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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattatcaattttttttttttttgacaacaagtttagattgttttgactgattcgtggtttccgatctctttctaatgttctcctttgtatcatctccagGTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTACCCCTTTTCCTCTACAATTACTCCACCCACCAGCTTCATGGAGTTTTTGA

Basic information

species Vitis vinifera
transcript Vv02s0025g01720.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g01720.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os01g36950.3 (Oryza sativa), 3'ss of exon 1
-------------------------aattatcaattttttttttttttgacaac-aagtttagattgtttt--gactgattcgtggtttccgatctctttctaatgttctcct-------ttgtatcatctccagGTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTACCCCTTTTCCTCTACAATTACTCCACCCACCAGCTTCATGGAGTTTTTGA
                          || || ||    |       |||  |    |      ||| || |   ||  |    |  | ||| ||    ||  ||  ||||| |       | ||      | ||||  | ||  | || ||| | ||||||||| |||| || |  |||||  | ||||| ||||||||||| ||||||||||||||||| || ||  | || ||
gtaagcataaccaacctataaattcgatgataaaaccatccaagaattggtacttgaaccctaattattcttgaaccaagaaattatgtcccataaaatt--aagtttctcatgaacaaatcgtgcttgatgcagGGCTTCCATCGAGATACAGGGATTCAGTGAGGGCGATCAGGCCAGGGCTGCCCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGA

upper sequence: Vv02s0025g01720.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AC207342.3_FGT008 (Zea mays), 3'ss of exon 1
--------------------------------------------------aattatcaattttttttttttttgacaacaagtttagattgtt--ttgactgat--------tcgtggtttccgatct---ctttctaatgttctcctttgtatcatctccagGTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTACCCCTTTTCCTCTACAATTACTCCACCCACCAGCTTCATGGAGTTTTTGA
                                                    |    |||   |        ||| || |||      |||||  |||| ||||         ||   |   | | |    ||   | ||  | |    ||       | ||||  ||||  | |||||| | || || |||||||| ||   ||| ||  | ||||| ||||||||||| ||||||||||||||||| || ||  | ||  |
gtgagccactgaccgcgcgcgcaggcacaagaaccgtatcgtttcgtttctgtctgaaatagctagggcagctgaaaagaagcgatatttgttgattgattgatgatgaacaccggaataaaccagcagagctgattgattgtgtttgatggggtggatgcagGGCTGCCGTCGAGGTACAGGGACTCGGTGCGGGCCATCCGCCCGGGGCTGCCCCTCTTCCTCTACAACTACTCCACCCACCAGCTGCACGGCATCTTCAA

upper sequence: Vv02s0025g01720.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM5G860590_T01 (Zea mays), 3'ss of exon 1
--------------------------------------aattatcaattttttttttttttgacaacaagtttag----attgtttt---gactgattcgt--ggtttccgatctctttctaatgttctcc-tttgtatcatctccagGTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTACCCCTTTTCCTCTACAATTACTCCACCCACCAGCTTCATGGAGTTTTTGA
                                       ||      ||   |   | ||  |  | | | |||     || |  |    ||  || ||       ||  ||| | |||       ||||  |   |||   || ||||  ||||  |||||||| | ||||| ||| |||| || |  || ||  | ||||| ||||||||||| ||||||||||||||||| || ||  | |||||
gtaatatctctttcattttcctgtccattcattgatttgatcgaacgttacgtacatattccagcataggattaaccgaatcggatccaagatcgactcccccaagttgtgattttttttcgtctctctcgatacatatt-cctgcagGGCTGCCGTCCAGGTACAGGGATTCTGTGAGGGCCATCAGGCCCGGCCTGCCCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTTGA

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|110726776|gb|EE102853.1|EE102853
EST:     TGTCTGCAACAACGATACTATGCAAGAGAATCTCAAGAGACAGCTCTTTG                         GTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTAC
genomic: TGTCTGCAACAACGATACTATGCAAGAGAATCTCAAGAGACAGCTCTTTGgtaagccccc ... tcatctccagGTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTAC
EST: gi|29783652|gb|CB349968.2|CB349968
EST:     GCAAGAGAATCTCAAGAGACAGCTCTTTG                         GTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTAC
genomic: GCAAGAGAATCTCAAGAGACAGCTCTTTGgtaagccccc ... tcatctccagGTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTAC
EST: gi|110406653|gb|EC972233.1|EC972233
EST:     TGTCTGCAACAACGATACTATGCAAGAGAATCTCAAGAGACAGCTCTTTG                         GTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTAC
genomic: TGTCTGCAACAACGATACTATGCAAGAGAATCTCAAGAGACAGCTCTTTGgtaagccccc ... tcatctccagGTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTAC
EST: gi|352777407|gb|FQ474041.1|FQ474041
EST:     AGAGAATCTCAAGAGACAGCTCTTTG                         GTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTAC
genomic: AGAGAATCTCAAGAGACAGCTCTTTGgtaagccccc ... tcatctccagGTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTAC
EST: gi|34547922|gb|CF516154.1|CF516154
EST:     CTGCAACAACGATACTATGCAAGAGAATCTCAAGAGACAGCTCTTTG                         GTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTAC
genomic: CTGCAACAACGATACTATGCAAGAGAATCTCAAGAGACAGCTCTTTGgtaagccccc ... tcatctccagGTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTAC
EST: gi|30137123|gb|CB922461.1|CB922461
EST:     AGAGACAGCTCTTTG                         GTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTAC
genomic: AGAGACAGCTCTTTGgtaagccccc ... tcatctccagGTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTAC
EST: gi|352768383|gb|FQ469558.1|FQ469558
EST:     GAATCTCAAGAGACAGCTCTTTG                         GTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTAC
genomic: GAATCTCAAGAGACAGCTCTTTGgtaagccccc ... tcatctccagGTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTAC
EST: gi|110726023|gb|EE103098.1|EE103098
EST:     TGTCTGCAACAACGATACTATGCAAGAGAATCTCAAGAGACAGCTCTTTG                         GTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTAC
genomic: TGTCTGCAACAACGATACTATGCAAGAGAATCTCAAGAGACAGCTCTTTGgtaagccccc ... tcatctccagGTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTAC
EST: gi|32458755|gb|CD799929.1|CD799929
EST:     CAAGAGACAGCTCTTTG                         GTTTGCCTCCCAGAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATT
genomic: CAAGAGACAGCTCTTTGgtaagccccc ... tcatctccagGTTTGCCTCCC--AGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATT
EST: gi|33406561|gb|CF212188.1|CF212188
EST:     TGTCTGCAACAACGATACTATGCAAGAGAATCTCAAGAGACAGCTCTTTG                         GTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTAC
genomic: TGTCTGCAACAACGATACTATGCAAGAGAATCTCAAGAGACAGCTCTTTGgtaagccccc ... tcatctccagGTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTAC
EST: gi|352776555|gb|FQ474857.1|FQ474857
EST:     AGAGATTCTCAAGAGACAGCTCTTTG                         GTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTAC
genomic: AGAGAATCTCAAGAGACAGCTCTTTGgtaagccccc ... tcatctccagGTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTAC
EST: gi|29783826|gb|CB350276.2|CB350276
EST:     GCAAGAGAATCTCAAGAGACAGCTCTTTG                         GTNTGCCTCCCAGGTTCCGTGATTCAGTGCGGGCTATAACCCCAGGATTAC
genomic: GCAAGAGAATCTCAAGAGACAGCTCTTTGgtaagccccc ... tcatctccagGTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTAC
EST: gi|28965525|gb|CB344558.1|CB344558
EST:     GCAACAACGATACTATGCAAGAGAATCTCAAGAGACAGCTCTTTG                         GTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTAC
genomic: GCAACAACGATACTATGCAAGAGAATCTCAAGAGACAGCTCTTTGgtaagccccc ... tcatctccagGTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTAC
EST: gi|110732396|gb|EE107656.1|EE107656
EST:     CTGCAACAACGATACTATGCAAGAGAATCTCAAGAGACAGCTCTTTG                         GTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTAC
genomic: CTGCAACAACGATACTATGCAAGAGAATCTCAAGAGACAGCTCTTTGgtaagccccc ... tcatctccagGTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTAC
EST: gi|110376766|gb|EC941841.1|EC941841
EST:     GACAGCTCTTTG                         GTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTAC
genomic: GACAGCTCTTTGgtaagccccc ... tcatctccagGTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTAC
EST: gi|110725858|gb|EE102801.1|EE102801
EST:     CAAGAGAATCTCAAGAGACAGCTCTTTG                         GTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTAC
genomic: CAAGAGAATCTCAAGAGACAGCTCTTTGgtaagccccc ... tcatctccagGTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTAC
EST: gi|22012251|gb|BQ797285.1|BQ797285
EST:     TGTCTGCAACAACGATACTATGCAAGAGAATCTCAAGAGACAGCTCTTTG                         GTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTAC
genomic: TGTCTGCAACAACGATACTATGCAAGAGAATCTCAAGAGACAGCTCTTTGgtaagccccc ... tcatctccagGTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gactgattcgtggtttccgatctctttctaatgttctcctttgtatcatctccagGTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTACCCCTTTTCCTCTACAATTACTCCACCCACCAGCTTCATGGAGTTTTTGA
                         ttctaat  putative branch site (score: 2)
                                 ttctcctttgtatc  CT-rich tract
                        tttctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattatcaattttttttttttttgacaacaagtttagattgttttgactgattcgtggtttccgatctctttctaatgttctcctttgtatcatctccagGTTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTACCCCTTTTCCTCTACAATTACTCCACCCACCAGCTTCATGGAGTTTTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - acaacaa
- - - - - - - - - - - - - - - - - - - - - - tgactga