Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGCTATGGAAATTGTGAGATCTAGAAGAACAGTGAACCGTCTTCATGAAAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGTTGgtaagataacatatctaaacatgtgtatcctgttgcacatgttactatctaaaactgcaacttcctctaaaatacatccctgcagagcagtgcctgttgt...

Basic information

species Vitis vinifera
transcript Vv06s0061g00540.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0061g00540.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os07g29630.1 (Oryza sativa), 5'ss of exon 3
CTTGCTATGGAAATTGTGAGATCTAGAAGAACAGTGAACCGTCTTCATGAAAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGTTGgtaagataacatatctaaacatgtgtatcctgttgcacatgttactatctaaaactgcaactt--cctctaaaata-catccctgcagagcagtgcctgttgt----
||||||| |||| | ||||| || ||| |  | || || |||||  ||||||||||||||||| | |||||  |||||||||| ||||| |||| |||||||| | |    |   |     | | |   ||| |  | | |  | |   ||  | | || | |  |||  |   || || |||   ||  |  |||  |   |    
CTTGCTAAGGAACTAGTGAGGTCAAGACGTGCTGTTAATCGTCTCTATGAAAACAAGGCTCAACTAAATTCAGTATCAATGCATCTTGGAGAAATTGTTGgtatgttctttttctt-----tttatgagctgatagagagg--atttattagcaattcagcctaaccttcatcgtatcagcccacaagttccttgcaggcaattaca

upper sequence: Vv06s0061g00540.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G165195_T01 (Zea mays), 5'ss of exon 3
CTTGCTATGGAAATTGTGAGATCTAGAAGAACAGTGAACCGTCTTCATGAAAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGTTGgtaagataacatatctaaacatgtgtatcc-tgttgcacatgttactatctaaaactgcaacttcctctaaaatacatccctgcagagcagtgcctgttgt------
||||||| |||| |||| ||||| ||| |  | || || |||||| |||| |||||||||||| | |||||  |||||||||||||||| |||| ||| |||| |      |    |    | | | |   | | |    ||    | || || |    ||  |||| | || |     |  | ||||   | |   | ||      
CTTGCTAAGGAACTTGTAAGATCAAGACGTGCTGTTAATCGTCTTTATGAGAACAAGGCTCAACTAAATTCAGTATCAATGCACCTTGGAGAAATTGTCGgtatggcttttttatgatttttttttgttggtttggtgtctgacgttgtccaagag---aatgtccttttaatt----tctggaagagtgattctgttagttaatat

upper sequence: Vv06s0061g00540.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G165195_T02 (Zea mays), 5'ss of exon 3
CTTGCTATGGAAATTGTGAGATCTAGAAGAACAGTGAACCGTCTTCATGAAAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGTTGgtaagataacatatctaaacatgtgtatcctgttg-cacatgttactatctaaaactgcaacttcctctaaaatacatccctgcagagcagtgcctgttgt------
         ||| |||| ||||| ||| |  | || || |||||| |||| |||||||||||| | |||||  |||||||||||||||| |||| ||| |||| |      |    |    | | | |    |||     ||    | || || |    ||  |||| | || |     |  | ||||   | |   | ||      
---------GAACTTGTAAGATCAAGACGTGCTGTTAATCGTCTTTATGAGAACAAGGCTCAACTAAATTCAGTATCAATGCACCTTGGAGAAATTGTCGgtatggcttttttatgatttttttttgttggtttggtgtctgacgttgtccaagag---aatgtccttttaatt----tctggaagagtgattctgttagttaatat

upper sequence: Vv06s0061g00540.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA04G21900.1 (Glycine max), 5'ss of exon 3
CTTGCTATGGAAATTGTGAGATCTAGAAGAACAGTGAACCGTCTTCATGAAAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGTTGgtaagataacatatctaaacatgtgtatcctgttgcacatgttactatctaaaactgcaacttcctctaaaatacatccctgcagagcagtgcctgttgt-----
||||||| |||| ||||||||||||| | ||| |||||||||||| ||||||| || || ||| ||||||| ||||||||||||||||| || |||||||||| | |    | || |    |   || |||       || ||    | ||  |    |   |  |||||| ||  |   ||  |   ||| || | |       
CTTGCTAAGGAACTTGTGAGATCTAGGAAAACTGTGAACCGTCTTTATGAAAATAAAGCACAAATGAATTCAATATCAATGCACCTTGGAGAGAGTGTTGgtaggtt----tttccatgttttgttagccttaacttaattttgacttatagcaaataaggattgtctaaattagttatttgt-gtttagtaccaggttcttgat

upper sequence: Vv06s0061g00540.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA12G08510.1 (Glycine max), 5'ss of exon 3
CTTGCTATGGAAATTGTGAGATCTAGAAGAACAGTGAACCGTCTTCATGAAAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGTTGgtaagataa--catatctaaacatg--tgtatcctgttgcacatgtt-actatctaaaactgcaacttcctctaaaatacatccctgcagagcagtgcctgttgt
||||||| |||| ||||||||||||| | ||| |||||||||||| ||||||| || || ||| ||||||| ||||||||||||||||| || |||||||||| | |    |||  || || ||   | |  | |||  || ||    ||| |||||    |  || |   ||  | |||     |  |||  | |         
CTTGCTAAGGAACTTGTGAGATCTAGGAAAACGGTGAACCGTCTTTATGAAAATAAAGCACAAATGAATTCAATATCAATGCACCTTGGAGAGAGTGTTGgtaggtttttccatgccttaagataattttgccttgtaacaaataaggactctctaagttagttacctgtacttga-taccaggttttagataattattcc----

upper sequence: Vv06s0061g00540.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA11G19930.1 (Glycine max), 5'ss of exon 4
CTTGCTATGGAAATTGTGAGATCTAGAAGAACAGTGAACCGTCTTCATGAAAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGTTGgtaagataacatatctaaacatgtgtatcctgttgcacatgttactat-ctaaaactgcaacttcctctaaaatacatccctgcagagcagtgcctgttgt----
||| ||| |||| ||||||||||||| | ||| |||||||||||| ||||||| || || ||| ||||||| ||||||||||||||||| || |||||||||| | |    | || |    |   || |||   |   || || |  |  ||| |    |     ||||||  ||  | ||||  |     | || | | |    
CTTACTAAGGAACTTGTGAGATCTAGGAAAACGGTGAACCGTCTTTATGAAAATAAAGCACAAATGAATTCAATATCAATGCACCTTGGAGAGAGTGTTGgtaggtt----tttccatgttttattagccttaagataattttgccttgttaacaaataaggactctctaagttagttacctgt-gcttgataccaggtttttga

upper sequence: Vv06s0061g00540.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA06G23570.2 (Glycine max), 5'ss of exon 4
CTTGCTATGGAAATTGTGAGATCTAGAAGAACAGTGAACCGTCTTCATGAAAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGTTGgtaagataacatatctaaacatgtgtatcctgttgcacatgttactatctaaaactgcaacttcctctaaaatacatccctgcagagcagtgcctgttgt-----
||||| | |||| |||||||||||||   ||| |||||||| ||| |||||||||| || ||| ||||||| ||||||||||||||||| || |||||||||| | |    | |  |    |   || |||       || || |  | ||  |    |   |  |||||  ||  | | ||  |   | | || | |       
CTTGCCAAGGAACTTGTGAGATCTAGGCAAACTGTGAACCGCCTTTATGAAAACAAAGCACAAATGAATTCAATATCAATGCACCTTGGAGAGAGTGTTGgtaggtt----ttttcatgttttattagccttaacttaatttttccttatagcaaataaggattgtctaagttagttacttgt-gtttaataccaggttcttgat

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|30296312|gb|CB973106.1|CB973106
EST:     AAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGCTG                         CAATTGCTCGTACGGTGGGGCATTTGTCGAAGAGTGCAGAGGTAATGAAAC
genomic: AAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGTTGgtaagataac ... gatttttcagCAATTGCTCGTACGGTGGGGCATTTGTCGAAGAGTGCAGAGGTAATGAAAC
EST: gi|110718482|gb|EE095363.1|EE095363
EST:     AAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGTTG                         CAATTGCTCGTACGGTGGGGCATCTGTCGAAGAGTGCAGAGGTAATGAAAC
genomic: AAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGTTGgtaagataac ... gatttttcagCAATTGCTCGTACGGTGGGGCATTTGTCGAAGAGTGCAGAGGTAATGAAAC
EST: gi|110718154|gb|EE094659.1|EE094659
EST:     AAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGTTG                         CAATTGCTCGTACGGTGGGGCATTTGTCGAAGAGTGCAGAGGTAATGAAAC
genomic: AAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGTTGgtaagataac ... gatttttcagCAATTGCTCGTACGGTGGGGCATTTGTCGAAGAGTGCAGAGGTAATGAAAC
EST: gi|26257618|gb|CA808681.1|CA808681
EST:     AAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGTTG                         CAATTGCTCGTACGGTGGGGCATTTGTCGAAGAGTGCAGAGGTAATGAAAC
genomic: AAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGTTGgtaagataac ... gatttttcagCAATTGCTCGTACGGTGGGGCATTTGTCGAAGAGTGCAGAGGTAATGAAAC
EST: gi|110702376|gb|EE081020.1|EE081020
EST:     AAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGTTG                         CAATTGCTCGTACGGTGGGGCATTTGTCGAAGAGTGCAGAGGTAATGAAAC
genomic: AAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGTTGgtaagataac ... gatttttcagCAATTGCTCGTACGGTGGGGCATTTGTCGAAGAGTGCAGAGGTAATGAAAC
EST: gi|351031409|gb|FQ445434.1|FQ445434
EST:     AAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGTTG                         CAATTGCTCGTACGGTGGGGCATTTGTCGAAGAGTGCAGAGGTAATGAAAC
genomic: AAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGTTGgtaagataac ... gatttttcagCAATTGCTCGTACGGTGGGGCATTTGTCGAAGAGTGCAGAGGTAATGAAAC
EST: gi|110702630|gb|EE078767.1|EE078767
EST:     AAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGTTG                         CAATTGCTCGTACGGTGGGGCATTTGTCGAAGAGTGCAGAGGTAATGAAAC
genomic: AAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGTTGgtaagataac ... gatttttcagCAATTGCTCGTACGGTGGGGCATTTGTCGAAGAGTGCAGAGGTAATGAAAC
EST: gi|110722756|gb|EE099290.1|EE099290
EST:     AAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGTTG                         CAATTGCTCGTACGGTGGGGCATTTGTCGAAGAGTGCAGAGGTAATGAAAC
genomic: AAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGTTGgtaagataac ... gatttttcagCAATTGCTCGTACGGTGGGGCATTTGTCGAAGAGTGCAGAGGTAATGAAAC
EST: gi|110362725|gb|EC926275.1|EC926275
EST:     AAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGTTG                         CAATTGCTCGTACGGTGGGGCATTTGTCGAAGAGTGCAGAGGTAATGAAAC
genomic: AAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGTTGgtaagataac ... gatttttcagCAATTGCTCGTACGGTGGGGCATTTGTCGAAGAGTGCAGAGGTAATGAAAC
EST: gi|351014990|gb|FQ444279.1|FQ444279
EST:     AAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGTTG                         CAATTGCTCGTACGGTGGGGCATTTGTCGAAGAGTGCAGAGGTAATGAAAC
genomic: AAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGTTGgtaagataac ... gatttttcagCAATTGCTCGTACGGTGGGGCATTTGTCGAAGAGTGCAGAGGTAATGAAAC
EST: gi|110396776|gb|EC962475.1|EC962475
EST:     AAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGTTG                         CAATTGCTCGTACGGTGGGGCATTTGTCGAAGAGTGCAGAGGTAATGAAAC
genomic: AAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGTTGgtaagataac ... gatttttcagCAATTGCTCGTACGGTGGGGCATTTGTCGAAGAGTGCAGAGGTAATGAAAC
EST: gi|26257678|gb|CA808741.1|CA808741
EST:     AAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGTTG                         CAATTGCTCGTACGGTGGGGCATTTGTCGAAGAGTGCAGAGGTAATGAAAC
genomic: AAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGTTGgtaagataac ... gatttttcagCAATTGCTCGTACGGTGGGGCATTTGTCGAAGAGTGCAGAGGTAATGAAAC
EST: gi|110714302|gb|EE091055.1|EE091055
EST:     AAACAAAGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGTTG                         CAATTGCTCGTACGGTGGGGCATTTGTCGAAGAGTGCAGAGGTAATGAAAC
genomic: AAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGTTGgtaagataac ... gatttttcagCAATTGCTCGTACGGTGGGGCATTTGTCGAAGAGTGCAGAGGTAATGAAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGCTATGGAAATTGTGAGATCTAGAAGAACAGTGAACCGTCTTCATGAAAACAAGGCTCAATTGAATTCTATATCAATGCACCTTGGGGAAAGTGTTGgtaagataacatatctaaacatgtgtatcctgttgcacatgttactatctaaaactgcaacttcctctaaaatacatccctgcagagcagtgcctgttgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttcctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaataca