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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCAgtaagctaagctctctctactaagaacggttttgtattccactttattgttaaatcatgctgattttttatttttttttactgaagttacttgaggctat...

Basic information

species Vitis vinifera
transcript Vv19s0015g01010.t01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0015g01010.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: LOC_Os01g50760.1 (Oryza sativa), 5'ss of exon 6
TCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCAgtaagctaagctctctctactaagaacggtttt-gtattccactttattgttaaatcatgctgattttttatttttttttactgaagttacttgaggctat-----
|||||||||||||||||||||||| || ||||| |||||||| || ||||| ||| | |   |  | ||| ||| | |   |||   | ||  |  |     ||   | ||       |  |  |  |   ||   |   || ||     |||     
TCACCGCCGCATTGTTCAGTACAAGACAGCTTACTACTCATTCTATCTTCCGgtaggatttaccat-tctcctatggattttttccatctttaaactctcacttcggtaatctgcgaatagttgtcatcactagcaataatatttttctttatccaag

upper sequence: Vv19s0015g01010.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G098569_T01 (Zea mays), 5'ss of exon 6
TCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCAgtaagctaagctctctctactaagaacggttttgtattccactttattgttaaatcatgctgattttttatttttttttactgaagt-tacttgaggctat
|||||||||||| ||||||||||| || |||||||| ||||| |||||||| |||||   || | |   | ||    |   | || |    ||  |   |||||   |||    |||| ||   | |  | |      | ||||  |  | | 
TCACCGCCGCATCGTTCAGTACAAGACAGCTTATTATTCATTCTACCTTCCTgtaag---agttat---tgctctatatattcttctcagtcatctggatgttag--catttcaatttgttgagtgtggtaataagtttctactccattcaag

upper sequence: Vv19s0015g01010.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G147721_T01 (Zea mays), 5'ss of exon 6
TCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCAgtaagctaagctctctctactaagaacggttttgtattccactttattgttaaatcatgctgattttttatttttttttactgaagttacttgaggctat----
|| ||||| ||| ||||||||||| || |||||||| |||||||||||||| |||||   || |  |   |||    |   |  | |    || ||   |||||   ||| || ||||  |   | |  | ||  ||||| | |    || |    
TCGCCGCCACATCGTTCAGTACAAGACAGCTTATTATTCATTTTACCTTCCTgtaag---agttacc---actctatatattcctctcagtcatttggatgtta--ccattctaatttgatgagtgtggtaac--aagtt-cctactcctctcaag

upper sequence: Vv19s0015g01010.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA09G01820.3 (Glycine max), 5'ss of exon 7
TCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCAgtaagctaagctctctctactaagaacggttttgtattccactttattgttaaatcatgctgattttttatttttttttactgaagttacttgaggctat--------
 || || || || ||||||||||| ||||| || || ||||||||||||||||||||      |   | |||         |||| | ||  |     |   ||| |  || |   || ||  |   |||| ||  || ||||   | | |         
GCATCGACGTATAGTTCAGTACAAGACTGCATACTATTCATTTTACCTTCCAgtaagtattaattcttgtac--------atttttttttgtatagcctccctaatttttggtttcttctttgtcccttttcctagagatactaatgtcaaatggttctt

upper sequence: Vv19s0015g01010.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA15G12780.1 (Glycine max), 5'ss of exon 7
TCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCAgtaagctaagctctctctactaagaacggttttgtattccactttattgttaaatcatgctgattttttatttttttttactgaagttacttgaggctat-------
 || || || |||||||||||||| ||||| ||||| || ||||||||||| |||||      | | | |||         |||| | |||   |    |    | | ||| |   || ||  |   |||| ||  || ||||   | | |        
GCATCGACGTATTGTTCAGTACAAGACTGCATATTATTCCTTTTACCTTCCGgtaagtattaatttttgtac-------attttttttttcgtatagcctccctagttatggtttcttctttgtcccttttcctagagatactaacgtcaaatgattct

upper sequence: Vv19s0015g01010.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: AT4G17190.1 (Arabidopsis thaliana), 5'ss of exon 6
TCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCAgtaag----ctaag---ctctctctactaagaacggttttgtattccactttattgttaaatcatgctgattttttatttttttttactgaagttacttgaggctat
 || || || |||||| |||||||||| ||||||||||||||||| ||||| || ||    || |    |||||||||   | |    | | |  |  ||| |   | | | |   ||| |  |  ||  |||  |   ||  |   | |         
CCATCGGCGTATTGTTGAGTACAAAACAGCTTATTACTCATTTTATCTTCCTgtgagtactctgaatccctctctctatatatatatatatagagtcacacgtaggt-tcagaggttgcagcataatttatttcgtaagctagacacattctg------

upper sequence: Vv19s0015g01010.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: AT5G47770.1 (Arabidopsis thaliana), 5'ss of exon 7
TCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCAgtaagctaagctctctctactaagaacggttttgtattccactttattgttaaatcatgctgattttttatttttttttactgaagttacttgaggctat------------------------
 ||||| || ||||| ||||||||||| ||||||||||||||||| || || || || || |   ||||| ||      |   |  ||||     | |     || ||||| |  |  |||  | |   | | || | ||  | ||  |  |                        
CCACCGTCGTATTGTCCAGTACAAAACGGCTTATTACTCATTTTATCTCCCTgtgag-tatggattctcttcttccctag---tcatatttggggtcaaaaacaa-tcatgttattccttttgtctccatcattgcaattg-tagatcccgtgacaagctgtgtttttctattcag

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|161718315|gb|FC067264.1|FC067264
EST:     ACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCA                         GTTGCATGTGCATTGCTTATTGCAGGCGAAAATTTGGACAATCACACTTCT
genomic: ACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCAgtaagctaag ... atacacctagGTTGCATGTGCATTGCTTATGGCAGGCGAAAATTTGGACAATCACACTTCT
EST: gi|110702878|gb|EE079232.1|EE079232
EST:     ACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCA                         GTTGCATGTGCATTGCTTATGGCAAGCGAATATTTGGACAATCACACTTCT
genomic: ACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCAgtaagctaag ... atacacctagGTTGCATGTGCATTGCTTATGGCAGGCGAAAATTTGGACAATCACACTTCT
EST: gi|110396453|gb|EC962139.1|EC962139
EST:     ACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCA                         GTTGCATGTGCATTGCTTATTGCAGGCGAAAATTTGGACAATCACACTTCT
genomic: ACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCAgtaagctaag ... atacacctagGTTGCATGTGCATTGCTTATGGCAGGCGAAAATTTGGACAATCACACTTCT
EST: gi|22013972|gb|BQ799006.1|BQ799006
EST:     ACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCA                         GTTGCATGTGCATTGCTTATGGCAGGCGAAAATTTGGACAATCACACTTCT
genomic: ACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCAgtaagctaag ... atacacctagGTTGCATGTGCATTGCTTATGGCAGGCGAAAATTTGGACAATCACACTTCT
EST: gi|110729204|gb|EE105291.1|EE105291
EST:     ACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCA                         GTTGCATGTGCATTGCTTATGGCAAGCGAAAATTTGGACAATCACACTTCT
genomic: ACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCAgtaagctaag ... atacacctagGTTGCATGTGCATTGCTTATGGCAGGCGAAAATTTGGACAATCACACTTCT
EST: gi|71877000|gb|DT026055.1|DT026055
EST:     ACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCA                         GTTGCATGTGCATTGCTTATTGCAGGC
genomic: ACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCAgtaagctaag ... atacacctagGTTGCATGTGCATTGCTTATGGCAGGC
EST: gi|30256278|gb|CB972121.1|CB972121
EST:     ACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCA                         GTTGCATGTGCATTGCTTATGGCNGGCGAAAATTTGGACAATCACACTTCT
genomic: ACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCAgtaagctaag ... atacacctagGTTGCATGTGCATTGCTTATGGCAGGCGAAAATTTGGACAATCACACTTCT
EST: gi|46917987|gb|CN547316.1|CN547316
EST:     ACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCA                         GTTGCATGTGCATTGCTTA
genomic: ACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCAgtaagctaag ... atacacctagGTTGCATGTGCATTGCTTA
EST: gi|110698392|gb|EE075834.1|EE075834
EST:     ACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCA                         GTTGCATGTGCATTGCTTATGGCAGGCGAAAATTTGGACAATCACACTTCT
genomic: ACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCAgtaagctaag ... atacacctagGTTGCATGTGCATTGCTTATGGCAGGCGAAAATTTGGACAATCACACTTCT
EST: gi|77579770|gb|DV218763.1|DV218763
EST:     ACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCA                         GTTGCATGTGCATTGCTTATGGC
genomic: ACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCAgtaagctaag ... atacacctagGTTGCATGTGCATTGCTTATGGC
EST: gi|110375001|gb|EC939952.1|EC939952
EST:     ACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCA                         GTTGCATGTGCATTGCTTATGGCAGGCGAAAATTTGGACAATCACACTTCT
genomic: ACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCAgtaagctaag ... atacacctagGTTGCATGTGCATTGCTTATGGCAGGCGAAAATTTGGACAATCACACTTCT
EST: gi|30128757|gb|CB914096.1|CB914096
EST:     ACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCA                         GTTGCATGTGCATTGCTTATGGCAGGCGAAAATTTGGACAATCACACTTCT
genomic: ACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCAgtaagctaag ... atacacctagGTTGCATGTGCATTGCTTATGGCAGGCGAAAATTTGGACAATCACACTTCT
EST: gi|110687343|gb|EE064671.1|EE064671
EST:     ACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCA                         GTTGCATGTGCATTGCTTATTGCANGCGAAAATTTGGACAATCACACTTCT
genomic: ACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCAgtaagctaag ... atacacctagGTTGCATGTGCATTGCTTATGGCAGGCGAAAATTTGGACAATCACACTTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCACCGCCGCATTGTTCAGTACAAAACTGCTTATTACTCATTTTACCTTCCAgtaagctaagctctctctactaagaacggttttgtattccactttattgttaaatcatgctgattttttatttttttttactgaagttacttgaggctat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actaagaa