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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttggctgtgcgggttatcattttctttcattgttactttcttttgtttactgctacatctgtgctctttgcttactctgctggttctgggtattcacagGTAAATAGCGGTGTCAAAGACAATATGATGCAAAGCTTCTTCCTTGCTGAGACACTCAAATATCTCTATCTTCTTTTCTCACCTTCGACGGTCATTTCAT

Basic information

species Vitis vinifera
transcript Vv09s0054g00370.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0054g00370.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA08G23730.1 (Glycine max), 3'ss of exon 13
cttggctgtgcgggttatcattttctttcattgtt--actttcttttgtttactgctacatctgtgctctttgcttactc--tgctggttctgggtatt-cacagGTAAATAGCGGTGTCAAAGACAATATGATGCAAAGCTTCTTCCTTGCTGAGACACTCAAATATCTCTATCTTCTTTTCTCACCTTCGACGGTCATTTCAT
        |||    | | || ||  |  | || |  ||   | |||  |  |     || || | ||   | || |     |     || |    ||| | ||||| ||||| || ||||||||||| ||||||||||||||||| ||||| ||||| || || ||| | |||||||| |||||||||||  | ||||| ||||
-----tcttgcttcctttgatatttatctaatgctggacaaccatttagtatcccaagcaactattctgcctactcatgtattatcacttgttcacatttctcagGTTAATAGTGGAGTCAAAGACAACATGATGCAAAGCTTCTTTCTTGCGGAGACCCTGAAGTATTTTTATCTTCTCTTCTCACCTTCTTCAGTCATCTCAT

upper sequence: Vv09s0054g00370.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA07G02290.1 (Glycine max), 3'ss of exon 12
-cttggctgtgcgggttatcattttctttcattgttactttcttttgtttactgctacatctgtgc-tctttgcttactctgctggttctgggtattcacagGTAAATAGCGGTGTCAAAGACAATATGATGCAAAGCTTCTTCCTTGCTGAGACACTCAAATATCTCTATCTTCTTTTCTCACCTTCGACGGTCATTTCAT
 ||||  | |   | |  | || |  |         ||  | |  | | |   |||||   | ||| |  |    || | |      |     | ||| ||||| ||||| || ||||||||||| ||||||||||||||||| ||||| ||||| || || ||| | |||||||| |||||||||||  | |||||  |||
tcttgcttcttttgatatttatctaatgctgg-acaaccatttagtatctcaagctactattctgcctactcatgtattataacttgttcacat-ttctcagGTTAATAGTGGAGTCAAAGACAACATGATGCAAAGCTTCTTTCTTGCGGAGACCCTGAAGTATTTTTATCTTCTCTTCTCACCTTCTTCTGTCATCCCAT

upper sequence: Vv09s0054g00370.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT3G21160.1 (Arabidopsis thaliana), 3'ss of exon 13
-----------------------cttggctgtgcgg-gttatcattttctttcattg-------ttactttcttttgtttactgctacatctgtg---ctctttgcttactct-gctggttctgggtattcacagGTAAATAGCGGTGTCAAAGACAATATGATGCAAAGCTTCTTCCTTGCTGAGACACTCAAATATCTCTATCTTCTTTTCTCACCTTCGACGGTCATTTCAT
                        | |    |||   ||||  |  ||  |  ||||       | | |      | | || |  ||  |  |||   ||  | |   | |||   |  ||      |||  ||||| ||||  || || || ||||| | ||||||||| ||||||||||| ||||||||||| ||||||||||| || ||||| ||  | || |||||| | |
gtaagttttccgtaggcgcttaattagatcctgcattgttaaaaccttggtgaattgaattatatcattccaccatctatattagtaattgagtgtaactgatggtagattcttatttctttcaatcatttccagGTTAATACAGGCGTTAAGGACAACAAGATGCAAAGTTTCTTCCTTGCAGAGACACTCAAGTATCTCTATCTACTCTTCTCGCCGACAACAGTCATTCCTT

upper sequence: Vv09s0054g00370.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT1G51590.1 (Arabidopsis thaliana), 3'ss of exon 13
cttggctgtg---cgggttatcattttctttcattgttactttcttttgtttactgctacatctgt-----gctctttgcttactctgctggttctgggtattcacagGTAAATAGCGGTGTCAAAGACAATATGATGCAAAGCTTCTTCCTTGCTGAGACACTCAAATATCTCTATCTTCTTTTCTCACCTTCGACGGTCATTTCAT
 |  | |  |   |||| |  | ||  |        |  | | ||   ||   |   | ||||| |      | | ||| | ||  |  || ||||    |||  ||||| ||||  ||||  |||||||| | |||||||||||||||| | |||||||| || || ||||| |||||||| || || |||||  | || |||||||
gtaagtttcgagccgggctgaccttaaccaatcagataccctcctcgagtgggcctttccatctttcggaaacacgttgttaacgtt--tgcttctt--cattttcagGTCAATACAGGTGCTAAAGACAACAAGATGCAAAGCTTCTTCTTAGCTGAGACTCTTAAGTATCTATATCTTCTCTTTTCGCCTTCATCTGTTATTTCAT

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|352768272|gb|FQ469447.1|FQ469447
EST:     CATTTGAAAAGAACTCCCGCATAGAGTCAGGATACGTTGGACTGAAGGAT                         GTAAATAGCGGTGTCAAAGACAATATGATGCAAAGCTTCTTCCTTGCTGAG
genomic: CATTTGAAAAGAACTCCCGCATAGAGTCAGGATACGTTGGACTGAAGGATgtaagtacac ... gtattcacagGTAAATAGCGGTGTCAAAGACAATATGATGCAAAGCTTCTTCCTTGCTGAG
EST: gi|110415337|gb|EC981235.1|EC981235
EST:     CATTTGAAAAGAACTCCCGCATAGAGTCAGGATACGTTGGACTGAAGGAT                         GTAAATAGCGGTGTCAAAGACAATATGATGCAAAGCTTCTTCCTTGCTGAG
genomic: CATTTGAAAAGAACTCCCGCATAGAGTCAGGATACGTTGGACTGAAGGATgtaagtacac ... gtattcacagGTAAATAGCGGTGTCAAAGACAATATGATGCAAAGCTTCTTCCTTGCTGAG
EST: gi|77586886|gb|DV222591.1|DV222591
EST:     CATTTGAAAAGAACTCCCGCATAGAGTCAGGATACGTTGGACTGAAGGAT                         GTAAATAGCGGTGTCAAAGACAATATGATGCAAAGCTTCTTCCTTGCTGAG
genomic: CATTTGAAAAGAACTCCCGCATAGAGTCAGGATACGTTGGACTGAAGGATgtaagtacac ... gtattcacagGTAAATAGCGGTGTCAAAGACAATATGATGCAAAGCTTCTTCCTTGCTGAG
EST: gi|33402283|gb|CF207910.1|CF207910
EST:     CATTTGAAAAGAACTCCCGCATAGAGTCAGGATACGTTGGACTGAAGGAT                         GTAAATAGCGGTGTCAAAGACAATATGATGCAAAGCTTCTTCCTTGCTGAG
genomic: CATTTGAAAAGAACTCCCGCATAGAGTCAGGATACGTTGGACTGAAGGATgtaagtacac ... gtattcacagGTAAATAGCGGTGTCAAAGACAATATGATGCAAAGCTTCTTCCTTGCTGAG
EST: gi|110382080|gb|EC938428.1|EC938428
EST:     GTTGGACTGAAGGAT                         GTAAATAGCGGTGTCAAAGACAATATGATGCAAAGCTTCTTCCTTGCTGAG
genomic: GTTGGACTGAAGGATgtaagtacac ... gtattcacagGTAAATAGCGGTGTCAAAGACAATATGATGCAAAGCTTCTTCCTTGCTGAG
EST: gi|352763646|gb|FQ473349.1|FQ473349
EST:     CATTTGAAAAGAACTCCCGCATAGAGTCAGGATACGTTGGACTGAAGGAT                         GTAAATAGCGGTGTCAAAGACAATATGATGCAAAGCTTCTTCCTTGCTGAG
genomic: CATTTGAAAAGAACTCCCGCATAGAGTCAGGATACGTTGGACTGAAGGATgtaagtacac ... gtattcacagGTAAATAGCGGTGTCAAAGACAATATGATGCAAAGCTTCTTCCTTGCTGAG
EST: gi|71863682|gb|DT012737.1|DT012737
EST:     CATTTGAAAAGAACTCCCGCATAGAGTCAGGATACGTTGGACTGAAGGAT                         GTAAATAGCGGTGTCAAAGACAATATGATGCAAAGCTTCTTCCTTGCTG
genomic: CATTTGAAAAGAACTCCCGCATAGAGTCAGGATACGTTGGACTGAAGGATgtaagtacac ... gtattcacagGTAAATAGCGGTGTCAAAGACAATATGATGCAAAGCTTCTTCCTTGCTG
EST: gi|352781335|gb|FQ467781.1|FQ467781
EST:     CATTTGAAAAGAACTCCCGCATAGAGTCCGGATACGTTGGACTGAAGGAT                         GTAAATAGCGGTGTCAAAGACAATATGATGCAAAGCTTCTTCCTTGCTGAG
genomic: CATTTGAAAAGAACTCCCGCATAGAGTCAGGATACGTTGGACTGAAGGATgtaagtacac ... gtattcacagGTAAATAGCGGTGTCAAAGACAATATGATGCAAAGCTTCTTCCTTGCTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttactgctacatctgtgctctttgcttactctgctggttctgggtattcacagGTAAATAGCGGTGTCAAAGACAATATGATGCAAAGCTTCTTCCTTGCTGAGACACTCAAATATCTCTATCTTCTTTTCTCACCTTCGACGGTCATTTCAT
                        tgcttac  putative branch site (score: 2)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttggctgtgcgggttatcattttctttcattgttactttcttttgtttactgctacatctgtgctctttgcttactctgctggttctgggtattcacagGTAAATAGCGGTGTCAAAGACAATATGATGCAAAGCTTCTTCCTTGCTGAGACACTCAAATATCTCTATCTTCTTTTCTCACCTTCGACGGTCATTTCAT

- tggctgt
- - - - - - - - - - - - - - - - - - - - - - - - - ctgctac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctggttc