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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGTTCGGAACTTTAGAGGACCTCTTCTAGAGTTACTGCAATCAGGGGATATAGATCTTTGCTTTGCCAATGAGGATGAAGCAAGAGAGCTGTTAAGgtgattgccaattgatttttccagacctatcatgctaaaacagtcggtgatgaaagagaattaatcctcctcatccagcttaaaatttttggtgcaatctgtggtaaatggtgctaatttctcttatgatggttgtag

Basic information

species Vitis vinifera
transcript Vv18s0001g12750.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g12750.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: LOC_Os01g01620.1 (Oryza sativa), 5'ss of exon 6
ATGGTTCGGAACTTTAGAGGACCTCTTCTAGAGTTACTGCAATCAGGGGATATAGATCTTTGCTTTGCCAATGAGGATGAAGCAAGAGAGCTGTTAAGgtgattgccaattgatttttccagacctatcatgctaaaacagtcggtgatgaaagagaattaatcctcctcatccagcttaaaatttttggtgcaatctgtggtaaatggtgctaatttctcttatgatggttgtag
||||||||  ||| |||   ||  ||  | ||  |  || || | ||  | || || |||||||||||||||||||||||||| ||||||||  || ||||||         |   |    | | |||  |  | | |   ||     |||  || |  || |       |||     |     | ||  | ||                                          
ATGGTTCGTGACTATAGGACACAACTCATTGACCTTTTGGAAACTGGCAACATTGACCTTTGCTTTGCCAATGAGGATGAAGCTAGAGAGCTTCTAGGgtgat---------accctcatcgccttattgt-ttcagatgttcttcagtgagtgatacctattatagtatatctgatgtgtgcgtgttttttcag-----------------------------------------

upper sequence: Vv18s0001g12750.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G051842_T01 (Zea mays), 5'ss of exon 4
ATGGTTCGGAACTTTAGAGGACCTCTTCTAGAGTTACTGCAATCAGGGGATATAGATCTTTGCTTTGCCAATGAGGATGAAGCAAGAGAGCTGTTAAGgtgattgccaattgatttttccagacctatcatgctaaaacagtcggtgatgaaagag-aattaatcctcctcatccagcttaaaatttttggtgcaatctgtggtaa-atggtgc---taatttctcttatgatggttgtag------------------------
||||| ||  ||| |||       ||| |  |  |  || |  | ||  | || || |||||||| ||||||||||||||||| |||||| |  || |||||  | |  |  |   |   | |   |     ||||  |||   |  ||||||||   |  ||| |   |     |    | |  |  |       | ||  || | || ||||    ||| |    |||| ||  || ||                        
ATGGTCCGTGACTCTAGGTCTAAGCTTATTAACCTTTTGGAGACCGGTAACATTGACCTTTGCTTCGCCAATGAGGATGAAGCTAGAGAGGTTATAGGgtga--gtctttccaaaatcgtatattaacgcatctaagtcagaaaggaatgaaagaatgacgaattcaaatggataaaaaaatatatgctcacatcttttgaagtgacatagtgcaaccaatctaaggtatg-tgcctggagttcacctgttgcttttatctgcag

upper sequence: Vv18s0001g12750.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA14G07980.2 (Glycine max), 5'ss of exon 6
ATGGTTCGGAACTTTAGAGGACCTCTTCTAGAGTTACTGCAATCAGGGGATATAGATCTTTGCTTTGCCAATGAGGATGAAGCAAGAGAGCTGTTAAGgtgattgccaattg-atttttccagacctatcatgctaaaacagtcggtgatgaaagagaatta--atcctcctcatccagcttaaaatttttggtgcaatctgtggtaaatggtgctaatttctcttatgatggttgtag
|||||| |||| || | |  ||| |||||  || ||||| | || ||| ||||||| ||||||||||||||||||||||| |||| ||||||  || ||| |||| |  ||  | ||  ||   | |    | | ||| ||     |  |  |||  | | |  ||  || |  |    ||||| |  |    ||     |||  |  ||      |  |  | |||  |||| | |||
ATGGTTAGGAATTTCAAACAACCACTTCTGAAGCTACTGGAGTCTGGGAATATAGACCTTTGCTTTGCCAATGAGGATGAGGCAACAGAGCTTCTACGgtaattgtcttttttacttaaccctgcttg--gtaccaaagcatgaattattccaagttattcatcattgtcttagtttcacttaataactaatctgttgattgttttttata-cataatgtcattttacaatggatttag

upper sequence: Vv18s0001g12750.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA17G37040.1 (Glycine max), 5'ss of exon 6
ATGGTTCGGAACTTTAGAGGACCTCTTCTAGAGTTACTGCAATCAGGGGATATAGATCTTTGCTTTGCCAATGAGGATGAAGCAAGAGAGCTGTTAAGgtgattgccaattgatttttccagacctatcatgctaaaacagtcggtgatgaaagagaattaatcctcctcatccagcttaa-aatt---tttggtgcaatctgtggtaaatggtgctaatttctcttatgatggttgtag
 ||||| |||| |||| |  ||| |||||  || ||||| | || ||| ||||||| ||||||||||||||||||||||| |||| ||||||  |||||| | | | | ||  |||    |  |||    || |  || | |  |   |   |    | | ||  || |  |    ||||| || |   | || ||   | | |  || ||| ||  | |||    |||||     |   
-TGGTTAGGAATTTTAAACAACCACTTCTGAAGCTACTGGAGTCTGGGAATATAGACCTTTGCTTTGCCAATGAGGATGAGGCAACAGAGCTTCTAAGGtaact-ctattt--tttacttaaccctgctttgttctaaga-tatgcatttttaagttactcattgtcttagtttcacttaataagtaaatctgttgattttttttatacatgatgtcactttac--tatgaacacagg--

upper sequence: Vv18s0001g12750.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA04G03290.1 (Glycine max), 5'ss of exon 6
ATGGTTCGGAACTTTAGAGGACCTCTTCTAGAGTTACTGCAATCAGGGGATATAGATCTTTGCTTTGCCAATGAGGATGAAGCAAGAGAGCTGTTAAGgtgattgccaattg-atttttccagacctatcatgctaaaacagtcggtgatgaaagagaattaa--------tcctcctcatccagcttaaaatttttg------gtgcaatctgt------ggtaaatggtgctaattt-ctcttatgatggttgtag
|||||  ||||||||| |  ||| |||||  || ||||| |||| ||| | ||||| || ||||||||||||||||||||||||   || || ||||||||| || || ||| ||    ||   | |   ||    |  || | | |||  | | |   |||         ||||  | ||  |   |   |||||         || | | |||        ||| || |   ||||| || ||  |  | || |||
ATGGTGAGGAACTTTAAACTACCGCTTCTCAAGCTACTGGAATCTGGGAACATAGACCTCTGCTTTGCCAATGAGGATGAAGCAGCTGAACTTTTAAGgtgactgtcatttggatcagacccagctttatatcaagatgcatttgttgaaaatacaattttatcttcagtttcctagttattgactatcttattttcatttaatatgtattttgtcttgtaaataagtgatatcaatttacttttccgtggattttag

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|110717578|gb|EE093555.1|EE093555
EST:     GATATAGATCTTTGCTTTGCCAATGAGGATGAAGCAAGAGAGCTGTTAAG                         AGATGACGAAAATGCTAGTCCTGAGGCTGCTCTTGAATTTCTTGCTAAGCA
genomic: GATATAGATCTTTGCTTTGCCAATGAGGATGAAGCAAGAGAGCTGTTAAGgtgattgcca ... atggttgtagAGATGACGAAAATGCTAGTCCTGAGGCTGCTCTTGAATTTCTTGCTAAGCA
EST: gi|110697937|gb|EE075379.1|EE075379
EST:     GATATAGATCTTTGCTTTGCCAATGAGGATGAAGCAAGAGAGCTGTTAAG                         AGATGACGAAAATGCTAGTCCTGAGGCTGCTCTTGAATTTCTCGCTAAGCA
genomic: GATATAGATCTTTGCTTTGCCAATGAGGATGAAGCAAGAGAGCTGTTAAGgtgattgcca ... atggttgtagAGATGACGAAAATGCTAGTCCTGAGGCTGCTCTTGAATTTCTTGCTAAGCA
EST: gi|110697939|gb|EE075381.1|EE075381
EST:     GATATAGATCTTTGCTTTGCCAATGAGGATGAAGCAAGAGAGCTGTTAAG                         AGATGACGAAAATGCTAGTCCTGAGGCTGCTCTTGAATTTCTCGCTAAGCA
genomic: GATATAGATCTTTGCTTTGCCAATGAGGATGAAGCAAGAGAGCTGTTAAGgtgattgcca ... atggttgtagAGATGACGAAAATGCTAGTCCTGAGGCTGCTCTTGAATTTCTTGCTAAGCA
EST: gi|110684947|gb|EE062806.1|EE062806
EST:     ATATAGATCTTTGCTTTTGC-AATGAGGATGAAGCAAGAGAGCTGTTAA-                         AGATGACGACA-TGCTAGTCCTGAAGCTGCTC
genomic: ATATAGATCTTTGCTTT-GCCAATGAGGATGAAGCAAGAGAGCTGTTAAGgtgattgcca ... atggttgtagAGATGACGAAAATGCTAGTCCTGAGGCTGCTC
EST: gi|110699416|gb|EE076394.1|EE076394
EST:     GATATAGATCTTTGCTTTGCCAATGAGGATGAAGCAAGAGAGCTGGTAAG                         AGATGACGAAAATGCTAGTCCTGAGGCTGCTCTTGAAT
genomic: GATATAGATCTTTGCTTTGCCAATGAGGATGAAGCAAGAGAGCTGTTAAGgtgattgcca ... atggttgtagAGATGACGAAAATGCTAGTCCTGAGGCTGCTCTTGAAT
EST: gi|33401764|gb|CF207391.1|CF207391
EST:     GATATAGATCTTTGCTTTGCCAATGAGGATGAAGCAAGAGAGCTGTTAAG                         AGATGACGAAAATGCTAGTCCTGAGGCTGCTCTTGAATTTCTTGCTAAGCA
genomic: GATATAGATCTTTGCTTTGCCAATGAGGATGAAGCAAGAGAGCTGTTAAGgtgattgcca ... atggttgtagAGATGACGAAAATGCTAGTCCTGAGGCTGCTCTTGAATTTCTTGCTAAGCA
EST: gi|33401843|gb|CF207470.1|CF207470
EST:     GATATAGATCTTTGCTTTGCCAATGAGGATGAAGCAAGAGAGCTGTTAAG                         AGATGACGAAAATGCTAGTCCTGAGGCTGCTCTTGAATTTCTTGCTAAGCA
genomic: GATATAGATCTTTGCTTTGCCAATGAGGATGAAGCAAGAGAGCTGTTAAGgtgattgcca ... atggttgtagAGATGACGAAAATGCTAGTCCTGAGGCTGCTCTTGAATTTCTTGCTAAGCA
EST: gi|110732830|gb|EE108461.1|EE108461
EST:     GATATAGATCTTTGCTTTGCCAATGAGGATGAAGCAAGAGAGCTGTTAAG                         AGATGACGAAAATGCTAGTCCTGAGGCTGCTCTTGAATTTCTCGCTAAGCA
genomic: GATATAGATCTTTGCTTTGCCAATGAGGATGAAGCAAGAGAGCTGTTAAGgtgattgcca ... atggttgtagAGATGACGAAAATGCTAGTCCTGAGGCTGCTCTTGAATTTCTTGCTAAGCA
EST: gi|110697936|gb|EE075378.1|EE075378
EST:     GATATAGATCTTTGCTTTGCCAATGAGGATGAAGCAAGAGAGCTGTTAAG                         AGATGACGAAAATGCTAGTCCTGAGGCTGCTCTTGAATTTCTCGCTAAGCA
genomic: GATATAGATCTTTGCTTTGCCAATGAGGATGAAGCAAGAGAGCTGTTAAGgtgattgcca ... atggttgtagAGATGACGAAAATGCTAGTCCTGAGGCTGCTCTTGAATTTCTTGCTAAGCA
EST: gi|110429129|gb|EC995617.1|EC995617
EST:     GATATAGATCTTTGCTTTGCCAATGAGGATGAAGCAAGAGAGCTGTTAAG                         AGATGACGAAAATGCTAGTCCTGAGGCTGCTCTTGAATTTCTTGCTAAGCA
genomic: GATATAGATCTTTGCTTTGCCAATGAGGATGAAGCAAGAGAGCTGTTAAGgtgattgcca ... atggttgtagAGATGACGAAAATGCTAGTCCTGAGGCTGCTCTTGAATTTCTTGCTAAGCA
EST: gi|110698651|gb|EE076389.1|EE076389
EST:     ATATAGATCCTTGCTTTGCCCATGGAG-ATGAAACAAGAGAGCTGTTAAG                         AGATGACGAAAATGCCTAATCCTGAGG
genomic: ATATAGATCTTTGCTTTGCCAATG-AGGATGAAGCAAGAGAGCTGTTAAGgtgattgcca ... atggttgtagAGATGACGAAAATGC-TAGTCCTGAGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGTTCGGAACTTTAGAGGACCTCTTCTAGAGTTACTGCAATCAGGGGATATAGATCTTTGCTTTGCCAATGAGGATGAAGCAAGAGAGCTGTTAAGgtgattgccaattgatttttccagacctatcatgctaaaacagtcggtgatgaaagagaattaatcctcctcatccagcttaaaatttttggtgcaatctgtggtaaatggtgctaatttctcttatgatggttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT