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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcatatcctggggcttgtgctttagaggccttatttaggagattgtaggcaatctgagaatggagtgtatttttgctttttaattgtccgaacccttattaagtatagttcaaatatgatcttgtagGTCATGAGGCTTAGGCGTATTGAGAGAGGAGCCCTAACTCTAGCTTCTGCAGAAGTCAAATTTCAAATTGATACTGAAACTCATGATCCTCTTGATATTG

Basic information

species Vitis vinifera
transcript Vv07s0031g02190.t01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g02190.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: LOC_Os03g03710.1 (Oryza sativa), 3'ss of exon 15
gtatgcatatcctggggcttgtgctttagaggccttatttaggagattgtaggcaat-ctgagaatggagtgtatttttgctttttaattgtccgaacccttattaagtatagttcaaatatgatcttgtagGTCATGAGGCTTAGGCGTATTGAGAGAGGAGCCCTAACTCTAGCTTCTGCAGAAGTCAAATTTCAAATTGATACTGAAACTCATGATCCTCTTGATATTG
                | |||   ||     | || || |   | | ||||    ||  |    ||  | ||  | ||| |  || || |||        ||||||  |||  ||| ||| |  ||    || | ||||||| | |||||  ||| ||||| || ||||| || ||||| ||||||||||||||  ||||||||| |||||| |||||||| ||||| || |
----------------gtttgcttttgtattgactcatctc--atactgtaattgatgttctttatctattgc-tatttaccattgaaatgttttttttattattat-tatgtttcgaatgt--tcacacagATTATGAGGCATCGGCGTTGTGAAAGAGGGGCTCTAACACTTGCTTCAGCAGAAGTCAAATTCGAAATTGATAGTGAAACCCATGATCCGCTTGACATAG

upper sequence: Vv07s0031g02190.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GRMZM2G031859_T04 (Zea mays), 3'ss of exon 10
gtatgcatatcctggggcttgtgctttagaggccttatttaggagattgtaggcaatctgaga-atggagtgtatttttgctttttaattgtccgaacccttattaagtatagttcaaatatgatcttgtagGTCATGAGGCTTAGGCGTATTGAGAGAGGAGCCCTAACTCTAGCTTCTGCAGAAGTCAAATTTCAAATTGATACTGAAACTCATGATCCTCTTGATATTG
                             |  |   |  ||  | |      | | | || ||    | | ||| | ||   |   |||      |  ||||||  | |   | |   ||    |  || || ||||| | |   | |||  ||| ||||| ||  | ||||| |||||||||||||| |||||| | ||||||| ||||||||||||||||||||| || |
----------------------------aaatctagagcta--aaacgactagtattttgggatggagggagtagtatttaatgcgaataacttca--ccttatgtattcatgctttgattgctttatgcagATCATGCGACAACGCCGTTGTGAAAGAGGGGCTTTGACTCTTGCTTCTGCAGAAGTAAAATTTGAGATTGATAGTGAAACTCATGATCCTCTTGACATAG

upper sequence: Vv07s0031g02190.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA04G39980.1 (Glycine max), 3'ss of exon 15
gtatgcatatcctggggcttgtgctttagaggccttatttaggagattgtaggcaatctgagaatggagtgtatttttgctttttaattgtccgaacccttattaagtatag-ttcaaatatgatcttgtagGTCATGAGGCTTAGGCGTATTGAGAGAGGAGCCCTAACTCTAGCTTCTGCAGAAGTCAAATTTCAAATTGATACTGAAACTCATGATCCTCTTGATATTG
||||| |  |  |||      ||||  ||| || ||  |||     ||     ||   | | ||    |  | | ||| |||  ||  |     ||   |||  |||||||| ||    ||||| ||   ||   |||||  | ||||||||||||||||||||  | ||||| || ||||| || ||||||||||||||||| || || ||||||||||| ||||||||||
gtatggaatttgtgga-----tgctc-agatgc-ttgcttattgttttactcacataattataagtatggttgtattttcttgctatataatgaaa---ttaaaaagtatagctttgtttatgacctatcagAAAATGAGATTAAGGCGTATTGAGAGAGGAGCTTTGACTCTTGCATCTGCTGAGGTCAAATTTCAAATTGACACGGAGACTCATGATCCACTTGATATTG

upper sequence: Vv07s0031g02190.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA06G14870.2 (Glycine max), 3'ss of exon 15
gtatgcatatcctggggcttgtgctttagaggccttatttaggagattgtaggcaatctgagaatggagtgtatttttgctttttaattgtccgaacccttattaagtatag-ttcaaatatgatcttgtagGTCATGAGGCTTAGGCGTATTGAGAGAGGAGCCCTAACTCTAGCTTCTGCAGAAGTCAAATTTCAAATTGATACTGAAACTCATGATCCTCTTGATATTG
||||| |  |  ||      | ||||     |  ||  | | |  | | |  | |   |   | | |  ||  |  ||||| | ||||     |||   ||   ||| |||| ||    ||||||||   ||   |||||  | ||||||||||||||||||||  | ||||| || ||||| |||||||||||||| ||||| || || |||||||| || ||||||||||
gtatggactttgtgaatgccg-gctt----agttttgatcacgtaactatcagtatggttgtatttgcttgc-taattgctatataat-----gaaa--ttgaaaagcatagctttgtttatgatctatcagAAAATGAGATTAAGGCGTATTGAGAGAGGAGCTTTGACTCTTGCATCTGCTGAAGTCAAATTTCAGATTGACACAGAGACTCATGACCCCCTTGATATTG

upper sequence: Vv07s0031g02190.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: AT2G17510.1 (Arabidopsis thaliana), 3'ss of exon 15
gtatgcatatcctggggcttgtgctttagaggccttatttaggagattgtaggcaatctgagaatggagtgtatttttgctttttaattgtccgaacccttattaagtatagttcaaatatgatcttgtagGTCATGAGGCTTAGGCGTATTGAGAGAGGAGCCCTAACTCTAGCTTCTGCAGAAGTCAAATTTCAAATTGATACTGAAACTCATGATCCTCTTGATATTG
                      | || |||  |||  | |   |  |||       |   ||||   |  | |      |     ||   |  || |  || ||   |    || |||      | ||||| | |||||||  |||||||| || || |||||| ||||||| |||||||| |||||||||||| | |||||| | || | ||||||||||||| | ||||
----------------------gtttgagacacctcctctcacaagttgccatatgttccagaaatcatagaaagaacac-----aacattttgacctgttttt---tgctcttgaaa------cctgtagATAATGAGGCAAAGGCGTATCGATAGGGGAGCCTTAACTCTTGCTTCTGCGGAAGTCAAATTTGATATTGATCCGGAGAATCATGATCCTCTTAACATTG

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|32247182|gb|CD713001.1|CD713001
EST:     TGATGGATCCATTAACTATGGATTTGCGAAATATGAATGCTTTGGCAAAG                         GTCATGAGGCTTANGCGTATTGAGAGAGGAGCCCTAACTCTAGCTTCTGCA
genomic: TGATGGATCCATTAACTATGGATTTGCGAAATATGAATGCTTTGGCAAAGgtatgcatat ... gatcttgtagGTCATGAGGCTTAGGCGTATTGAGAGAGGAGCCCTAACTCTAGCTTCTGCA
EST: gi|349815930|gb|FQ403547.1|FQ403547
EST:     TGATGGATCCATTAACTATGGATTTGCGAAATATGAATGCTTTGGCAAAG                         GTCATGAGGCTTAGGCGTATTGAGAGAGGAGCCCTAACTCTAGCTTCTGCA
genomic: TGATGGATCCATTAACTATGGATTTGCGAAATATGAATGCTTTGGCAAAGgtatgcatat ... gatcttgtagGTCATGAGGCTTAGGCGTATTGAGAGAGGAGCCCTAACTCTAGCTTCTGCA
EST: gi|351013790|gb|FQ433942.1|FQ433942
EST:     TGATGGATCCATTAACTATGGATTTGCGAAATATGAATGCTTTGGCAAAG                         GTCATGAGGCTTAGGCGTATTGAGAGAGGAGCCCTAACTCTAGCTTCTGCA
genomic: TGATGGATCCATTAACTATGGATTTGCGAAATATGAATGCTTTGGCAAAGgtatgcatat ... gatcttgtagGTCATGAGGCTTAGGCGTATTGAGAGAGGAGCCCTAACTCTAGCTTCTGCA
EST: gi|351054754|gb|FQ462784.1|FQ462784
EST:     TGATGGATCCATTAACTATGGATTTGCGAAATATGAATGCTTTGGCAAAG                         GTCATGAGGCTTAGGCGTATTGAGAGAGGAGCCCTAACTCTAGCTTCTGCA
genomic: TGATGGATCCATTAACTATGGATTTGCGAAATATGAATGCTTTGGCAAAGgtatgcatat ... gatcttgtagGTCATGAGGCTTAGGCGTATTGAGAGAGGAGCCCTAACTCTAGCTTCTGCA
EST: gi|351048032|gb|FQ441204.1|FQ441204
EST:     TGATGGATCCATTAACTATGGATTTGCGAAATATGAATGCTTTGGCAAAG                         GTCATGAGGCTTAGGCGTATTGAGAGAGGAGCCCTAACTCTAGCTTCTGCA
genomic: TGATGGATCCATTAACTATGGATTTGCGAAATATGAATGCTTTGGCAAAGgtatgcatat ... gatcttgtagGTCATGAGGCTTAGGCGTATTGAGAGAGGAGCCCTAACTCTAGCTTCTGCA
EST: gi|351055546|gb|FQ442342.1|FQ442342
EST:     TGATGGATCCATTAACTATGGATTTGCGAAATATGAATGCTTTGGCAAAG                         GTCATGAGGCTTAGGCGTATTGAGAGAGGAGCCCTAACTCTAGCTTCTGCA
genomic: TGATGGATCCATTAACTATGGATTTGCGAAATATGAATGCTTTGGCAAAGgtatgcatat ... gatcttgtagGTCATGAGGCTTAGGCGTATTGAGAGAGGAGCCCTAACTCTAGCTTCTGCA
EST: gi|32248522|gb|CD714341.1|CD714341
EST:     TGATGGATCCATTAACTATGGATTTGCGAAATATGAATGCTTTGGCAAAG                         GTCATGAGGCTTAGGCGTATTGAGAGAGGAGCCCTAACTCTAGCTTCTGCA
genomic: TGATGGATCCATTAACTATGGATTTGCGAAATATGAATGCTTTGGCAAAGgtatgcatat ... gatcttgtagGTCATGAGGCTTAGGCGTATTGAGAGAGGAGCCCTAACTCTAGCTTCTGCA
EST: gi|351025060|gb|FQ433477.1|FQ433477
EST:     TGATGGATCCATTAACTATGGATTTGCGAAATATGAATGCTTTGGCAAAG                         GTCATGAGGCTTAGGCGTATTGAGAGAGGAGCCCTAACTCTAGCTTCTGCA
genomic: TGATGGATCCATTAACTATGGATTTGCGAAATATGAATGCTTTGGCAAAGgtatgcatat ... gatcttgtagGTCATGAGGCTTAGGCGTATTGAGAGAGGAGCCCTAACTCTAGCTTCTGCA
EST: gi|351036566|gb|FQ457279.1|FQ457279
EST:     TGATGGATCCATTAACTACGGATTTGCGAAATATGAATGCTTTGGCAAAG                         GTCATGAGGCTTAGGCGTATTGAGAGAGGAGCCCTAACTCTAGCTTCTGCA
genomic: TGATGGATCCATTAACTATGGATTTGCGAAATATGAATGCTTTGGCAAAGgtatgcatat ... gatcttgtagGTCATGAGGCTTAGGCGTATTGAGAGAGGAGCCCTAACTCTAGCTTCTGCA
EST: gi|351033178|gb|FQ461950.1|FQ461950
EST:     TGATGGATCCATTAACTATGGATTTGCGAAATATGAATGCTTTGGCAAAG                         GTCATGAGGCTTAGGCGTATTGAGAGAGGAGCCCTAACTCTAGCTTCTGCA
genomic: TGATGGATCCATTAACTATGGATTTGCGAAATATGAATGCTTTGGCAAAGgtatgcatat ... gatcttgtagGTCATGAGGCTTAGGCGTATTGAGAGAGGAGCCCTAACTCTAGCTTCTGCA
EST: gi|351054627|gb|FQ456824.1|FQ456824
EST:     TGATGGATCCATTAACTATGGATTTGCGAAATATGAATGCTTTGGCAAAG                         GTCATGAGGCTTAGGCGTATTGAGAGAGGAGCCCTAACTCTAGCTTCTGCA
genomic: TGATGGATCCATTAACTATGGATTTGCGAAATATGAATGCTTTGGCAAAGgtatgcatat ... gatcttgtagGTCATGAGGCTTAGGCGTATTGAGAGAGGAGCCCTAACTCTAGCTTCTGCA
EST: gi|349830463|gb|FQ416761.1|FQ416761
EST:     TGATGGATCCATTAACTATGGATTTGCGAAATATGAATGCTTTGGCAAAG                         GTCATGAGGCTTAGGCGTATTGAGAGAGGAGCCCTAACTCTAGCTTCTGCA
genomic: TGATGGATCCATTAACTATGGATTTGCGAAATATGAATGCTTTGGCAAAGgtatgcatat ... gatcttgtagGTCATGAGGCTTAGGCGTATTGAGAGAGGAGCCCTAACTCTAGCTTCTGCA
EST: gi|349810328|gb|FQ401774.1|FQ401774
EST:     TGATGGATCCATTAACTATGGATTTGCGAAATATGAATGCTTTGGCAAAG                         GTCATGAGGCTTAGGCGTATTGAGAGAGGAGCCCTAACTCTAGCTTCTGCA
genomic: TGATGGATCCATTAACTATGGATTTGCGAAATATGAATGCTTTGGCAAAGgtatgcatat ... gatcttgtagGTCATGAGGCTTAGGCGTATTGAGAGAGGAGCCCTAACTCTAGCTTCTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctttttaattgtccgaacccttattaagtatagttcaaatatgatcttgtagGTCATGAGGCTTAGGCGTATTGAGAGAGGAGCCCTAACTCTAGCTTCTGCAGAAGTCAAATTTCAAATTGATACTGAAACTCATGATCCTCTTGATATTG
     ttttaat  putative branch site (score: 3)
                       ttattaagtatagttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcatatcctggggcttgtgctttagaggccttatttaggagattgtaggcaatctgagaatggagtgtatttttgctttttaattgtccgaacccttattaagtatagttcaaatatgatcttgtagGTCATGAGGCTTAGGCGTATTGAGAGAGGAGCCCTAACTCTAGCTTCTGCAGAAGTCAAATTTCAAATTGATACTGAAACTCATGATCCTCTTGATATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT