Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtattattttgtttgtttctaggaactttctttctgaagttgttacttaatggtaattctgcttgatttcagGCACTGGATAAGATTAGGTTCCTTTCCCTCACAGATAAGGAGATTTTAGGTGAAGGTGATACTGCAAAGCTTGATATCCAG

Basic information

species Vitis vinifera
transcript Vv18s0001g14500.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 3
--------------------gtaagtatt-attttgtttgtttctaggaactttctttctgaagtt-gttacttaatg-gtaattctgcttgat-ttcagGCACTGGATAAGATTAGGTTCCTTTCCCTCACAGATAAGGAGATTTTAGGTGAAGGTGATACTGCAAAGCTTGATATCCAG
                      |||  |  | |     ||   |    |  ||  |    || | | |  | |||||| ||  || |  || || |  ||||  |||| ||||||||||||||  | ||||| ||||||||| |||| || |||||||| ||||| |||||||| ||||||
attcctatgaaattcccgggaaaagcctccaatccaaatgagcccttaaggttattagtagatgctaggaatttaatgtgtgctttttttttatgtgtagGCTTTGGACAAGATTAGGTTCCTGGCTCTCACTGATAAGGAGGTTTTGGGCGAAGGTGACACTGCTAAGCTTGAAATCCAG

upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G110574_T01 (Zea mays), 3'ss of exon 7
gtaagtattattttgtttgtttctaggaactttctttc--tgaagttgtt----acttaatggtaattctgcttgatttcagGCACTGGATAAGATTAGGTTCCTTTCCCTCACAGATAAGGAGATTTTAGGTGAAGGTGATACTGCAAAGCTTGATATCCAG
||| ||||||  |    ||   ||||    | |  | |  ||  | || |    | | | | |   |||||| ||  |  ||||  ||||||||||||||||||||||||| || ||||||||  |||| |||||||| || |||||||||||||| || |||
gtatgtattacata--ctgaccctagtgtttgttctacattgtggatgctcgaaattaactaggtgttctgcatgtctgtagGCGTTGGATAAGATTAGGTTCCTTTCCCTTACTGATAAGGAAGTTTTGGGTGAAGGGGACACTGCAAAGCTTGAGATTCAG

upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G399073_T03 (Zea mays), 3'ss of exon 3
gtaagtattattttgtttgtttctaggaactttctttctgaagttgtt--acttaatggtaat--tctgcttgatttcagGCACTGGATAAGATTAGGTTCCTTTCCCTCACAGATAAGGAGATTTTAGGTGAAGGTGATACTGCAAAGCTTGATATCCAG
||| |||||  ||        | |    | | |   |      | ||   | ||||  ||  |  ||||| ||  |  ||||| |||||||||| |||||||||||||| || ||||||||  || | ||||||||||| |||||||||||||| || |||
gtatgtattgcttctgacccctgtgtttattctgcattgtggatggtcgaaattaactgtggtgttctgcatgtctgtagGCATTGGATAAGATCAGGTTCCTTTCCCTTACTGATAAGGAAGTTCTGGGTGAAGGTGACACTGCAAAGCTTGAGATTCAG

upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G022909_T01 (Zea mays), 3'ss of exon 4
gtaagtattattttgtttgtttctaggaactttct---ttctgaa--gttgttacttaatggtaattctgcttgatttcagGCACTGGATAAGATTAGGTTCCTTTCCCTCACAGATAAGGAGATTTTAGGTGAAGGTGATACTGCAAAGCTTGATATCCAG
||| ||| ||  |   |     ||  |    ||||   || || |   | |  | | | |||   |||| | ||  |  ||||  ||||||||||||||||||||||||| || ||||||||  || | |||||||| || |||||||||||||| || |||
gtatgtactacat-actgacccctgtgtttgttctgcattgtggatgctcgaaattaactgggtgttctacatgtctgtagGC--TGGATAAGATTAGGTTCCTTTCCCTTACTGATAAGGAAGTTCTGGGTGAAGGGGACACTGCAAAGCTTGAGATTCAG

upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G141931_T01 (Zea mays), 3'ss of exon 3
gtaagtatta--ttttgtttgtttctaggaactttctttctgaagttgttacttaa-tggtaattctgcttgatttcagGCACTGGATAAGATTAGGTTCCTTTCCCTCACAGATAAGGAGATTTTAGGTGAAGGTGATACTGCAAAGCTTGATATCCAG
||| ||||||  | |      | | |  |  ||   ||   || | |   | |||| |||   |||||| ||  |  ||||  ||||||||||||||||||||||||| || ||||||||  || | |||||||| || |||||||||||||| || |||
gtatgtattacatctgacccctgtgtttgttctgcattgtggatgctcgaaattaactgggtgttctgcatgtctgtagGCGTTGGATAAGATTAGGTTCCTTTCCCTTACTGATAAGGAAGTTCTGGGTGAAGGGGACACTGCAAAGCTTGAGATTCAG

upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G063988_T02 (Zea mays), 3'ss of exon 10
gtaagtattattttgtttgtttctaggaactttct---ttctgaag--ttgttacttaatggtaattctgcttgatttcagGCACTGGATAAGATTAGGTTCCTTTCCCTCACAGATAAGGAGATTTTAGGTGAAGGTGATACTGCAAAGCTTGATATCCAG
||| ||||||  |   |     ||  |    ||||   || || |   | |  | | | |||   |||||| ||  |  ||||  ||||||||||||||||||||||||| || ||||||||  |||| |||||| | || |||||||||||||| || |||
gtatgtattacat-actgacccctgtgtttgttctacattgtggatgctcgaaattaactgggtgttctgcatgtctgtagGCGTTGGATAAGATTAGGTTCCTTTCCCTTACTGATAAGGAAGTTTTGGGTGAAAGGGACACTGCAAAGCTTGAGATTCAG

upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------------------------------gtaagtattattttgtttgtttctaggaactttctttctgaagttgttact--taatggtaattc-tgcttg-atttcagGCACTGGATAAGATTAGGTTCCTTTCCCTCACAGATAAGGAGATTTTAGGTGAAGGTGATACTGCAAAGCTTGATATCCAG
                                                                        | |  ||   |   |||   | |     |   ||      |  ||||| |  |||||  || |  |||||| |||  ||||  |||| ||||||||||||||||||||||| ||||||||  |||| || ||||||||||   | ||||||||||| || 
tgtaagcgttttttttttattgttatttatttgagttaaaacctacatctattcatatgcttgtttacattttgaaaatccatgcatttaaattttcatccaaactccaacgatgtgttattgttaatgacaaatgatgcttgcattctaGGCTTTGGACAAGATTAGGTTCCTTTCCCTCACGGATAAGGACGTTTTGGGAGAAGGTGATAACACCAAGCTTGATATTCA-

upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA14G40320.4 (Glycine max), 3'ss of exon 3
------------------gtaagtattattttgtttgt---ttctag-----gaactttctttctgaa--gttg-----ttacttaatggt-aattctgcttg-atttcagGCACTGGATAAGATTAGGTTCCTTTCCCTCACAGATAAGGAGATTTTAGGTGAAGGTGATACTGCAAAGCTTGATATCCAG
                    ||  ||  ||||||||     | || |      || ||| | | ||||  ||||     ||  |||||||  |||  ||     |||  ||||  |||| |||||||||||||| |||||||| ||||||||| | || || ||||||||||   | ||||||||||| |||
gtaagcgctttttttttaaaaaaaatatttttgtttaaaaatccttgcatttaaattttttatttgaattgttgaacgatttgttaatggcgaataatgtgcacattctagGCTTTGGACAAGATTAGGTTCCTCTCCCTCACGGATAAGGAGGTGTTGGGAGAAGGTGATAACACCAAGCTTGATATTCAG

upper sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT4G24190.2 (Arabidopsis thaliana), 3'ss of exon 3
------------gtaagtattatttt-gtttgtttctaggaactttctttc--tgaagttgttacttaatggtaattctgcttgatttcagGCACTGGATAAGATTAGGTTCCTTTCCCTCACAGATAAGGAGATTTTAGGTGAAGGTGATACTGCAAAGCTTGATATCCAG
            ||    ||| |||| ||  |||| | |||    || ||   |   |    || | | ||    |  || |   ||||||||  |||| || |||||||||||| | ||||| || || ||  |||| ||||||||||| ||||| |||||||| ||||||
gtaagcagcttcgtgtacattgttttagtgagtttttgggatacctcgttaaataggggaactaataagtgtctgtgttggtgattttcagGCCTTGGACAAAATTAGGTTCCTTGCACTCACTGACAAAGACGTTTTGGGTGAAGGTGACACTGCTAAGCTTGAGATCCAG

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|110723753|gb|EE101423.1|EE101423
EST:     ATAGCAACAAAGACATTTTCTTAAGGGAGTTGATCTCCAATGCTTCTGAT                         GCACTGGATAAGATTAGGTTCCTTTCCCTCACAGATAAGGAGATTTTAGGT
genomic: ATAGCAACAAAGACATTTTCTTAAGGGAGTTGATCTCCAATGCTTCTGATgtaagtatta ... ttgatttcagGCACTGGATAAGATTAGGTTCCTTTCCCTCACAGATAAGGAGATTTTAGGT
EST: gi|161705792|gb|FC056663.1|FC056663
EST:     ATAGCAACAAAGACATTTTCTTAAGGGAGTTGATCTCCAATGCTTCTGAT                         GCACTGGATAAGATTAGGTTCCTTTCCC
genomic: ATAGCAACAAAGACATTTTCTTAAGGGAGTTGATCTCCAATGCTTCTGATgtaagtatta ... ttgatttcagGCACTGGATAAGATTAGGTTCCTTTCCC
EST: gi|110710305|gb|EE086522.1|EE086522
EST:     ATAGCAACAAAGACATTTTCTTAAGGGAGTTGATCTCCAATGCTTCTGAT                         GCACTGGATAAGATTAGGTTCCTTTCCCTCACAGATAAGGAGATTTTAGGT
genomic: ATAGCAACAAAGACATTTTCTTAAGGGAGTTGATCTCCAATGCTTCTGATgtaagtatta ... ttgatttcagGCACTGGATAAGATTAGGTTCCTTTCCCTCACAGATAAGGAGATTTTAGGT
EST: gi|352764021|gb|FQ467591.1|FQ467591
EST:     ATAGCAACAAAGACATTTTCTTAAGGGAGTTGATCTCCAATGCTTCTGAT                         GCACTGGATAAGATTAGGTTCCTTTCCCTCACAGATGAGGAGATTTTAGGT
genomic: ATAGCAACAAAGACATTTTCTTAAGGGAGTTGATCTCCAATGCTTCTGATgtaagtatta ... ttgatttcagGCACTGGATAAGATTAGGTTCCTTTCCCTCACAGATAAGGAGATTTTAGGT
EST: gi|110709700|gb|EE085391.1|EE085391
EST:     ATAGCAACAAAGACATTTTCTTAAGGGAGTTGATCTCCAATGCTTCTGAT                         GCACTGGATAAGATTAGGTTCCTTTCCCTCACAGATAAGGAGATTTTAGGT
genomic: ATAGCAACAAAGACATTTTCTTAAGGGAGTTGATCTCCAATGCTTCTGATgtaagtatta ... ttgatttcagGCACTGGATAAGATTAGGTTCCTTTCCCTCACAGATAAGGAGATTTTAGGT
EST: gi|110726118|gb|EE101621.1|EE101621
EST:     ATAGCAACAAAGACATTTTCTTAAGGGAGTTGATCTCCAATGCTTCTGAT                         GCACTGGATAAGATTAGGTTCCTTTCCCTCACAGATAAGGAGATTTTAGGT
genomic: ATAGCAACAAAGACATTTTCTTAAGGGAGTTGATCTCCAATGCTTCTGATgtaagtatta ... ttgatttcagGCACTGGATAAGATTAGGTTCCTTTCCCTCACAGATAAGGAGATTTTAGGT
EST: gi|110724805|gb|EE100952.1|EE100952
EST:     ATAGCAACAAAGACATTTTCTTAAGGGAGTTGATCTCCAATGCTTCTGAT                         GCACTGGATAAGATTAGGTTCCTTTCCCTCACAGATAAGGAGATTTTAGGT
genomic: ATAGCAACAAAGACATTTTCTTAAGGGAGTTGATCTCCAATGCTTCTGATgtaagtatta ... ttgatttcagGCACTGGATAAGATTAGGTTCCTTTCCCTCACAGATAAGGAGATTTTAGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaggaactttctttctgaagttgttacttaatggtaattctgcttgatttcagGCACTGGATAAGATTAGGTTCCTTTCCCTCACAGATAAGGAGATTTTAGGTGAAGGTGATACTGCAAAGCTTGATATCCAG
                                       ttctgctt  CT-rich tract
                         ttacttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtattattttgtttgtttctaggaactttctttctgaagttgttacttaatggtaattctgcttgatttcagGCACTGGATAAGATTAGGTTCCTTTCCCTCACAGATAAGGAGATTTTAGGTGAAGGTGATACTGCAAAGCTTGATATCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG