgttgcagGATGCGCAGGACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG

upper sequence: Vv13s0019g04680.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM5G863105_T01 (Zea mays), 3'ss of exon 2
------------gtgagtgtcata--ctatttgtctgaatgcttcagcttttcctatgtattcacaaaatgtgctttaacacgtgtttattttattcttgaagGATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAG
                |  |||    |    |||| |   |||  |  |    ||    |    | | ||||  || |  |  ||    | |  || |||  |||||     || ||||||||||||||    ||||| || ||||| || || || |||||||||||||| |||||||| |||||||||
gaccatggaccgtccggcctcagggccggactgtccgccagctcaaaatggcgctcaacaactgctatatgttattgacaatatg---gtgtacttgttgcggGATGCACAGGACTATGCAGAGAAGAACAAAATGTTTTTCATTGAGACGTCAGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG

upper sequence: Vv13s0019g04680.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA10G35230.3 (Glycine max), 3'ss of exon 6
gtgagtgtcatactatttgtctgaatgcttcagcttttcctatgtattcacaaaatgtgc-tttaacacgtgtttattttattcttgaagGATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAG
|| ||||  | ||||| |     | |  |      |   | |  || |||     |   | | ||  | |  |||| | | | | |||||||||| | ||| ||||||||||||||||||||||| || || || ||||||||||||||||| ||||| |||||  | |||||||||
gt-agtgcaacactatgtaatatagttgtc--atataaacaaaataatcatttttttctcatatagtatgc-tttactgtttccatgaaggatggcactgactatgcagAGAAGAATGGTATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG

upper sequence: Vv13s0019g04680.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA20G32320.1 (Glycine max), 3'ss of exon 6
gtgagtgtcatactatttgtctgaatgcttcagcttttcctatgtattcacaaaatgtgctttaacacgtg---tttattttattcttgaagGATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAG
|| ||||  | |||   |||   |  | |      |   | |  || |       | | ||   | |  |    |||| | | | | |||||||||| | ||| |||||||||||||||| |||||| || || || ||||||||||||||||| ||||| |||||  | |||||||||
gt-agtgcaacact--ctgtaatatagttgtcatataaacaaaataattgtttgtttttctcatatatatatgctttactgtttccatgaagGATGGCACTGACTATGCAGAGAAGAATGATATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG

upper sequence: Vv13s0019g04680.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT3G54840.1 (Arabidopsis thaliana), 3'ss of exon 6
----gtgagtgtcatactatttgtctgaatgcttcagc---ttttcctat-gtattcacaaaatgtgctttaacacgtgttt---atttta---ttcttga-agGATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAG
    ||  | || |   | ||  |||  || |   |||   ||||  | |    ||||       |||||   ||   || |   |||||    ||||| | ||||||| || ||   |||||||||||| || |||||||| ||||| || || || |||||||| ||||||||||| || |||||||||
gtgagtttgcgtaaacgtcttcatctagattccgtagcgcattttgttgtcactttcattgtccttgcttcttcagtggtatcacattttcaatttcttaacagGATGGAATGGAGCTTGCAGAGAAGAACGGCATGTTCTTCATTGAGACGTCAGCCAAGACAGCCGATAACATAAATCAACTGTTTGAG

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|351049141|gb|FQ449863.1|FQ449863
EST:     TAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAA                         GATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCT
genomic: TAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAAgtgagtgtca ... attcttgaagGATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCT
EST: gi|351031329|gb|FQ445354.1|FQ445354
EST:     TAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAA                         GATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAGACATCT
genomic: TAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAAgtgagtgtca ... attcttgaagGATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCT
EST: gi|110378503|gb|EC943640.1|EC943640
EST:     TAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAA                         GATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAGACATCT
genomic: TAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAAgtgagtgtca ... attcttgaagGATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCT
EST: gi|110386522|gb|EC951122.1|EC951122
EST:     TAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAA                         GATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAGACATCT
genomic: TAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAAgtgagtgtca ... attcttgaagGATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCT
EST: gi|110707796|gb|EE084605.1|EE084605
EST:     TAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAA                         GATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAGACATCT
genomic: TAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAAgtgagtgtca ... attcttgaagGATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCT
EST: gi|351029650|gb|FQ427490.1|FQ427490
EST:     TAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAA                         GATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAGACATCT
genomic: TAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAAgtgagtgtca ... attcttgaagGATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCT
EST: gi|351031354|gb|FQ445379.1|FQ445379
EST:     TAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAA                         GATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAGACATCT
genomic: TAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAAgtgagtgtca ... attcttgaagGATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCT
EST: gi|351036602|gb|FQ457315.1|FQ457315
EST:     TAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAA                         GATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCT
genomic: TAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAAgtgagtgtca ... attcttgaagGATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCT
EST: gi|110390981|gb|EC955931.1|EC955931
EST:     TAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAA                         GATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAGACATCT
genomic: TAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAAgtgagtgtca ... attcttgaagGATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCT
EST: gi|351033397|gb|FQ462048.1|FQ462048
EST:     TAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAA                         GATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCT
genomic: TAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAAgtgagtgtca ... attcttgaagGATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCT
EST: gi|30302011|gb|CB978805.1|CB978805
EST:     TAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAA                         GATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAGACATCT
genomic: TAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAAgtgagtgtca ... attcttgaagGATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCT
EST: gi|349830843|gb|FQ418151.1|FQ418151
EST:     TAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCGA                         GATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAGACATCT
genomic: TAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAAgtgagtgtca ... attcttgaagGATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCT
EST: gi|110428129|gb|EC994591.1|EC994591
EST:     TAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAA                         GATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAGACATCT
genomic: TAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAAgtgagtgtca ... attcttgaagGATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCT
EST: gi|351016862|gb|FQ424289.1|FQ424289
EST:     TAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAA                         GATGGTATTGATTATGCAGAGAAAAATGGTATGTTCTTTATTGAAACATCT
genomic: TAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAAgtgagtgtca ... attcttgaagGATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCT
EST: gi|110691925|gb|EE070587.1|EE070587
EST:     TAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAA                         GATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAGACATCT
genomic: TAGTTGGGAACAAAGCTGATCTTCATGAGAATCGAGAAGTACCAGTTCAAgtgagtgtca ... attcttgaagGATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcctatgtattcacaaaatgtgctttaacacgtgtttattttattcttgaagGATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAG
                         ctttaac  putative branch site (score: 3)
                                     tttattttattctt  putative PPT
                                     tttattttattcttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgtcatactatttgtctgaatgcttcagcttttcctatgtattcacaaaatgtgctttaacacgtgtttattttattcttgaagGATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT