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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgcgaccaattgagctaagggcatgtttagctaatacaatgtcactatagatacataaaatggagtcatcaattgacgggcgtgtgtgttctcatgcagGATGCTGCTGCATGGCTTGAATATTTTGAATCAAAAGCTTTAGAGCAGCAAGAAGCAGCAAGAAATGGAACTCCAAAGCCAGATGCATCTATTGCAAGCA

Basic information

species Vitis vinifera
transcript Vv09s0002g07530.t01
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g07530.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: LOC_Os04g55230.1 (Oryza sativa), 3'ss of exon 20
atgcgaccaattgagctaagggcatgtttagctaatacaatgtc-actatagatacataaaatggagtcatcaattgacgggcgtgtgtgttctcat---gcagGATGCTGCTGCATGGCTTGAATATTTTGAATCAAAAGCTTTAGAGCAGCAAGAAGCAGCAAGAAATGGAACTCCAAAGCCAGATGCATCTATTGCAAGCA
              | |         || |    || ||||| | | |  | |||| |   |||   || |  | |    | | ||    || || |   |||||||||||||||||||||||| |||||||| |||||||| ||||| || ||||| || ||  |||  || |  ||||| || ||  |||||||||||||||
--------------gttttttttcccttcaaaatatgcaatgacgagtccaaatac-tgctatgttctcttggactattagacatgataattttcctgctgcagGATGCTGCTGCATGGCTTGAGTATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCCGCCCGAAGGGGCATCCCAAAACCTGACTCATCTATTGCAAGCA

upper sequence: Vv09s0002g07530.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GRMZM5G892758_T01 (Zea mays), 3'ss of exon 3
atgcgaccaattgagctaagggcatgtttagctaatacaatgtcactatagatacataaaatggagtcatcaattgacgggcgtgtgtgttctcatgcagGATGCTGCTGCATGGCTTGAATATTTTGAATCAAAAGCTTTAGAGCAGCAAGAAGCAGCAAGAAATGGAACTCCAAAGCCAGATGCATCTATTGCAAGCA
                        |  | |||  | | ||    |  ||| |||| |   |||   || | |||| ||       |   ||   ||||||||||||||||||||||| ||||||||||| |||||||| ||||| || ||||| || ||  |||  || |  ||||| || ||| ||||||||||||| |
-----------------gttctttttctcagcgtacaaaaacataggatatatac-tccgatgttctcttgaattaacacat---tacttttcgatgcagGATGCTGCTGCATGGCTAGAATATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCTGCCCGAAGAGGCATGCCAAAACCTGATTCATCTATTGCAAGTA

upper sequence: Vv09s0002g07530.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GRMZM2G086030_T01 (Zea mays), 3'ss of exon 20
atgcgaccaattgagctaagggcatgtttagctaataca-atgtcactatagatacataaaatggagtcatcaattga-cgggcgtgtgtgttctcatgcagGATGCTGCTGCATGGCTTGAATATTTTGAATCAAAAGCTTTAGAGCAGCAAGAAGCAGCAAGAAATGGAACTCCAAAGCCAGATGCATCTATTGCAAGCA
                        | |||    |   || ||   | |||||  | ||| | |    || ||  ||||     |   |   |  |  |||||||||||||||||||||| ||||||||||| |||||||| ||||| || ||||| || ||  |||  || |  ||||| || ||| ||||||||||||| |
----------------------gttcttttttcagggcatataaaaatatagg-atatatactctgatcttctcttgaattaacacattattgttgttgcagGATGCTGCTGCATGGCTAGAATATTTTGAGTCAAAAGCATTAGAACAACAAGAGGCGGCTCGAAGAGGCATGCCAAAACCTGATTCATCTATTGCAAGTA

upper sequence: Vv09s0002g07530.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA08G22850.1 (Glycine max), 3'ss of exon 19
------------------------------atgcgaccaa-----ttgagctaagggcatgtttagc--taatacaatgtcactatagatacataaaat-----ggagtcatcaattg-acgggcgtgtgtgttctcatgcagGATGCTGCTGCATGGCTTGAATATTTTGAATCAAAAGCTTTAGAGCAGCAAGAAGCAGCAAGAAATGGAACTCCAAAGCCAGATGCATCTATTGCAAGCA
                              || || | ||     |||  ||| |       |  ||  |   | | | |    || |||| ||  | |        || | || ||  | |   || | |   |  |||||||||||||||||||||||||| |||||||||||||||||  ||||||||||||||||||| | |||||||||||||||||| |||||||| |||||||| |
gtcatttccttttctgatagtagtgctagaatacgtcaaagaatattggtctaggattgaactacgcattggcaaactatggggattgatagattgatttgtttaatgttaccattttcatgaaagttttttccccaatgcagGATGCTGCTGCATGGCTTGAGTATTTTGAATCAAAAGCCCTAGAGCAGCAAGAAGCAGCTAAAAATGGAACTCCAAAGCCTGATGCATCCATTGCAAGTA

upper sequence: Vv09s0002g07530.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA07G03250.1 (Glycine max), 3'ss of exon 21
----------------------atgcgaccaat-tgagctaagggcatgtttagc--taatacaatgtcactatagatacataaaatgga-----gtcatcaattgacgggcg----tgtgtgttctcatgcagGATGCTGCTGCATGGCTTGAATATTTTGAATCAAAAGCTTTAGAGCAGCAAGAAGCAGCAAGAAATGGAACTCCAAAGCCAGATGCATCTATTGCAAGCA
                       | | |  | | ||  ||| |       | |||  |   | ||| |     | |||| ||    | |      || | || ||  |  |      | | | |||  |||||||||||||| || ||||||||||||||||||||||||||  ||||||||||||||||| | | |||||||||||||||||| |||||||| |||||||| |
gtcatttccttttctgattgtagtactagaattctggtctaggattgaactaagcattggcaaaatatgggggttgatagatggttttggctaatgttaccatttttcatgaaaggtttttttttccaatgcagGATGCTGCCGCGTGGCTTGAATATTTTGAATCAAAAGCCATAGAGCAGCAAGAAGCAACTAAAAATGGAACTCCAAAGCCTGATGCATCCATTGCAAGTA

upper sequence: Vv09s0002g07530.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: AT1G15290.1 (Arabidopsis thaliana), 3'ss of exon 18
---------atgcgaccaattgagctaagggcatgttt--agctaatacaa---tgtcacta-tagatacataaaatgga-gtcatcaatt----gacgggcgtgtgtgtt------------ctcatgcagGATGCTGCTGCATGGCTTGAATATTTTGAATCAAAAGCTTTAGAGCAGCAAGAAGCAGCAAGAAATGGAACTCCAAAGCCAGATGCATCTATTGCAAGCA
          |||  |   || |        ||  | |    | ||||  |   | | ||||  | |   | ||| || | ||  | || |    |||   | ||| ||||            |||   |||||||||||||||||||| |||||||||||||||| |||  |||||||||| |||||||   |||||||||  |||||||| ||||| || || || ||||
gtgattgatttgcttctggttcattcgcatacaaatctcagacgaatattaatttcttactagcaaagtaacaaagtgaacgttttgaactctgagacatacatgtttgttttctccatttgtctctcacagGATGCTGCTGCATGGCTCGAATATTTTGAATCAAGAGCCATAGAGCAGCAGGAAGCAGGCCGAAATGGAATCCCAAAGCCTGATGCTTCCATCGCGAGCA

upper sequence: Vv09s0002g07530.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: EFJ26424 (Selaginella moellendorffii), 3'ss of exon 20
atgcgaccaattgagctaagggcatgtttagctaatacaatgtcactatagatacataaaatggagtcatcaattgacgggcgtgtgtgttctcatgcagGATGCTGCTGCATGGCTTGAATATTTTGAATCAAAAGCTTTAGAGCAGCAAGAAGCAGCAAGAAATGGAACTCCAAAGCCAGATGCATCTATTGCAAGCA
                                   ||| |  | | |   ||    |  | |    |  || |||        | | | |  | ||| ||||||| ||||| ||||| || ||||| || ||||||||| ||||||||||||| || ||| ||| |||  | ||||| |||||||| || || || ||||
----------------------------------gtactaacttatttgcga---gtgcactattttattcgatttgttc-tttttctttcattatgtagGATGCAGCTGCTTGGCTGGACTATTTCGACTCAAAAGCTGTAGAGCAGCAAGAGGCTGCACGAACTGGGGCACCAAAACCAGATGCTTCAATCGCCAGCA

upper sequence: Vv09s0002g07530.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: EFJ26734 (Selaginella moellendorffii), 3'ss of exon 20
atgcgaccaattgagctaagggcatgtttagctaatacaatgtcactatagatacataaaatggagtcatcaattgacgggcgtgtgtgttctcatgcagGATGCTGCTGCATGGCTTGAATATTTTGAATCAAAAGCTTTAGAGCAGCAAGAAGCAGCAAGAAATGGAACTCCAAAGCCAGATGCATCTATTGCAAGCA
                                   ||| |  | | |   ||    |    |    |  || |||        |   | |  | ||| ||||||| ||||| ||||| || ||||| || ||||||||| ||||||||||||| || ||| ||| |||  | ||||| |||||||| || || || ||||
----------------------------------gtactaacttatttgcga---gtgcgctattttattcgatttgttctttttcttttcattatgtagGATGCAGCTGCTTGGCTGGACTATTTCGACTCAAAAGCTGTAGAGCAGCAAGAGGCTGCACGAACTGGGGCACCAAAACCAGATGCTTCAATCGCCAGCA

upper sequence: Vv09s0002g07530.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: EFJ08067 (Selaginella moellendorffii), 3'ss of exon 20
atgcgaccaattgagctaagggcatgtttagctaatacaatgtcactatagatacataaaatggagtcatcaattgacgggcgtgtgtgttctcatgcagGATGCTGCTGCATGGCTTGAATATTTTGAATCAAAAGCTTTAGAGCAGCAAGAAGCAGCAAGAAATGGAACTCCAAAGCCAGATGCATCTATTGCAAGCA
                              | | || | |  || || | |||   | |||   ||||    ||  | |    | ||||||||  | |||||||||||||| |||||||| |||||||| || |||||  | ||||| ||||||||  |||| |  ||  | || ||||| ||| | ||| |||||||||
------------------------------gttgat-cgac-tccctcttgat-tgtgaaac--agtctctcatgcatga---tatgtgttctt-tacagGATGCTGCTGCCTGGCTTGATTATTTTGATTCTAAAGCAGTTGAGCAACAAGAAGCCACAAGGACAGGGGCACCTAAGCCTGATCCTTCTGTTGCAAGCA

upper sequence: Vv09s0002g07530.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: EFJ24726 (Selaginella moellendorffii), 3'ss of exon 20
atgcgaccaattgagctaagggcatgtttagctaatacaatgtcactatagatacataaaatggagtcatcaattgacgggcgtgtgtgttctcatgcagGATGCTGCTGCATGGCTTGAATATTTTGAATCAAAAGCTTTAGAGCAGCAAGAAGCAGCAAGAAATGGAACTCCAAAGCCAGATGCATCTATTGCAAGCA
                              | | || | |  || || | |||   | |||   ||||    ||  | |    | ||||||||  | |||||||||||||| |||||||| |||||||| || |||||  | ||||||||||||||  |||| |  ||  | || ||||| ||| | ||| |||||||||
------------------------------gttgat-cgac-tccctcttgat-tgtgaaac--agtctctcatgcatga---tatgtgttctt-tacagGATGCTGCTGCCTGGCTTGATTATTTTGATTCTAAAGCAGTTGAGCAGCAAGAAGCCACAAGGACAGGGGCACCTAAGCCTGATCCTTCTGTTGCAAGCA

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|110698822|gb|EE076760.1|EE076760
EST:     CACTCCAGATACTCCAAGCAAAACTTGGGCCAGAGGATCTCCGTACTCAG                         GATGCTGCTGCATGGCTTGAATATTTTGAATCAAAAGCTTTAGAGCAGCAA
genomic: CACTCCAGATACTCCAAGCAAAACTTGGGCCAGAGGATCTCCGTACTCAGgtaccaagat ... tctcatgcagGATGCTGCTGCATGGCTTGAATATTTTGAATCAAAAGCTTTAGAGCAGCAA
EST: gi|110698721|gb|EE076539.1|EE076539
EST:     GCCAGAGTGTTCTCCGTACTCAG                         GATGCTGCTGCATGGCTTGAATATTTTGAATCAAAAGCTTTAGAGCAGCAA
genomic: GCCAGAG-GATCTCCGTACTCAGgtaccaagat ... tctcatgcagGATGCTGCTGCATGGCTTGAATATTTTGAATCAAAAGCTTTAGAGCAGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatagatacataaaatggagtcatcaattgacgggcgtgtgtgttctcatgcagGATGCTGCTGCATGGCTTGAATATTTTGAATCAAAAGCTTTAGAGCAGCAAGAAGCAGCAAGAAATGGAACTCCAAAGCCAGATGCATCTATTGCAAGCA
                          aattgac  putative branch site (score: 3)
                                          tgttctc  putative PPT
      atacataaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgcgaccaattgagctaagggcatgtttagctaatacaatgtcactatagatacataaaatggagtcatcaattgacgggcgtgtgtgttctcatgcagGATGCTGCTGCATGGCTTGAATATTTTGAATCAAAAGCTTTAGAGCAGCAAGAAGCAGCAAGAAATGGAACTCCAAAGCCAGATGCATCTATTGCAAGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- -cgaccaa
- - - - - - - - - - -gcatgtt
- - - - - - - - - - - - - - - - - - -caatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - -acataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggcgtg