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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGTTTGTTGATTCATGCAAGCGCTTGCGTATAATGAAAGGATCAGAAGCAATTGGTCTTGgtaagcaattgatcagcaggaattatttttctagccttcaaacagatcatgaacaatgcatcatagagggttgggcattatgatcagctcaaccttatatttattgcaatccaaactttttattattattattaatcttcttttcctatatataagtatataactaatgctagttccattaattatcag

Basic information

species Vitis vinifera
transcript Vv05s0020g04690.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g04690.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os12g40890.1 (Oryza sativa), 5'ss of exon 4
GATGTTTGTTGATTCATGCAAGCGCTTGCGTATAATGAAAGGATCAGAAGCAATTGGTCTTGgtaagcaattgatcagcaggaattatttttctagccttcaaacagatcatgaacaatgcatcatagagggttgggcattatgatcagctcaaccttatatttattgcaatccaaactttttattattattattaatcttcttttcctatatataagtatataactaatgctagttccattaattatcag
|||||||||||| |||||||||||| |  | |||||||||||||||||||| ||||| |||||| ||    | ||||     | || | ||||||      ||  || || |      |  ||  ||    ||||||  |||   | || |  |     |||   || |   |  |||  |  | ||| || ||   | || ||||    | | | ||                                 
GATGTTTGTTGAATCATGCAAGCGCCTTAGGATAATGAAAGGATCAGAAGCTATTGGCCTTGgtcagtgcat-atca-----agttttatttctacatacaaattagctcctttgggtttgattttaa---gttggggtttaatttaagttgga-----tatcagttactgacagaacagtgaaatataat-atattttttgttttgaattgtttcag---------------------------------

upper sequence: Vv05s0020g04690.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G138268_T01 (Zea mays), 5'ss of exon 4
GATGTTTGTTGATTCATGCAAGCGCTTGCGTATAATGAAAGGATCAGAAGCAATTGGTCTTGgtaagcaattgatcagcaggaattatttttctagccttcaaacagatcatgaacaatgcatcatagagggttgggcattatgatcagctcaaccttatatttattgcaatccaaactttttattattattattaatcttcttttcctatatataagtatataactaatgctagttccattaattatcag
|||||| || || |||||||||||| | || || ||||||||||||||||| ||||| || ||| ||   ||||     | || ||||| || |  |  | |     |  |  ||  |  | |  ||| |   |  |||    | |    |||  ||  | | |||     ||  || |||  |                                                                   
GATGTTCGTCGAATCATGCAAGCGCCTTCGGATCATGAAAGGATCAGAAGCCATTGGCCTGGgtgag---ttgacatatatga-ttattattattac--taatctcaacaacaaaagagactttctagggtagtaagcagcccgtttgtttca-tctggtctctatc----tctgaattttccag------------------------------------------------------------------

upper sequence: Vv05s0020g04690.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G138268_T02 (Zea mays), 5'ss of exon 3
--------------------------------------GATGTTTGTTGATTCATGCAAGCGCTTGCGTATAATGAAAGGATCAGAAGCAATTGGTCTTGgtaagcaattgatcagcaggaattatttttctagccttcaaacagatcatgaacaatgcatcatagagggttgggcattatgatcagctcaaccttatatttattgcaatccaaactttttattattattattaatcttcttttcctatatataagtatataactaatgctagttccattaattatcag
                                      |||||| || || |||||||||||| | || || ||||||||||||||||| ||||| || ||| ||   ||||     | || ||||| || |  |  | |     |  |  ||  |  | |  ||| |   |  |||    | |    |||  ||  | | |||     ||  || |||  |                                                                   
TAATCGGAAAATAATAATAATTTCCATTTCATTTTCAGGATGTTCGTCGAATCATGCAAGCGCCTTCGGATCATGAAAGGATCAGAAGCCATTGGCCTGGgtgag---ttgacatatatga-ttattattattac--taatctcaacaacaaaagagactttctagggtagtaagcagcccgtttgtttca-tctggtctctatc----tctgaattttccag------------------------------------------------------------------

upper sequence: Vv05s0020g04690.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA10G32340.1 (Glycine max), 5'ss of exon 4
GATGTTTGTTGATTCATGCAAGCGCTTGCGTATAATGAAAGGATCAGAAGCAATTGGTCTTGgtaagca--attgatcagcaggaattatttttctagccttcaaacagatcatgaacaatgcatcatagagggttgggcattatgatcagctcaaccttatatttattgcaatccaaactttttattattattattaatcttcttttcctatatataagtatataactaatgctagttccattaattatcag
|||||||||||  |||||||||||| |||| |||||||| ||||||||||| ||||| ||||||| |||  |||    |         || |   |   |||   ||   ||||| | |||  ||||| |    |    |   || | ||  ||||   |||||  ||  || |  ||  ||||   |||| | |||||| |  ||  |    || |   ||| ||  |   |                    
GATGTTTGTTGGGTCATGCAAGCGCCTGCGAATAATGAAGGGATCAGAAGCGATTGGCCTTGgtatgcatcattatataattaattccatctactttttcttttcac---tcatgga-aattaatcattgttt-tgaaactcaattaccaa-tcaataatatatacatgccatt--aattttttggctattctaattaatgtg-ttggcgcgcatctttttatgtactttcag--------------------

upper sequence: Vv05s0020g04690.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA20G35270.1 (Glycine max), 5'ss of exon 5
GATGTTTGTTGATTCATGCAAGCGCTTGCGTATAATGAAAGGATCAGAAGCAATTGGTCTTGgtaagcaattgatcagcaggaattatttttctagccttcaaacagatcatgaacaatgca-tcatagagggttgggcattatgatcagctcaaccttatatttattgcaatccaaactttttattattattattaatcttcttttcctatatataagtatataactaatgctagttccattaattatcag
|||||||||||| |||||||||||  |||| |||||||| ||||||||||| ||||| ||||||| |||       | |   |  |   ||  |  | |  |   |  |  |   |  | || |||| ||       |  ||   | |   ||||   || ||  ||  || |  ||  | ||   |||| | ||      | ||  |    || |   ||| ||  |   |                    
GATGTTTGTTGAGTCATGCAAGCGTCTGCGAATAATGAAGGGATCAGAAGCGATTGGGCTTGgtatgcatcattatatcttaagcttaattaattacatctagctacttttt---cttttcactcatggaaatcattgttttgaaaactaatcaataatacatacatgccatt--aatttgttggctattctaatg-----tgttggcgcgcatctttttatgtactttcag--------------------

upper sequence: Vv05s0020g04690.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT4G14550.1 (Arabidopsis thaliana), 5'ss of exon 4
GATGTTTGTTGATTCATGCAAGCGCTTGCGTATAATGAAAGGATCAGAAGCAATTGGTCTTGgtaagcaattgatcagcaggaattatttttctagccttcaaacagatcatgaacaatgcatcatagagggttgggcattatgatcagctcaaccttatatttattgcaatccaaactttttattattattattaatcttcttttcctatatataagtatataactaatgctagttccattaattatcag
||||||||| || |||||||| || ||||| |||||||||||||| ||||||||||| |||||||||   |             ||  | |||    ||  ||   | || |      |    ||   | | | | |  || |  ||||                                                                                                      
GATGTTTGTCGAGTCATGCAAACGTTTGCGCATAATGAAAGGATCCGAAGCAATTGGACTTGgtaagttttct-----------tttctgttcgtttctataagtggctcttttctgtttttccaataatgctcgtgtttttttttcag------------------------------------------------------------------------------------------------------

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|34548112|gb|CF516344.1|CF516344
EST:     TTCATGCAAGCGCTTGCGTATNATGAAAGGATCAGAAGCAATTGGTCTTG                         CACCAAGAGCAATGG
genomic: TTCATGCAAGCGCTTGCGTATAATGAAAGGATCAGAAGCAATTGGTCTTGgtaagcaatt ... taattatcagCACCAAGAGCAATGG
EST: gi|351026381|gb|FQ428393.1|FQ428393
EST:     TTCATGCAAGCGCTTGCGTATAATGAAAGGATCAGAAGCATTTGGTCTTG                         CACCAAGAGCAATGGAGAAGTG
genomic: TTCATGCAAGCGCTTGCGTATAATGAAAGGATCAGAAGCAATTGGTCTTGgtaagcaatt ... taattatcagCACCAAGAGCAATGGAGAAGTG
EST: gi|110362275|gb|EC925796.1|EC925796
EST:     TTCATGCAAGCGCTTGCGTATAATGAAAGGATCAGAAGCAATTGGTCTTG                         CCCCAAGAGCAATGGAGAAGTGTAAGAATAGATGGTGAACCAGCACAGCCT
genomic: TTCATGCAAGCGCTTGCGTATAATGAAAGGATCAGAAGCAATTGGTCTTGgtaagcaatt ... taattatcagCACCAAGAGCAATGGAGAAGTGTAAGAATAGATGCTGAACCAGCACAGCCT
EST: gi|110421143|gb|EC987432.1|EC987432
EST:     TTCATGCAAGCGCTTGCGTATAATGAAAGGATCAGAAGCAATTGGTCTTG                         CACCAAGAGCAATGGAGAAGTGTAAGAATAGATGCTGAACCAGCACAGCCT
genomic: TTCATGCAAGCGCTTGCGTATAATGAAAGGATCAGAAGCAATTGGTCTTGgtaagcaatt ... taattatcagCACCAAGAGCAATGGAGAAGTGTAAGAATAGATGCTGAACCAGCACAGCCT
EST: gi|110390251|gb|EC955151.1|EC955151
EST:     TTCATGCAAGCGCTTGCGTATAATGAAAGGATCAGAAGCAATTGGTCTTG                         CACCAAGAGCAATGGAGAAGTGTAAGAATAGATGCTGAACCAGCACAGCCT
genomic: TTCATGCAAGCGCTTGCGTATAATGAAAGGATCAGAAGCAATTGGTCTTGgtaagcaatt ... taattatcagCACCAAGAGCAATGGAGAAGTGTAAGAATAGATGCTGAACCAGCACAGCCT
EST: gi|110390209|gb|EC955109.1|EC955109
EST:     TTCATGCAAGCGCTTGCGTATAATGAAAGGATCAGAAGCAATTGGTCTTG                         CACCAAGAGCAATGGAGAAGTGTAAGAATAGATGCTGAACCAGCACAGCCT
genomic: TTCATGCAAGCGCTTGCGTATAATGAAAGGATCAGAAGCAATTGGTCTTGgtaagcaatt ... taattatcagCACCAAGAGCAATGGAGAAGTGTAAGAATAGATGCTGAACCAGCACAGCCT
EST: gi|351045641|gb|FQ440826.1|FQ440826
EST:     TTCATGCAAGCGCTTGCGTATAATGAAAGGATCAGAAGCAATTGGTCTTG                         CACCAAAGAGCA-TGGAGAAATGTAAGAATAGATGCTGAACCAGCACA
genomic: TTCATGCAAGCGCTTGCGTATAATGAAAGGATCAGAAGCAATTGGTCTTGgtaagcaatt ... taattatcagCACCAA-GAGCAATGGAGAAGTGTAAGAATAGATGCTGAACCAGCACA
EST: gi|110382108|gb|EC938506.1|EC938506
EST:     TTCATGCAAGCGCTTGCGTATAATGAAAGGATCAGAAGCAATTGGTCTTG                         CACCAAGAGCAATGGAGAAGTGTAAGAATAGATGCTGAACCAGCACAGCCT
genomic: TTCATGCAAGCGCTTGCGTATAATGAAAGGATCAGAAGCAATTGGTCTTGgtaagcaatt ... taattatcagCACCAAGAGCAATGGAGAAGTGTAAGAATAGATGCTGAACCAGCACAGCCT
EST: gi|110378509|gb|EC943646.1|EC943646
EST:     TTCATGCAAGCGCTTGCGTATAATGAAAGGATCAGAAGCAATTGGTCTTG                         CACCAAGAGCAATGGAGAAGTGTAAGAATAGATGCTGAACCAGCACAGCCT
genomic: TTCATGCAAGCGCTTGCGTATAATGAAAGGATCAGAAGCAATTGGTCTTGgtaagcaatt ... taattatcagCACCAAGAGCAATGGAGAAGTGTAAGAATAGATGCTGAACCAGCACAGCCT
EST: gi|34551059|gb|CF519257.1|CF519257
EST:     TTCATGCAAGCGCTTGCGTATAATGAAAGGATCAGAAGCAATTGGTCTTG                         CACCAAGAGCAATGGAGAAGTGTAAGAATAGATGCTGAACCAGCACAGCCT
genomic: TTCATGCAAGCGCTTGCGTATAATGAAAGGATCAGAAGCAATTGGTCTTGgtaagcaatt ... taattatcagCACCAAGAGCAATGGAGAAGTGTAAGAATAGATGCTGAACCAGCACAGCCT
EST: gi|351056255|gb|FQ453717.1|FQ453717
EST:     TCATGCAAGCGCTTGCGTATAATGAAAAGG-TCAGAAGCAATTGGTCTTG                         CACCAAGAGCAATGAAGAAGTG
genomic: TCATGCAAGCGCTTGCGTATAATGAAA-GGATCAGAAGCAATTGGTCTTGgtaagcaatt ... taattatcagCACCAAGAGCAATGGAGAAGTG
EST: gi|30328719|gb|CD011981.1|CD011981
EST:     TTCATGCAAGCGCTTGCGTATAATGAAAGGATCAGAAGCAATTGGTCTTG                         CCCCAAGAGCAATGGAGAAGTGTAAGAATAGATGCTGAACCAGCACAGCCT
genomic: TTCATGCAAGCGCTTGCGTATAATGAAAGGATCAGAAGCAATTGGTCTTGgtaagcaatt ... taattatcagCACCAAGAGCAATGGAGAAGTGTAAGAATAGATGCTGAACCAGCACAGCCT
EST: gi|30328414|gb|CD011676.1|CD011676
EST:     TTCATGCAAGCGCTTGCGTATAATGAAAGGATCAGAAGCAATTGGTCTTG                         CACCAAGAGCAATGGAGAAGTGTAAGAATAGATGCTGAACCAGCACAGCCT
genomic: TTCATGCAAGCGCTTGCGTATAATGAAAGGATCAGAAGCAATTGGTCTTGgtaagcaatt ... taattatcagCACCAAGAGCAATGGAGAAGTGTAAGAATAGATGCTGAACCAGCACAGCCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGTTTGTTGATTCATGCAAGCGCTTGCGTATAATGAAAGGATCAGAAGCAATTGGTCTTGgtaagcaattgatcagcaggaattatttttctagccttcaaacagatcatgaacaatgcatcatagagggttgggcattatgatcagctcaaccttatatttattgcaatccaaactttttattattattattaatcttcttttcctatatataagtatataactaatgctagttccattaattatcag

- - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - -  AAGCAA