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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCGGGGTGTAATATATGGTTGTGGGGATTTGATATTCTCATCTCACATGATCTTCACTCTAGTCTTTGTGCTCACATATCAGAAATATGGCACCCGAAGgtataacattcttgtcatatagtagattcaaatctaacaaactgaaaattttatactatgttttacatatgtttgatgttccttactttaaggtgcatgt...

Basic information

species Vitis vinifera
transcript Vv08s0007g01510.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g01510.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: LOC_Os01g63060.1 (Oryza sativa), 5'ss of exon 8
CTCGGGGTGTAATATATGGTTGTGGGGATTTGATATTCTCATCTCACATGATCTTCACTCTAGTCTTTGTGCTCACATATCAGAAATATGGCACCCGAAGgtataacattcttgtcatatagtagattcaaatctaacaaactgaaaattttatactatgttttacatatgtttgatgtt----ccttactttaaggtgcatgt----------------------------------------------------------
|||| || ||  | | ||||||||| ||| |||| || ||||||||||||||||| || || || || ||||  |||||||| ||||||||  ||  ||||||| | | | | |  ||  | ||    || |       |  ||    |||         ||||     |||   ||||       ||  || ||| ||||||                                                           
CTCGTGGAGTGCTTTTTGGTTGTGGCGATCTGATTTTTTCATCTCACATGATCTTTACACTTGTTTTCGTGCGTACATATCATAAATATGGATCCAAAAGgtattaaaatataga-atgca-tatgcgcacacacgcttatttgtctctttccctggtcattttttgcctgtaatatgtcataaatttggttcaagttgcatgctaactcagtactctgacatctgatcttctaatctcattggttgttcctgttttgttag

upper sequence: Vv08s0007g01510.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: LOC_Os05g21180.4 (Oryza sativa), 5'ss of exon 7
CTCGGGGTGTAATATATGGTTGTGGGGATTTGATATTCTCATCTCACATGATCTTCACTCTAGTCTTTGTGCTCACATATCAGAAATATGGCACCCGAAGgtataacattcttgtcatatagtagattcaaatctaacaaact---gaaaattttatactatgttttacatatg----tttgatgttccttacttt----aaggtgcatgt---
|  | || ||||| || || || || || |||||||| ||||| |||||||| |||||| ||||||| ||  | ||||| ||||||||||| |    |||||   |  || |||| ||  ||  ||| |    |    |  ||   || || || |  || | |   | |||      | | |  |||  || |||    ||    ||| |   
CAAGAGGAGTAATTTACGGGTGCGGTGACTTGATATTTTCATCCCACATGATTTTCACTATAGTCTTCGTTGTAACATACCAGAAATATGGAAATATAAGgtg--atgtttttgt-attgagaggatccctcacaggaattcttgcgagaaattcagtctgtctaggaaatacaacaatctaagattctgtatttttttcaaaactcatttcag

upper sequence: Vv08s0007g01510.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G169293_T01 (Zea mays), 5'ss of exon 8
CTCGGGGTGTAATATATGGTTGTGGGGATTTGATATTCTCATCTCACATGATCTTCACTCTAGTCTTTGTGCTCACATATCAGAAATATGGCACCCGAAGgtataacattctt--------gtcatatagtagattcaaatctaacaaac-tgaaaattttatactatgttttacatatgtttgatgttccttactttaaggt-----gcatgt--------
|||| || ||  | | ||||||||| ||| ||||||| ||||||||||||||||||||||| || ||||||| |||||| || ||||||||| |    |||||    | |||          |||| | ||    ||   | |     || || || || | |   || ||  | || | || | |   |   |  | ||  |      |||||        
CTCGTGGAGTGCTTTTTGGTTGTGGTGATCTGATATTTTCATCTCACATGATCTTCACTCTGGTTTTTGTGCGCACATACCATAAATATGGCTCAAACAGgtacggaaatctattatggcgatcatgt-gtgttctcccgtgtgttttacatgcaagttgtgtgacatcttacaaat-tattagttccccacgaactcaaccttcttcacatgttcttgtag

upper sequence: Vv08s0007g01510.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G004949_T01 (Zea mays), 5'ss of exon 6
CTCGGGGTGTAATATATGGTTGTGGGGATTTGATATTCTCATCTCACATGATCTTCACTCTAGTCTTTGTGCTCACATATCAGAAATATGGCACCCGAAGgta--taacattcttgt------catatagtagattcaaatctaacaaactgaaaattttatactatgttttacatatgttt--gatgttccttactttaag---gtgcatgt--
|||| || ||  | | ||||||||| ||| ||||||| |||||||||||||||||||| ||||| || |||| ||| || || ||||||||| |    |||||  |||  || ||||      ||| |   ||   |        |    || || || | ||  || ||| | ||  |||    |    |   || ||      || | |||  
CTCGCGGAGTGCTTTTTGGTTGTGGCGATCTGATATTTTCATCTCACATGATCTTCACCCTAGTTTTCGTGCGCACGTACCATAAATATGGCTCAAACAGgtacgtaaatttattgtggtgagcatgtgtgagccccggtgtgttctgcatgtaatttgtgtaacatttttcaaattggttccccacaaactcaaccttgtacgcgttcttgtag

upper sequence: Vv08s0007g01510.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G067036_T01 (Zea mays), 5'ss of exon 8
CTCGGGGTGTAATATATGGTTGTGGGGATTTGATATTCTCATCTCACATGATCTTCACTCTAGTCTTTGTGCTCACATATCAGAAATATGGCACCCGAAGgta-taacattcttgtcatatagtag-attcaaatctaacaaactgaaaattttatactatgttttacatatgtttgatgttccttactttaaggtgcatgt--
|||| || ||| | | ||||||||| ||||||||||| |||||||||||||| |||||||| || || || |  || || || ||||||||  |   |||||| |    || |   | |||  |    ||  || |  |  || |    | | | |  | ||  |  |       ||| | |      | |    ||  |    
CTCGTGGGGTACTTTTTGGTTGTGGTGATTTGATATTTTCATCTCACATGATTTTCACTCTGGTTTTCGTTCGAACTTACCAAAAATATGGTTCGAAAAGgtaattgtgttttgcacttatctttttgtttgaaccctatcaagttccgactgtctcttgtgggtatccctgaaatgaagctgaactatgtgtattgtgttcag

upper sequence: Vv08s0007g01510.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G147724_T01 (Zea mays), 5'ss of exon 8
CTCGGGGTGTAATATATGGTTGTGGGGATTTGATATTCTCATCTCACATGATCTTCACTCTAGTCTTTGTGCTCACATATCAGAAATATGGCACCCGAAGgtataacattcttgtc-atatagtag---attcaaatctaacaaactgaaaattttatactatgttttacatatgtttgatgttccttactttaaggtg-catgt---
|  | || || || ||||| ||||| || |||||||| ||||| |||||||| ||||| ||||| |||||  | ||||| ||||||||||| | |   ||||| |   || ||||| ||||  |      ||    ||     |  ||  || | |||  |   |  |   || ||    | ||  ||  |  ||     |||||   
CAAGAGGAGTGATTTATGGATGTGGTGACTTGATATTTTCATCCCACATGATTTTCACCCTAGTTTTTGTCATTACATACCAGAAATATGGAAGCATGAGgtaaagatttgttgtccatatgttttcttgtttgtgtcagcgtatttgtgaaatatatgttcaatgatgtttaagtcctgtttttttttttaaaaaaaatcatgtcag

upper sequence: Vv08s0007g01510.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G045976_T01 (Zea mays), 5'ss of exon 8
CTCGGGGTGTAATATATGGTTGTGGGGATTTGATATTCTCATCTCACATGATCTTCACTCTAGTCTTTGTGCTCACATATCAGAAATATGGCACCCGAAGgtataacattcttgtc-atatagtagattcaaatcta-acaaactgaaaattttatactatgttttacatatgtttga--tgttccttactttaaggtgcatgt---
|    || || || ||||| ||||| || |||||||| ||||| |||||||| ||||| ||||| || ||  | ||||| ||||||||||| | |  |||||     ||| ||||| |  || |   |||   | ||      || |    |  |   ||||||  |   |||||| |    ||  ||  ||     | |||||   
CAACAGGAGTGATTTATGGATGTGGTGACTTGATATTTTCATCCCACATGATTTTCACCCTAGTTTTCGTCATAACATACCAGAAATATGGAAGCATAAGgtgagtaattgttgtccaattattttcttcttgtttatgttggctcatttgtgaaagatatgttgaatg-atgtttaagtccttttttttttgccaattcatgtcag

upper sequence: Vv08s0007g01510.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA03G15850.1 (Glycine max), 5'ss of exon 8
CTCGGGGTGTAATATATGGTTGTGGGGATTTGATATTCTCATCTCACATGATCTTCACTCTAGTCTTTGTGCTCACATATCAGAAATATGGCACCCGAAGgtataacattcttgtca-tatagtagattcaaatctaacaaactgaaaattttatactatgttttacatatgtttgatgttccttactttaaggtgcatgt-----
| || || ||  | ||||| ||||| ||||||||||||||||| ||||||||||| ||||| |||||||||||||| ||||||||||||||||| |||||||| ||    ||| | | | |  |  ||   | ||  |  |  | | | ||||  |  |  ||| ||  ||     ||      |  |  |||| | ||||     
CGCGTGGCGTGGTCTATGGATGTGGTGATTTGATATTCTCATCACACATGATCTTTACTCTTGTCTTTGTGCTCACGTATCAGAAATATGGCACTCGAAGgtaaaattggcttataaatgtcttctatctcactc--atgatttaatagttttcgataaattttaacgaataagaaat----tatgttagaaggagtatgttggta

upper sequence: Vv08s0007g01510.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA01G26700.1 (Glycine max), 5'ss of exon 8
CTCGGGGTGTAATATATGGTTGTGGGGATTTGATATTCTCATCTCACATGATCTTCACTCTAGTCTTTGTGCTCACATATCAGAAATATGGCACCCGAAGgtataacattcttgtca-tatagtagattcaaatctaacaaactgaaaattttat-actatgttttacatatgtttgatgttccttactttaaggtgc-atgt
| || |||||  | ||||| ||||| ||||||||||||||||| ||||||||||| || || || ||||||||||| ||||||||||||||||| |||||||| ||    ||| | | |    |  ||     | |    ||     || | | | |  || ||||||    ||   |  ||  |||   |||  |   ||| 
CACGTGGTGTGGTCTATGGATGTGGTGATTTGATATTCTCATCACACATGATCTTTACACTTGTTTTTGTGCTCACGTATCAGAAATATGGCACTCGAAGgtaaaattggcttataaattccttccatcttgttttgttgaagaatcaactctgtcaagatattttactgcagt--aacttttgttaggctaatttattatg-

upper sequence: Vv08s0007g01510.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA18G41820.1 (Glycine max), 5'ss of exon 8
CTCGGGGTGTAATATATGGTTGTGGGGATTTGATATTCTCATCTCACATGATCTTCACTCTAGTCTTTGTGCTCACATATCAGAAATATGGCACCCGAAGgtataacattcttgtcatatagtagattcaaatctaacaaactgaaaattttatactatgttttacatatgt----ttgatgttccttactttaaggtgcatgt
| || || || |||||||| ||||| ||||||||||| ||||| ||||||||||| ||||||||||||||    |||||||| | ||| |||||  ||||||| |         ||||      || |||  | |   ||  |  || ||||  |  |  ||| ||    ||    ||  | ||  || ||| |  ||  ||  
CACGTGGCGTGATATATGGATGTGGTGATTTGATATTTTCATCACACATGATCTTTACTCTAGTCTTTGTTAATACATATCATAGATACGGCACAAGAAGgtaaattggc----tcatgggtctgactcatttttgtgaagatttaagttttccagaagatttcactgccgtaacatttgttttggttgcttcattgtttattg

upper sequence: Vv08s0007g01510.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA07G17110.1 (Glycine max), 5'ss of exon 8
CTCGGGGTGTAATATATGGTTGTGGGGATTTGATATTCTCATCTCACATGATCTTCACTCTAGTCTTTGTGCTCACATATCAGAAATATGGCACCCGAAGgtataacattcttgtcatatagtagattcaaatctaacaaactgaaaattttatactatgtttt------acatatgtttgatgttccttactttaaggtgcatgt
| |  | ||  |||||||| || || ||||||||||| ||||| ||||||||||| ||||||||||||||    |||||||| | ||| ||||| |||||||| ||    ||  | |       || |||  | |   ||  |  || ||||  |  || ||||      |   |  |||  | ||  || ||| |  ||      
CACAAGATGCGATATATGGATGCGGTGATTTGATATTTTCATCACACATGATCTTTACTCTAGTCTTTGTTAATACATATCATAGATACGGCACACGAAGgta-aattggctcat-acgggtctgactcatttttgtgaagatttaagttttccagaatattttcactgcagtaacattttgttttggttgcttcactgttt----

upper sequence: Vv08s0007g01510.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: AT2G37940.1 (Arabidopsis thaliana), 5'ss of exon 8
CTCGGGGTGTAATATATGGTTGTGGGGATTTGATATTCTCATCTCACATGATCTTCACTCTAGTCTTTGTGCTCACATATCAGAAATATGGCACCCGAAGgtataacattcttgtcatatagtagattcaaatctaacaaactgaaaattttatactatgttttacatatgtttgatgttccttactttaaggtgcatgt
|||  || || || ||||| || || ||  |||| |||||||| |||||||| ||||||||||||||||| |  || || ||||||||||||||   |||||| ||| ||||| |   |    |  || ||  ||      ||| ||||   || || ||  | |  | | ||   | | || ||  | |          
CTCATGGGGTGATGTATGGATGCGGAGACCTGATTTTCTCATCGCACATGATATTCACTCTAGTCTTTGTCCGTACTTACCAGAAATATGGCACTAAAAGgtaaaac-ttcttttggca--acatcttaaaggcttct---ctgtaaatcacat-ctctgcatcat-tcttttgtttatcccatatctcag---------

upper sequence: Vv08s0007g01510.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: AT3G54020.1 (Arabidopsis thaliana), 5'ss of exon 8
CTCGGGGTGTAATATATGGTTGTGGGGATTTGATATTCTCATCTCACATGATCTTCACTCTAGTCTTTGTGCTCACATATCAGAAATATGGCACCCGAAGgtataacattctt---gtcatatagtagattca-aatctaacaaactgaaaattttatactatgttttacatatgtttgatgttccttactttaaggtgcatgt
|||| ||||| ||||| || ||||| ||  |||| |||||||| |||||||| ||||| ||||||||||| | ||| || |||||||| ||  |   |||||| ||  ||  |   |||| || ||| |   | || |  ||||| | | |  ||   | | | | |  || |                               
CTCGTGGTGTGATATACGGATGTGGAGACCTGATTTTCTCATCGCACATGATATTCACACTAGTCTTTGTCCGCACTTACCAGAAATACGGTTCTAAAAGgtacaaagtttctctagtcacatcgtaaaacaataaccggacaaaataatagcttgtaaatgtctctctcacag------------------------------

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|110417451|gb|EC983505.1|EC983505
EST:     ATCTTCACTCTAGTCTTTGTGCTCACATATCAGAAATATGGCACCCGAAG                         GTGCATAAAGCAGTTTGCATGGTTGATTGCTGTGGCACAAAGCTTCTTAAT
genomic: ATCTTCACTCTAGTCTTTGTGCTCACATATCAGAAATATGGCACCCGAAGgtataacatt ... gtccttgcagGTGCATAAAGCAGTTTGCATGGTTGATTGCTGTGGCACAAAGCTTCTTAAT
EST: gi|161713043|gb|FC062124.1|FC062124
EST:     ATCTTCACTCTAGTCTTTGTGCTCACATATCAGAAATATGGCACCCGAAC                         GTGCATAAAGCAGTTTGCATGGTTGATTGCTGTGGCACAAAGCTTCTTAAT
genomic: ATCTTCACTCTAGTCTTTGTGCTCACATATCAGAAATATGGCACCCGAAGgtataacatt ... gtccttgcagGTGCATAAAGCAGTTTGCATGGTTGATTGCTGTGGCACAAAGCTTCTTAAT
EST: gi|22009138|gb|BQ794172.1|BQ794172
EST:     ATCTTCACTCTAGTCTTGGTGCTCACATATCAGAAATATGGCACCCGAAG                         GTGCATAAAGCAGTTTGCATGGTTGATTGCTGTGGCACAAAGCTTCTTAAT
genomic: ATCTTCACTCTAGTCTTTGTGCTCACATATCAGAAATATGGCACCCGAAGgtataacatt ... gtccttgcagGTGCATAAAGCAGTTTGCATGGTTGATTGCTGTGGCACAAAGCTTCTTAAT
EST: gi|110703156|gb|EE079754.1|EE079754
EST:     ATCTTCACTCTAGTCTTTGTGCTCACATATCAGAAATATGGCACCCGAAG                         GTGCATAAAGCAGTTTGCATGGTTGATTGCTGTGGCACAAAGCTTCTTAAT
genomic: ATCTTCACTCTAGTCTTTGTGCTCACATATCAGAAATATGGCACCCGAAGgtataacatt ... gtccttgcagGTGCATAAAGCAGTTTGCATGGTTGATTGCTGTGGCACAAAGCTTCTTAAT
EST: gi|27580938|gb|CB003633.1|CB003633
EST:     ATCTTCACTCTAGTCTTTGTGCTCACATATCAGAAATATGGCACCCGAAG                         GTGCATAAAGCAGTTTGCATGGTTGATTGCTGTGGCACAAAGCTTCTTAAT
genomic: ATCTTCACTCTAGTCTTTGTGCTCACATATCAGAAATATGGCACCCGAAGgtataacatt ... gtccttgcagGTGCATAAAGCAGTTTGCATGGTTGATTGCTGTGGCACAAAGCTTCTTAAT
EST: gi|37188828|gb|CF608177.1|CF608177
EST:     ATCTTCACTCTAGTCTTTGTGCTCACATATCAGAAATATGGCACCCGAAG                         GTGCATAAAGCAGTTTGCATGGTTGATTGCTGTGGCACAAAGCTTCTTAAT
genomic: ATCTTCACTCTAGTCTTTGTGCTCACATATCAGAAATATGGCACCCGAAGgtataacatt ... gtccttgcagGTGCATAAAGCAGTTTGCATGGTTGATTGCTGTGGCACAAAGCTTCTTAAT
EST: gi|110419291|gb|EC985508.1|EC985508
EST:     ATCTTCACTCTAGTCTTTGTGCTCACATATCAGAAATATGGCACCCGAAG                         GTGCATAAAGCAGTTTGCATGGTTGATTGCTGTGGCACAAAGCTTCTTAAT
genomic: ATCTTCACTCTAGTCTTTGTGCTCACATATCAGAAATATGGCACCCGAAGgtataacatt ... gtccttgcagGTGCATAAAGCAGTTTGCATGGTTGATTGCTGTGGCACAAAGCTTCTTAAT
EST: gi|110428534|gb|EC995009.1|EC995009
EST:     ATCTTCACTCTAGTCTTTGTGCTCACATATCAGAAATATGGCACCCGAAG                         GTGCATAAAGCAGTTTGCATGGTTGATTGCTGTGGCACAAAGCTTCTTAAT
genomic: ATCTTCACTCTAGTCTTTGTGCTCACATATCAGAAATATGGCACCCGAAGgtataacatt ... gtccttgcagGTGCATAAAGCAGTTTGCATGGTTGATTGCTGTGGCACAAAGCTTCTTAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCGGGGTGTAATATATGGTTGTGGGGATTTGATATTCTCATCTCACATGATCTTCACTCTAGTCTTTGTGCTCACATATCAGAAATATGGCACCCGAAGgtataacattcttgtcatatagtagattcaaatctaacaaactgaaaattttatactatgttttacatatgtttgatgttccttactttaaggtgcatgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaatt