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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgggatttgacttcattttattcctttaaccaggatcataaatttctcaatttattaaattatgttaatgtttaacagGATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCCCCAAACTGAGAGCTATTGGGGAAATGTTAACCCAATAG

Basic information

species Vitis vinifera
transcript Vv06s0004g04390.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 6
gtttgggattt---gacttcattttattcctttaaccaggatcataa--atttctcaatttattaaa-ttatgttaatgtttaacagGATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCCCCAAACTGAGAGCTATTGGGGAAATGTTAACCCAATAG
||| | | |||    |      || | |  |   |      | || |  | |    |||  |   |  || |  |  |||    |||||| ||| | || || || || ||||| || || ||||| |||||||| || ||||| |||  ||| |||||||||||||||||||| |
gttggtgtttttttaatgctgattaacttgtcctatgcaacttatgagaactatataatgaagggaggtttttatgttgtactgcagGATTTTGTTGACTTCGACCTCTGAAGTTTACGGTGATCCGCTTGAGCACCCTCAAACAGAGGCCTACTGGGGAAATGTTAACCCAATTG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G157772_T02 (Zea mays), 3'ss of exon 3
gtttgggatttgacttcattttattcctttaaccaggatcataaatttctcaatttattaaattatgttaatgtttaacagGATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCCCCAAACTGAGAGCTATTGGGGAAATGTTAACCCAATAG
||  | | |     | |  || |||| | || |        | ||   |||| ||    || |||| ||    ||   |||||| ||| | |||||||| || ||||| ||||| ||||| ||||||||||| |||||||||  ||| ||||| ||||||||||| || |
gtcagtgttcatcatgccattgattcttctagcgcctcatgtgaaaaactcagttacagaatttatttttgaatt--gcagGATTTTGTTAACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 5
gtttgggatttgacttcattttattcctttaaccaggatc----ataaatttctcaatttattaaattatgttaatgtttaacagGATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCCCCAAACTGAGAGCTATTGGGGAAATGTTAACCCAATAG
    |  |||   | ||||   |||  ||   ||||   |     | ||   |||||||    || |||| ||    ||   |||||| ||| | |||||||| || ||||| ||||| ||||| ||||||||||| |||||||||  ||| ||||| ||||||||||| || |
----gtcattgttcatcatgccattgattcttccagcgcctcatgtgaaaaactcaattacagaatttatttttgaatt--gcagGATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCCTCAAACTGAGGCCTACTGGGGCAATGTTAACCCGATTG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 6
gtttgggatttgacttcattttattcctttaaccaggat-cataaatttctcaatttattaaattatgttaatgtttaacagGATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCCCCAAACTGAGAGCTATTGGGGAAATGTTAACCCAATAG
  |  |  ||   | |  | ||  | |||  |||        | ||   |||| ||    || |||| || |  |    |||||| ||| | |||||||| || ||||| ||||| ||||| ||||||||||| ||||| |||  ||| ||||| |||||||||||||| |
-gtcagtgttcatcatgctattgattcttccaccgcctcatgtgaaaaactcagttacagaatttattttgaatt---gcagGATTTTGTTGACATCAACATCTGAAGTTTATGGTGATCCGCTTGAGCATCCTCAAACCGAGGCCTACTGGGGCAATGTTAACCCAATTG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G382038_T01 (Zea mays), 3'ss of exon 7
gtttgggatttgacttcattttattcctttaaccaggatcataaatttctcaatttattaaattatgttaatgtttaacagGATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCCCCAAACTGAGAGCTATTGGGGAAATGTTAACCCAATAG
||  | | |     | |  || |||| |  |||        | ||   |||| ||  | || |||| ||    ||   |||||| ||| | |||||||| || ||||| ||||| ||||| ||||||||||| |||| ||||  ||| ||||| |||||||| || || |
gtcagtgttcatcatgccattgattcttccaacgcctcatgtgaaaaactcagttactgaatttatttttgaatt--gcagGATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCCTCAAATTGAGGCCTACTGGGGCAATGTTAATCCGATTG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 12
gtttgggatttgacttcattttattcctttaaccaggatcataaatttctcaatttattaaattatgttaatgtttaacagGATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCCCCAAACTGAGAGCTATTGGGGAAATGTTAACCCAATAG
||  | | |     | |  || |||| |  | |        | ||   |||| ||  | || |||| ||    ||   |||||| ||| | |||||||| || ||||| ||||| ||||| ||||||||||| |||| ||||  ||| ||||| |||||||| || || |
gtcagtgttcatcatgccattgattcttccagcgcctcatgtgaaaaactcagttactgaatttatttttgaatt--gcagGATTTTGTTGACATCAACCTCTGAAGTTTATGGTGATCCACTTGAGCATCCTCAAATTGAGGCCTACTGGGGCAATGTTAATCCGATTG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA13G40960.1 (Glycine max), 3'ss of exon 7
gtttgggatttgacttcattttattcctttaaccaggatcataaatttctcaatttattaaattatgttaatgtttaacagGATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCCCCAAACTGAGAGCTATTGGGGAAATGTTAACCCAATAG
  ||||||| |    | |    ||    | |||      ||| | ||  ||  || ||||  |    ||  |  || ||||||| |||||||||||||||||||| |||||||| |||||||||| |||||||||| |||| || |||||||| ||||||||||| || |
-gttgggatattttcttaaacaataatctcaactgctgccattagttggtc--ttaattagttctaatt--ttattgacagGATTTTGCTTACATCAACTTCAGAGGTATATGGGGATCCTCTTGTGCATCCCCAACCTGAAAGTTATTGGGGCAATGTTAACCCTATTG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA15G04500.2 (Glycine max), 3'ss of exon 7
gtttgggatttgacttcattttattcctttaaccaggatcataaatttctcaatttattaaattatgttaatgtttaacagGATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCCCCAAACTGAGAGCTATTGGGGAAATGTTAACCCAATAG
  ||||||| |    | |    ||   || |||      ||| | ||  ||  || ||||  ||   ||  |  ||  ||||||  ||||||||||||||||||| |||||||| |||||||||| |||||||||| |||| || |||||||| ||||||||||| || |
-gttgggatattttcttaaacaataatttcaactgctgccattagttggtc--ttaattagtttgaatt--ttattggcagGATTCTGCTTACATCAACTTCAGAGGTATATGGGGATCCTCTTGTGCATCCCCAACCTGAAAGTTATTGGGGCAATGTTAACCCTATTG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 5
-----------gtttgggatttgacttcattttattcctttaaccaggatcataaatttctcaatttattaaattatgttaatgtttaacagGATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCCCCAAACTGAGAGCTATTGGGGAAATGTTAACCCAATAG
            ||| | | |  ||   | || ||  | |  ||||  | |||     | |  ||||   || || |  |  || || ||||||| ||||||||||| ||||||||||||||||| || |||||||||||||| ||| | || ||||||||||| |||||||| || || |
gttatctctctttttcgaaat--acaaaagttgatagcctataccattaccat----ctgttgattttacaagttgtaattttgattgacagGATTTTGCTTACATCTACTTCAGAAGTATATGGGGACCCTCTTGAGCATCCACAACCAGAAAGCTATTGGGGCAATGTTAATCCTATTG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 6
gtttgggatttgacttcattttatt-cctttaaccaggatcataa--atttctcaatttattaaattatgttaatgtttaacagGATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCCCCAAACTGAGAGCTATTGGGGAAATGTTAACCCAATAG
|||     |||  ||  ||   |       | | |   |||||    ||   |  || |   || |  |  |  || || ||||||| ||||||||||| ||||||||||||||||| || ||||||| |||||| ||| | || ||||||||||| ||||| ||||| || |
gttatctctttttctaaatacaaaagtggatgatctacatcattgccatccgtgtatcttacaagtagtaattttgattgacagGATTTTGCTTACATCTACTTCAGAAGTATATGGGGACCCTCTTGTGCATCCACAACCAGAAAGCTATTGGGGCAATGTAAACCCCATTG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA12G06990.1 (Glycine max), 3'ss of exon 6
-------------gtttgggatttga---cttcattttattcctttaaccaggatcataaatttctcaatttattaaattatgttaatgtt----taacagGATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCCCCAAACTGAGAGCTATTGGGGAAATGTTAACCCAATAG
              ||||| |  |||    ||||  || |  | | |    |  |      ||| ||   || |||   |  |||  | ||    |  |||||| || || |||||||| || || |||||||| |||||||||| |||||||||| |||| ||||||||||| ||||| ||||| || |
gttggtaaattgtctttggaaaatgataatttcagcttctatcatcagttggtctttattctttttcttcttgttagtcttagttcttattttattggcagGATTTTACTCACATCAACATCTGAGGTATATGGGGATCCTCTTGTGCATCCCCAACCTGAAAGCTATTGGGGCAATGTGAACCCTATTG

upper sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 5
gtttgggatttga---cttcattttattcctttaaccaggatcataaatttctcaatttattaaattatgttaatgtttaacagGATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCCCCAAACTGAGAGCTATTGGGGAAATGTTAACCCAATAG
|||||  |  |||   | || ||||||| |||  ||     |      |  |     | | ||| |||   |  |     ||||||| |||||||| ||||| || || |||||||||||||||||    ||||||||  |||||||||||||||||||||| |||||||| |
gtttgcaaaatgataccctctttttattactt--acttctgttgatcttcgcctttgtgactaacttactcttctaccggacagGATTTTGCTTACCTCAACCTCGGAGGTATATGGAGATCCTCTCATTCATCCCCAGCCTGAGAGCTATTGGGGAAATGTCAACCCAATTG

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|33409748|gb|CF215375.1|CF215375
EST:     GTCATTGGTACACTGAATATGCTGGGACTTGCCAAACGAGTTGGAGCAAG                         GATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCC
genomic: GTCATTGGTACACTGAATATGCTGGGACTTGCCAAACGAGTTGGAGCAAGgtttgggatt ... tgtttaacagGATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCC
EST: gi|33408202|gb|CF213829.1|CF213829
EST:     GTCATTGGTACACTGAATATGCTGGGACTTGCCAAACGAGTTGGAGCAAG                         GATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCC
genomic: GTCATTGGTACACTGAATATGCTGGGACTTGCCAAACGAGTTGGAGCAAGgtttgggatt ... tgtttaacagGATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCC
EST: gi|71879035|gb|DT028090.1|DT028090
EST:     GTCATTGGTACACTGAATATGCTGGGACTTGCCAAACGAGTTGGAGCAAG                         GATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCC
genomic: GTCATTGGTACACTGAATATGCTGGGACTTGCCAAACGAGTTGGAGCAAGgtttgggatt ... tgtttaacagGATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCC
EST: gi|71879209|gb|DT028264.1|DT028264
EST:     GTCATTGGTACACTGAATATGCTGGGACTTGCCAAACGAGTTGGAGCAAG                         GATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCC
genomic: GTCATTGGTACACTGAATATGCTGGGACTTGCCAAACGAGTTGGAGCAAGgtttgggatt ... tgtttaacagGATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCC
EST: gi|33407209|gb|CF212836.1|CF212836
EST:     GTCATTGGTACACTGAATATGCTGGGACTTGCCAAACGAGTTGGAGCAAG                         GATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCC
genomic: GTCATTGGTACACTGAATATGCTGGGACTTGCCAAACGAGTTGGAGCAAGgtttgggatt ... tgtttaacagGATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCC
EST: gi|71881039|gb|DT030094.1|DT030094
EST:     GTCATTGGTACACTGAATATGCTGGGACTTGCCAAACGAGTTGGAGCAAG                         GATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCC
genomic: GTCATTGGTACACTGAATATGCTGGGACTTGCCAAACGAGTTGGAGCAAGgtttgggatt ... tgtttaacagGATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCC
EST: gi|30297461|gb|CB974255.1|CB974255
EST:     GTCATTGGTACACTGAATATGCTGGGACTTGCCAAACGAGTTGGAGCAAG                         GATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCC
genomic: GTCATTGGTACACTGAATATGCTGGGACTTGCCAAACGAGTTGGAGCAAGgtttgggatt ... tgtttaacagGATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCC
EST: gi|33407983|gb|CF213610.1|CF213610
EST:     GTCATTGGTACACTGAATATGCTGGGACTTGCCAAACGAGTTGGAGCAAG                         GATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCC
genomic: GTCATTGGTACACTGAATATGCTGGGACTTGCCAAACGAGTTGGAGCAAGgtttgggatt ... tgtttaacagGATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCC
EST: gi|56408375|gb|CX016627.1|CX016627
EST:     ACTGAATATGCTGGGACTTGCCAAACGAGTTGGAGCAAG                         GATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCC
genomic: ACTGAATATGCTGGGACTTGCCAAACGAGTTGGAGCAAGgtttgggatt ... tgtttaacagGATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCC
EST: gi|33406260|gb|CF211887.1|CF211887
EST:     GTCATTGGTACACTGAATATGCTGGGACTTGCCAAACGAGTTGGAGCAAG                         GATATTGCTTACATCAACTTCAGCAGTATATGGAGATCCTCTTGAGCATCC
genomic: GTCATTGGTACACTGAATATGCTGGGACTTGCCAAACGAGTTGGAGCAAGgtttgggatt ... tgtttaacagGATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttaaccaggatcataaatttctcaatttattaaattatgttaatgtttaacagGATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCCCCAAACTGAGAGCTATTGGGGAAATGTTAACCCAATAG
                                       tgttaat  putative branch site (score: 3)
              ataaatttctcaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgggatttgacttcattttattcctttaaccaggatcataaatttctcaatttattaaattatgttaatgtttaacagGATATTGCTTACATCAACTTCAGAAGTATATGGAGATCCTCTTGAGCATCCCCAAACTGAGAGCTATTGGGGAAATGTTAACCCAATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT