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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctacgaattcaactgtttgggatatgctaccttgcattagaaaattaataaaaactgaaccactaacttggtggtgtgaacctgtatttgattttgacagGATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCATGATTACCATGTGGACTGCATCAAGAAATGGTTATTGATGAAGAACTCAT

Basic information

species Vitis vinifera
transcript Vv08s0040g02160.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0040g02160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA03G33670.1 (Glycine max), 3'ss of exon 8
ctacgaattcaactgtttgggatatgctaccttgcattagaaaattaataaaaactgaaccactaacttggtggt-gtgaacctgtatttgattttgacagGATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCATGATTACCATGTGGACTGCATCAAGAAATGGTTATTGATGAAGAACTCAT
 || | ||| |  | ||    | ||  ||  |    |||||    |    | |||      | |||   |||| |   ||   | | ||  | ||  |||||| ||||||||||||||||| |||||||| ||||| |   ||||  | ||||| |||||||||  |||||| || ||||||||||   ||| ||| | ||
gtatgtattta-ttcttccatacataataaat-attttagatgtctttggacaac------attaatcgggtgcttacgagtttttgttgaaatt--acagGAAGAGTACAAGAACATGGACGATGTTGGAACACTTAAAACATGTGGGCATGACTACCATGTGAGCTGCATTAAAAAATGGTTATCTTTGAGGAAATTAT

upper sequence: Vv08s0040g02160.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G20210.1 (Glycine max), 3'ss of exon 7
------------------------------------------------------------------ctacgaattcaactgtttgggatatgctaccttgcattagaa-aattaataa--aaactgaaccactaacttggtggt--gtga---acctgtatttgattttgacagGATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCATGATTACCATGTGGACTGCATCAAGAAATGGTTATTGATGAAGAACTCAT
                                                                    ||  |  | |  ||     ||    ||  |   | | ||| || || | |  ||    |  |  |||   |||| |   |||   | |  ||||  |  ||| ||||| || |||||||||||||| ||||||||||| ||||  || ||  | ||||||||||||||||  ||||| |  || ||||| |  ||||||||    |
gtatgcttccttctaccattcagaatacataatatacagtgacagtaacaggacaaccatattccatcactgaaccgaacgtccattattaaataagtaaaacttgaataaatattgatgaagtacaggccttaatccggtgcttaatgatccatccttattgaaaattg-cagGAAGAATACAAGAACATGGACGATGTTGGGACGCTGAAAGCTTGTGGACATGATTACCATGTGGGTTGCATAAGAAAGTGGTTGTCTATGAAGAAAGTTT
















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|110386709|gb|EC951326.1|EC951326
EST:     ATTGTTCATCTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTG                         GATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCAT
genomic: ATTGTTCATCTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTGgtaagaattt ... attttgacagGATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCAT
EST: gi|28962111|gb|CB341144.1|CB341144
EST:     ATTGTTCATCTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTG                         GATGAGTACAAGAGCATGGATGATGTTGGGACACTGAGCGCATGCCGCCAT
genomic: ATTGTTCATCTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTGgtaagaattt ... attttgacagGATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCAT
EST: gi|110698522|gb|EE076116.1|EE076116
EST:     ATTGTTCATCTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTG                         GATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCAT
genomic: ATTGTTCATCTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTGgtaagaattt ... attttgacagGATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCAT
EST: gi|71880900|gb|DT029955.1|DT029955
EST:     ATTGTTCATCTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTG                         GATGAGTACAAGAACATGGATGATGTTAGGACACTGAGCGCATGCCGCCAT
genomic: ATTGTTCATCTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTGgtaagaattt ... attttgacagGATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCAT
EST: gi|110360203|gb|EC922989.1|EC922989
EST:     ATTGTTCATCTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTG                         GATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCAT
genomic: ATTGTTCATCTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTGgtaagaattt ... attttgacagGATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCAT
EST: gi|110359745|gb|EC921816.1|EC921816
EST:     ATTGTTCATCTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTG                         GATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCAT
genomic: ATTGTTCATCTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTGgtaagaattt ... attttgacagGATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCAT
EST: gi|110359702|gb|EC921626.1|EC921626
EST:     ATTGTTCATCTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTG                         GATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCAT
genomic: ATTGTTCATCTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTGgtaagaattt ... attttgacagGATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCAT
EST: gi|110359655|gb|EC921489.1|EC921489
EST:     ATTGTTCATCTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTG                         GATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCAT
genomic: ATTGTTCATCTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTGgtaagaattt ... attttgacagGATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCAT
EST: gi|71883091|gb|DT032146.1|DT032146
EST:     ATTGTTCATCTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTG                         GATGAGTACAATAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCAT
genomic: ATTGTTCATCTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTGgtaagaattt ... attttgacagGATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCAT
EST: gi|22015326|gb|BQ800360.1|BQ800360
EST:     ATTGTTCATCTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTG                         GATTAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCAT
genomic: ATTGTTCATCTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTGgtaagaattt ... attttgacagGATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCAT
EST: gi|110358811|gb|EC923300.1|EC923300
EST:     ATTGTTCATCTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTG                         GATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCAT
genomic: ATTGTTCATCTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTGgtaagaattt ... attttgacagGATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCAT
EST: gi|77583866|gb|DV220970.1|DV220970
EST:     ATTGTTCATCTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTG                         GATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCAT
genomic: ATTGTTCATCTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTGgtaagaattt ... attttgacagGATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCAT
EST: gi|77578962|gb|DV218312.1|DV218312
EST:     ATTGTTCATCTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTG                         GATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCAT
genomic: ATTGTTCATCTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTGgtaagaattt ... attttgacagGATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCAT
EST: gi|32460924|gb|CD802098.1|CD802098
EST:     ATTGTTCATCTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTG                         GATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCAT
genomic: ATTGTTCATCTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTGgtaagaattt ... attttgacagGATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCAT
EST: gi|71886918|gb|DT035973.1|DT035973
EST:     ATTGTTCATCTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTG                         GATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCAT
genomic: ATTGTTCATCTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTGgtaagaattt ... attttgacagGATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCAT
EST: gi|71879182|gb|DT028237.1|DT028237
EST:     ATTGTTCATCTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTG                         GATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCAT
genomic: ATTGTTCATCTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTGgtaagaattt ... attttgacagGATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCAT
EST: gi|110375438|gb|EC940426.1|EC940426
EST:     ATTGTTCATCTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTG                         GATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCAT
genomic: ATTGTTCATCTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTGgtaagaattt ... attttgacagGATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCAT
EST: gi|28961515|gb|CB340765.1|CB340765
EST:     ATTGTTCATTTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTG                         GATGAGTACAAGAGCATGGATGATGTTGGGACACTGAGCGCATGCCGCCAT
genomic: ATTGTTCATCTGATCAACTCCAGGAGGAAGGGGCATGTGTAATCTGTCTGgtaagaattt ... attttgacagGATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taataaaaactgaaccactaacttggtggtgtgaacctgtatttgattttgacagGATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCATGATTACCATGTGGACTGCATCAAGAAATGGTTATTGATGAAGAACTCAT
                                       tatttgatttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctacgaattcaactgtttgggatatgctaccttgcattagaaaattaataaaaactgaaccactaacttggtggtgtgaacctgtatttgattttgacagGATGAGTACAAGAACATGGATGATGTTGGGACACTGAGCGCATGCCGCCATGATTACCATGTGGACTGCATCAAGAAATGGTTATTGATGAAGAACTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - -tgtttgg
- - - - - - - - - - gatatgc
- - - - - - - - - - - - - - -ccttgca
- - - - - - - - - - - - - - - - - - - agaaaat
- - - - - - - - - - - - - - - - - - - - - - - aataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acctgta