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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgactgacttgatggactatttcttgtctgttgtaaaattatcaaactgaataatttcaaaacctaagaatcttttgttatttctttttttggctgatttcatgcaaacagGAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAGTTGGTTGCATGTATGGGATTGGGTAAATCAGATGCTAAAAATGAGCCAC

Basic information

species Vitis vinifera
transcript Vv01s0011g05370.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 9
gtttgactgacttgatggactatttcttgtctgttgtaaaattatcaaactgaataatttcaaaacctaagaatcttttgttatttctttttttggctgatttcatgcaaacagGAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAGTTGGTTGCATGTATGGGATTGGGTAAATCAGATGCTAAAAATGAGCCAC---
                     |||| || |||  |     || ||||        ||||| ||||    ||||| |    |  | |   || ||  ||  | |  |    |||||||||||||||||| || |||||||||||||| || ||||||||||| ||  | ||||   | |||||  | || |||||     | ||   ||| || |   
------------------gtaatttgttttcttct-----atcatca-------caatttgaaaat---agaatttagattggtgttcattctttacttgtattttt---acagGAAGACTTTGGAGGGGGCCATCCAGATCCTAACCTCACCTATGCAAAAGAACTTGTTGACCGGATGGGCCTTGGAAAATC---CTCAAATGCTGAACCCCCAG

upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 9
gtttgactgacttgatggactatttcttgtctgttgtaaaattatcaaactgaataatttcaaaacctaagaatcttttgttatttctttttttggctgatttcatgcaaacagGAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAGTTGGTTGCATGTATGGGATTGGGTAAATCAGATGCTAAAAATGAGCCAC
                                ||  | |  |  || |     | || ||   |    ||  ||   |||  | ||| |   ||   || |||        ||||| ||||||||||| || ||||| |||||||| || ||||||||||| |||||||||| | | |||||  | || || |||    | ||   ||| || |
--------------------------------gtaatgagttcttctattgtcacaagtttctacttaaaatatggcttgggaattcatcactta--tgtttttg------cagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTCACCTATGCAAAAGAGTTGGTTGAACGGATGGGTCTTGGAAAGTCATCCTCAAATGTTGAACCTC

upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G109383_T02 (Zea mays), 3'ss of exon 9
gtttgactgacttgatggactatttcttgtctgttgtaaaattatcaaactgaataatttcaaaacctaagaatcttttgttatttctttttttggctgatttcatgcaaacagGAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAGTTGGTTGCATGTATGGGATTGGGTAAATCAGATGCTAAAAATGAGCCAC---
            | |||   | ||   |   |||   |||  |||| |  |  ||||| |    |  ||  |||   |  | | || | ||||||                ||||| ||||||||||| || ||||| |||||||| || ||||||||||| |||||||||| | | |||||  | || || |||    | ||   |||||| |   
-----------gtaatgagttcttctat---tgtcacaaa--tatctactt--ataatgtggctaggtattaat---tcatcacttatatttttg----------------caggagGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAGTTGGTTGAACGCATGGGTCTTGGAAAGTCATCCTCAAATGTTGAGCCTCCTG

upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G109383_T01 (Zea mays), 3'ss of exon 9
gtttgactgacttgatggactatttcttgtctgttgtaaaattatcaaactgaataatttcaaaacctaagaatcttttgttatttctttttttggctgatttcatgcaaacagGAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAGTTGGTTGCATGTATGGGATTGGGTAAATCAGATGCTAAAAATGAGCCAC
            | |||   | ||   |   |||   |||  |||| |  |  ||||| |    |  ||  |||   |  | | || | ||||||                ||||| ||||||||||| || ||||| |||||||| || ||||||||||| |||||||||| | | |||||  | || || |||    | ||   |||||| |
-----------gtaatgagttcttctat---tgtcacaaa--tatctactt--ataatgtggctaggtattaat---tcatcacttatatttttg----------------cagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAGTTGGTTGAACGCATGGGTCTTGGAAAGTCATCCTCAAATGTTGAGCCTC

upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA05G34790.1 (Glycine max), 3'ss of exon 9
gtttgactgacttgatggactatt-tcttgtctgttg-taaaattatcaaactgaataatttcaaaacctaagaatcttttgttatttctttttttggctgatttcatgcaaacagGAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAGTTGGTTGCATGTATGGGATTGGGTAAATCAGATGCTAAAAATGAGCCAC
                |   |||| ||||||   ||  |   |     |   | ||  |||   ||  | |    |  ||||    ||   ||| ||| ||| ||  || | ||||||||||||||||||||| || ||||| || ||| | || |||||||| |||||||||||  ||||||||||||| ||||| ||  |  || |||| || |
----------------gtcttattctcttgttgattaatgccaaggatagctttaaatattctgaatgccagttgtgatttgcc--tttgatttgtggatgacttgttggatacagGAAGACTTTGGAGGAGGACACCCAGACCCCAATTTGACATATGCAAAAGAGTTGGTTGCTCGTATGGGATTGGGCAAATCCGAACCACAAGATGATCCCC

upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA03G05150.1 (Glycine max), 3'ss of exon 2
gtttgactgacttgatggactatttcttgtctgttgtaaaattatcaaactgaataatttcaaaacctaagaatcttttgttatttctttttttggctgatttcatgcaaacagGAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAGTTGGTTGCATGTATGGGATTGGGTAAATCAGATGCTAAAAATGAGCCAC
                                   ||   ||| ||    ||| |||| |||           || |   ||   |   ||| ||| ||| ||  || | |||||||||||| |||||||| || ||||| || ||| | || |||||||| |||||||||||  ||||||||||||| ||||| ||  |  || ||||||| |
-----------------------------------gtcttattctcttgttgattaatgtcag----------tcgtgatttgccttgatttgtggatgacttgttggatacagGAAGACTTCGGAGGAGGACACCCAGACCCCAATTTGACATATGCAAAAGAGTTGGTTGCTCGTATGGGATTGGGCAAATCTGAACCCCAAGATGAGCCCC

upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA08G04890.1 (Glycine max), 3'ss of exon 9
gtttgactgacttgatggactatttcttgtctgttgtaaaattatcaaactgaataatttcaaaacctaagaatcttttgttatttctttttttggctgatttcatgcaaacagGAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAGTTGGTTGCATGTATGGGATTGGGTAAATCAGATGCTAAAAATGAGCCAC
        | |||  |   || ||  |  |   |   ||   || |    | |||| | | ||  ||    | || |   ||   |   ||| ||| ||| ||  || | |||||||||||| |||||||| || ||||| || ||| | || |||||||| |||||||||||  ||||||||||||| ||||| ||  |  || | ||||| |
--------gtcttatt---ctcttgttgattaatgccaaggatagct--ttaaatattctgaatgcc----agtcgtgatttgccttgatttgtggatgacttgttggatacagGAAGACTTCGGAGGAGGACACCCAGACCCCAATTTGACATATGCAAAAGAGTTGGTTGCTCGTATGGGATTGGGCAAATCCGAACCCCAAGAAGAGCCCC

upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 9
gtttgactgacttgatggactatttcttgtctgttgtaaaattatcaaactgaataatttcaaaacctaagaat-cttttgttatttctttttttggctgatttca--tgcaaacagGAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAGTTGGTTGCATGTATGGGATTGGGTAAATCAGATGCTAAAAATGAGCCAC
                        |||| | | ||||  ||  |  ||||   ||    | ||    ||  ||| |   |      ||  | |||  |  | | ||        ||||| |||||||||||||||||||| ||||| ||| | |||||||| |||||| | || ||| | |||||||| |||||||| ||  ||  |  ||| || |
-----------------------gtcttattt-ttgtctaaccaagaaacgctattccataaatgattacaaatacacctccaggctcaatatttaccacaatacaacgatttgcagGAGGACTTTGGAGGAGGGCATCCGGATCCCAATTTGACCTATGCTAAGGAGCTTGTGGCACGAATGGGATTAGGTAAATCCGACACTGGAGGTGAACCTC

upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT1G70730.1 (Arabidopsis thaliana), 3'ss of exon 9
gtttgactgacttgatggactatttcttgtctgttgtaaaattatcaaa--ctgaataatttcaaaaccta--------agaatcttttgttatttctttttttg-gctgatttcatg-caaacagGAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAGTTGGTTGCATGTATGGGATTGGGTAAATCAGATGCTAAAAATGAGCCAC
|| | | |   ||  |      | | |||| |     | || |||||    |||||    ||  |||   |        ||  |||||| | |||| |        |   ||   |      |||||| ||||||||||| || || || ||||| ||||| |||||||| |||||| | || ||| | ||||||||| ||||| | |||| |     ||     |
gtatcatttttttcttctttcttattttgtataaccaagaaatatcatttcctgaaaggattataaatacacgttgaacagtgtcttttatgatttataacaacacgacaatcggacaatgtacagGAGGACTTTGGAGGGGGCCACCCGGATCCCAATCTTACCTATGCTAAGGAGCTCGTGGCACGCATGGGATTGAGTAAAACTGATGATGCTGGTGGCGAGC

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|30132705|gb|CB918044.1|CB918044
EST:     TTGAAGAGCTTGGTGCACAAGAAAGCTCATTGCTGAACTGCGTTCCCAAG                         GAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAG
genomic: TTGAAGAGCTTGGTGCACAAGAAAGCTCATTGCTGAACTGCGTTCCCAAGgtttgactga ... atgcaaacagGAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAG
EST: gi|161709381|gb|FC059250.1|FC059250
EST:     TTGAAGAGCTTGGTGCACAAGAAAGCTCATTGCTGAACTGCGTTCCCAAG                         GAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAG
genomic: TTGAAGAGCTTGGTGCACAAGAAAGCTCATTGCTGAACTGCGTTCCCAAGgtttgactga ... atgcaaacagGAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAG
EST: gi|30305224|gb|CB982018.1|CB982018
EST:     TTGAAGAGCTTGGTGCACAAGAAAGCTCATTGCTGAACTGCGTTCCCAAG                         GAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAG
genomic: TTGAAGAGCTTGGTGCACAAGAAAGCTCATTGCTGAACTGCGTTCCCAAGgtttgactga ... atgcaaacagGAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAG
EST: gi|37183515|gb|CF602869.1|CF602869
EST:     TGCGTTCCCAAG                         GAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAG
genomic: TGCGTTCCCAAGgtttgactga ... atgcaaacagGAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAG
EST: gi|351015349|gb|FQ445633.1|FQ445633
EST:     TTGAAGAGCTTGGTGCACAAGAAAGCTCATTGCTGAACTGCGTTCCCAAG                         GAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAG
genomic: TTGAAGAGCTTGGTGCACAAGAAAGCTCATTGCTGAACTGCGTTCCCAAGgtttgactga ... atgcaaacagGAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAG
EST: gi|30125147|gb|CB910486.1|CB910486
EST:     TTGAAGAGCTTGGTGCACAAGAAAGCTCATTGCTGAACTGCGTTCCCAAG                         GAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAG
genomic: TTGAAGAGCTTGGTGCACAAGAAAGCTCATTGCTGAACTGCGTTCCCAAGgtttgactga ... atgcaaacagGAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAG
EST: gi|30136409|gb|CB921747.1|CB921747
EST:     TTGAAGAGCTTGGTGCACAAGAAAGCTCATTGCTGAACTGCGTTCCCAAG                         GAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAG
genomic: TTGAAGAGCTTGGTGCACAAGAAAGCTCATTGCTGAACTGCGTTCCCAAGgtttgactga ... atgcaaacagGAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAG
EST: gi|30305289|gb|CB982083.1|CB982083
EST:     TTGAAGAGCTTGGTGCACAAGAAAGCTCATTGCTGAACTGCGTTCCCAAG                         GAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAG
genomic: TTGAAGAGCTTGGTGCACAAGAAAGCTCATTGCTGAACTGCGTTCCCAAGgtttgactga ... atgcaaacagGAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAG
EST: gi|30125386|gb|CB910725.1|CB910725
EST:     TTGAAGAGCTTGGTGCACAAGAAAGCTCATTGCTGAACTGCGGTCCCAAG                         GAAGACTTTGGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGA
genomic: TTGAAGAGCTTGGTGCACAAGAAAGCTCATTGCTGAACTGCGTTCCCAAGgtttgactga ... atgcaaacagGAAGACTTTGG-AGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGA
EST: gi|349810189|gb|FQ401635.1|FQ401635
EST:     TTGAAGAGCTTGGTGCACAAGATAGCTCATTGCTGAACTGCGTTCCCGAG                         GAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAG
genomic: TTGAAGAGCTTGGTGCACAAGAAAGCTCATTGCTGAACTGCGTTCCCAAGgtttgactga ... atgcaaacagGAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAG
EST: gi|349818554|gb|FQ403189.1|FQ403189
EST:     TTGAAGAGCTTGGTGCACAAGAAAGCTCATTGCTGAACTGCGTTCCCAAG                         GAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAG
genomic: TTGAAGAGCTTGGTGCACAAGAAAGCTCATTGCTGAACTGCGTTCCCAAGgtttgactga ... atgcaaacagGAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAG
EST: gi|349827300|gb|FQ421573.1|FQ421573
EST:     TTGAAGAGCTTGGTGCACAAGAAAGCTCATTGCTGAACTGCGTTCCCAAG                         GAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAG
genomic: TTGAAGAGCTTGGTGCACAAGAAAGCTCATTGCTGAACTGCGTTCCCAAGgtttgactga ... atgcaaacagGAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAG
EST: gi|349810979|gb|FQ405967.1|FQ405967
EST:     TTGAAGAGCTTGGTGCACAAGAAAGCTCATTGCTGAACTGCGTTCCCAAG                         GAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAG
genomic: TTGAAGAGCTTGGTGCACAAGAAAGCTCATTGCTGAACTGCGTTCCCAAGgtttgactga ... atgcaaacagGAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAG
EST: gi|349810186|gb|FQ401632.1|FQ401632
EST:     TTGAAGAGCTTGGTGCACAAGAAAGCTCATTGCTGAACTGCGTTCCCGAG                         GAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAG
genomic: TTGAAGAGCTTGGTGCACAAGAAAGCTCATTGCTGAACTGCGTTCCCAAGgtttgactga ... atgcaaacagGAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAG
EST: gi|161715091|gb|FC063627.1|FC063627
EST:     TTGAAGAGCTTGGTGCACAAGAAAGCTCATTGCTGAACTGCGTTCCCAAG                         GAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAG
genomic: TTGAAGAGCTTGGTGCACAAGAAAGCTCATTGCTGAACTGCGTTCCCAAGgtttgactga ... atgcaaacagGAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaaacctaagaatcttttgttatttctttttttggctgatttcatgcaaacagGAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAGTTGGTTGCATGTATGGGATTGGGTAAATCAGATGCTAAAAATGAGCCAC
                                   ggctgat  putative branch site (score: 4)
        taagaatcttttgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgactgacttgatggactatttcttgtctgttgtaaaattatcaaactgaataatttcaaaacctaagaatcttttgttatttctttttttggctgatttcatgcaaacagGAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAGTTGGTTGCATGTATGGGATTGGGTAAATCAGATGCTAAAAATGAGCCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG