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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcaaaactaaaatccatcctcagattgtaggagcaaggaggagttttacttgtataacaaacttgctgaaaaaattctgaaccttgtaatgttggacagGTTTTGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTACTATGGAAAGAGTTCCCCCTTTCGGTCTCTGAGAACAGAAAATCTGAAAT

Basic information

species Vitis vinifera
transcript Vv04s0023g03020.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g03020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os10g36760.1 (Oryza sativa), 3'ss of exon 2
------------------------------------------------------------------ctcaaaactaaaatccatcctcagattgtaggagcaaggaggagttttacttgtataacaaacttgctgaaaaaattctgaaccttgtaatgttggacagGTTTTGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTACTATGGAAAGAGTTCCCCCTTTCGGTCTCTGAGAACAGAAAATCTGAAAT
                                                                   |   |  |   ||| || ||   |   || |   |      |  || || ||| |    ||| | |  |    ||  |     | || |||| |   ||||  |||||||||| ||||| || || ||||| || | ||||||||| ||||| |||||||||||||| |||  |  | ||| ||| |||||||| |  |
gtgagtatgctcaagtatatagttgtacagtttccaactggagcaattagacattatttgttacacattctaggtgtgatctatactttaagcatatggttatatttta-cttcacctgttttgataacatacacatgggatggtttgtgt-gtgatgt-gtgtagGTGATGGCAAAGAAGTTTGGTGCGGCAGTGGTCTCCCCTGAGCATCGGTACTACGGAAAGAGTTCCCCTTTTGAGAGTTTGACAACGGAAAATCTAAGGT

upper sequence: Vv04s0023g03020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G031572_T01 (Zea mays), 3'ss of exon 2
---------------------------------------------------ctcaaaa--ctaaaatccatcctcagattgtaggagcaaggaggagtt-ttacttgtataacaaacttgctgaaaaaattctgaaccttg--taatgt-------tggacagGTTT-----TGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTACTATGGAAAGAGTTCCCCCTTTCGGTCTCTGAGAACAGAAAATCTGAAAT
                                                    |  | |   || | | | | |||  | | |||     |     | |  | | ||    ||| |  |   || || || | ||    ||   |||  |       ||||  | ||      |||||||||||||||| || ||  ||||||||| ||||||||| ||||||||||||||||| || |||     | ||| ||||||||||||  | |
gtaagtttaatgagtatatagacatgcagtcacatatttttagttaaatgattggacatcttatactgcttactctaactctagacatgattcatattcataatttactcaaccatttgtgtgcaacaactttggctgttagataacatatacatatggatggattagGTGGTGGCAAAGAAATTTGGTGCTGCATTGGTTTCTCCTGAGCATCGATACTATGGAAAGAGTTCTCCTTTTAACAGTTTGACAACAGAAAATCTACAGT

upper sequence: Vv04s0023g03020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA16G24270.1 (Glycine max), 3'ss of exon 3
ctcaaaactaaaatccatcctcagattgtaggagcaaggaggag--ttttacttgtataacaaacttgctgaaa--aaattctgaaccttgtaatgt----tggacagGTTTTGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTACTATGGAAAGAGTTCCCCCTTTCGGTCTCTGAGAACAGAAAATCTGAAAT
        ||||     |    ||  | |   |  || || | |  | ||      | || | | |     |||  || |||    | || |  | |    |  | ||||  |||||||||| |||||||||||| ||||| ||||||| |||||||||||||||||||||||||| |||   ||| ||   ||||||||| ||||||
--------taaagagtgttgctagcatttctcaataatgatgtggctcttgtcaagaaaagataataatataaactaatttccatgcgttattttattttctctatagGTACTGGCAAAGAAGTTTGGAGCAGCTATGGTTACTCTTGAACATCGCTACTATGGAAAGAGTTCCCCATTTAATTCTTTGGAGACAGAAAATTTGAAAT

upper sequence: Vv04s0023g03020.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA16G24290.1 (Glycine max), 3'ss of exon 2
-ctcaaaactaaaatccatcctcagattgtaggagcaaggaggagttttacttgtataacaaacttgctgaaaaaattctgaaccttgtaatgttggacagGTTTTGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTACTATGGAAAGAGTTCCCCCTTTCGGTCTCTGAGAACAGAAAATCTGAAAT
  |      |    ||||     ||| ||  |  ||      ||     |      ||| |    |    | ||| |||    ||||||  | |   | ||||  |||||||||| |||||||||||| ||||| ||||||| ||||||||||| ||||||||| | || |||   ||| ||   ||||||||| ||||||
atttctctttttgttccagtaaaagaatgatgtggcttttgtgaagaaaaacctagtaatagtaatataaataaatttccatgccttgttttatca-atagGTACTGGCAAAGAAGTTTGGAGCAGCTATGGTTACTCTTGAACATCGCTACTACGGAAAGAGTACTCCATTTAATTCTTTGGAGACAGAAAATTTGAAAT

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|71855538|gb|DT004593.1|DT004593
EST:     AGATATGTGGAGAAGCTTCATGCGATGGGATACCCAATGATTATATCAGT                         GTTTTGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTAC
genomic: AGATATGTGGAGAAGCTTCATGCGATGGGATACCCAATGATTATATCAGTgtaagcaata ... tgttggacagGTTTTGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTAC
EST: gi|71888773|gb|DT037828.1|DT037828
EST:     GCGATGGGATACCCAATGATTATATCAGT                         GTTTTGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTAC
genomic: GCGATGGGATACCCAATGATTATATCAGTgtaagcaata ... tgttggacagGTTTTGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTAC
EST: gi|161714295|gb|FC063541.1|FC063541
EST:     AGATATGTGGAGAAGCTTCATGCGATGGGATACCCAATGATTATATCAGT                         GTTTTGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTAC
genomic: AGATATGTGGAGAAGCTTCATGCGATGGGATACCCAATGATTATATCAGTgtaagcaata ... tgttggacagGTTTTGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTAC
EST: gi|161716540|gb|FC065231.1|FC065231
EST:     AGATATGTGGAGAAGCTTCATGCGATGGGATACCCAATGATTATATCAGT                         GTTTTGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTAC
genomic: AGATATGTGGAGAAGCTTCATGCGATGGGATACCCAATGATTATATCAGTgtaagcaata ... tgttggacagGTTTTGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTAC
EST: gi|110703482|gb|EE080367.1|EE080367
EST:     AGATATGTGGAGAAGCTTCATGCGATGGGATACCCAATGATTATATCAGT                         GTTTTGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTAC
genomic: AGATATGTGGAGAAGCTTCATGCGATGGGATACCCAATGATTATATCAGTgtaagcaata ... tgttggacagGTTTTGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTAC
EST: gi|161714750|gb|FC063922.1|FC063922
EST:     AGATATGTGGAGAAGCTTCATGCGATGGGATACCCAATGATTATATCAGT                         GTTTTGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTAC
genomic: AGATATGTGGAGAAGCTTCATGCGATGGGATACCCAATGATTATATCAGTgtaagcaata ... tgttggacagGTTTTGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTAC
EST: gi|71885650|gb|DT034705.1|DT034705
EST:     GCGATGGGATACCCAATGATTATATCAGT                         GTTTTGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTAC
genomic: GCGATGGGATACCCAATGATTATATCAGTgtaagcaata ... tgttggacagGTTTTGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTAC
EST: gi|110710992|gb|EE087681.1|EE087681
EST:     GGAGAAGCTTCATGCGATGGGATACCCAATGATTATATCAGT                         GTTTTGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTAC
genomic: GGAGAAGCTTCATGCGATGGGATACCCAATGATTATATCAGTgtaagcaata ... tgttggacagGTTTTGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTAC
EST: gi|110719340|gb|EE097205.1|EE097205
EST:     AGATATGTGGAGAAGCTTCATGCGATGGGATACCCAATGATTATATCAGT                         GTTTTGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTAC
genomic: AGATATGTGGAGAAGCTTCATGCGATGGGATACCCAATGATTATATCAGTgtaagcaata ... tgttggacagGTTTTGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTAC
EST: gi|71882638|gb|DT031693.1|DT031693
EST:     GCGATGGGATACCCAATGATTATATCAGT                         GTTTTGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTAC
genomic: GCGATGGGATACCCAATGATTATATCAGTgtaagcaata ... tgttggacagGTTTTGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTAC
EST: gi|71886539|gb|DT035594.1|DT035594
EST:     GCGATGGGATACCCAATGATTATATCAGT                         GTTTTGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTAC
genomic: GCGATGGGATACCCAATGATTATATCAGTgtaagcaata ... tgttggacagGTTTTGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTAC
EST: gi|71887889|gb|DT036944.1|DT036944
EST:     GCGATGGGATACCCAATGATTATATCAGT                         GTTTTGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTAC
genomic: GCGATGGGATACCCAATGATTATATCAGTgtaagcaata ... tgttggacagGTTTTGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTAC
EST: gi|110367557|gb|EC931495.1|EC931495
EST:     AGATATGTGGAGAAGCTTCATGCGATGGGATACCCAATGATTATATCAGT                         GTTTTGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTAC
genomic: AGATATGTGGAGAAGCTTCATGCGATGGGATACCCAATGATTATATCAGTgtaagcaata ... tgttggacagGTTTTGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttacttgtataacaaacttgctgaaaaaattctgaaccttgtaatgttggacagGTTTTGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTACTATGGAAAGAGTTCCCCCTTTCGGTCTCTGAGAACAGAAAATCTGAAAT
       gtataac  putative branch site (score: 3)
                      tgaaaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcaaaactaaaatccatcctcagattgtaggagcaaggaggagttttacttgtataacaaacttgctgaaaaaattctgaaccttgtaatgttggacagGTTTTGGCAAAGAAATTTGGAGCAGCTGTGGTTTCTCTTGAGCATCGCTACTATGGAAAGAGTTCCCCCTTTCGGTCTCTGAGAACAGAAAATCTGAAAT

- - aaactaa
- - - - - - - ccatcct
- - - - - - - - - - - - - - - - -gcaagga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aacaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgaacc