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

GTATTTGACCTTGGTGGTGGTACTTTTGATGTCAGTGTCTTGACCATTGATAACGGAGTGTTTGAGGTTCTCTCCACAAATGGTGACACTCACTTGGGAGgtaaaatacttgtgaccacgaatgaattgttctgaattgcattaagaatgaattgttctgaattgcattgtgttcaataacaaatgattgctgtgccaat...

Basic information

species Arabidopsis thaliana
transcript AT5G42020.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G42020.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 4
GTATTTGACCTTGGTGGTGGTACTTTTGATGTCAGTGTCTTGACCATTGATAACGGAGTGTTTGAGGTTCTCTCCACAAATGGTGACACTCACTTGGGAGgtaaaa-tacttgtgaccacgaatgaattgttctgaattgcattaagaatgaattgtt-ctgaattgcattgt-gttcaataacaaatgattgctgtgccaat
|| ||||||||||||||||| || || ||||||||| ||||||||||||| ||||| |||||||||||  |  |||| ||||||||||||||  | |||||||  | | ||| |     |   |   |  |    |  ||| |    |    ||      || |  | | ||| |||  ||    |||||||    ||| |  
GTCTTTGACCTTGGTGGTGGGACATTCGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGTTGGCCACCAATGGTGACACTCATCTTGGAGgtatgactgcttttatttgcccttaggtactaaatatctgcttctgtacaacatcacagttgtagagtactgtagtttgat--tcaatgattttcatgcaac-

upper sequence: AT5G42020.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G415007_T01 (Zea mays), 5'ss of exon 4
GTATTTGACCTTGGTGGTGGTACTTTTGATGTCAGTGTCTTGACCATTGATAACGGAGTGTTTGAGGTTCTCTCCACAAATGGTGACACTCACTTGGGAGgtaaaatacttgtgaccacgaatgaattgttctgaattgcattaagaatga-attgttctgaattgcattgtgttcaataacaaatgattgctgtgccaat
|| ||||||||||||||||||||||||||||||||| ||||||||||||||||||| ||||||||||| ||  |||| ||||||||||| ||  | |||||||| | | | |  | |    || | ||        |||  ||    ||   |    ||   ||       |||      |  | |  ||| | ||    |
GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGATAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACCCATCTTGGAGgtaagaga-tagctatcctatattattttcagatgcttgtgtttgatatattaaaactcatgatgatgccatgtattcataggatttgttgatctgaatct

upper sequence: AT5G42020.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G114793_T01 (Zea mays), 5'ss of exon 4
GTATTTGACCTTGGTGGTGGTACTTTTGATGTCAGTGTCTTGACCATTGATAACGGAGTGTTTGAGGTTCTCTCCACAAATGGTGACACTCACTTGGGAGgtaaaata--cttgtgaccacgaatgaattgttctgaattgcattaag--aatgaattg-ttctga--attgcattgtg--ttcaataacaaatgattgctgtgccaat
|| ||||||||||||||||||||||||||||||||| ||||||||||||| ||||| ||||||||||| ||  |||| ||||||||||||||  | |||||||| | |   ||   |  |  | |   | | | |    |||| || |  |||||| |  ||||||  |||| | | |    | | || || ||| ||           
GTCTTTGACCTTGGTGGTGGTACTTTTGATGTCAGTATCTTGACCATTGACAACGGTGTGTTTGAGGTGCTGGCCACCAATGGTGACACTCATCTTGGAGgtaagagaattttcccattaaaactatctagctatcccatgcactacgacaatgaaatacttctgattattgtactattatcttattaccagatgcttat---------

upper sequence: AT5G42020.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA08G02940.1 (Glycine max), 5'ss of exon 4
GTATTTGACCTTGGTGGTGGTACTTTTGATGTCAGTGTCTTGACCATTGATAACGGAGTGTTTGAGGTTCTCTCCACAAATGGTGACACTCACTTGGGAGgtaaaatacttgtgaccacgaatgaattgttctgaattgcattaaga-atgaattgttctgaattgcattgtgttcaataacaaatgattgctgtgccaat-------------
|| ||||| ||||||||||| || |||||||||||| ||||||| ||||||||||| || ||||| |||||  | |||||||| || |||||  | |||||| |  ||||| |   |||  |   |       ||||   || ||   ||  ||| ||   |      ||   |||     | ||||  |||| |  |  |             
GTCTTTGATCTTGGTGGTGGGACCTTTGATGTCAGTATCTTGACAATTGATAACGGTGTTTTTGAAGTTCTTGCTACAAATGGAGATACTCATCTTGGAGgtgag-tacttttatacacatacacacaaga--gaatgaaatgaaattatatattctttccataaaattttctttctgatgctaatgtctgctatttctgtttccccttactag

upper sequence: AT5G42020.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA08G02960.1 (Glycine max), 5'ss of exon 4
GTATTTGACCTTGGTGGTGGTACTTTTGATGTCAGTGTCTTGACCATTGATAACGGAGTGTTTGAGGTTCTCTCCACAAATGGTGACACTCACTTGGGAGgtaaaatactt-----gtgaccacgaatgaattgttctgaat-tgcattaagaatgaattgttctgaattgcattgtgttcaataacaaatgattgctgtgccaat-------------
|| ||||||||||| ||||| || |||||||||||| ||||||| |||||||| || || |||||||||||  | |||||||| || |||||  | |||||| | |   ||      |||    |||| |      || | | || |  || |||    |  | |  |    ||| | |||       |||| ||||| |  |                
GTTTTTGACCTTGGGGGTGGAACATTTGATGTCAGTATCTTGACAATTGATAATGGTGTTTTTGAGGTTCTTGCTACAAATGGAGATACTCATCTTGGAGgtgagaattttttttaatgagtctgaataagaaaaacttattatgtagaaaaaatattattctttccacaaaattttcttctgatgttaatgcttgctatttctccttcaccttaccag

upper sequence: AT5G42020.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA05G36620.1 (Glycine max), 5'ss of exon 4
GTATTTGACCTTGGTGGTGGTACTTTTGATGTCAGTGTCTTGACCATTGATAACGGAGTGTTTGAGGTTCTCTCCACAAATGGTGACACTCACTTGGGAGgtaaa-------atacttgtgaccacgaatgaat---tgtt-ctgaattgcattaagaatgaattgttctgaattgcattgtg--ttcaataacaaatgattgctgtgccaat------------
|| ||||| ||||||||||| || |||||||||||| ||||||| |||||||| || || ||||| |||||  |||||||||| || |||||  | |||||| |        ||||   |   ||| |   |||   ||||  |  || | | | | | |  ||  |  |   ||  ||| |   ||   |  | ||||  |||| | |   |            
GTCTTTGATCTTGGTGGTGGGACCTTTGATGTCAGTATCTTGACAATTGATAATGGTGTTTTTGAAGTTCTTGCCACAAATGGAGATACTCATCTTGGAGgtgagtacttttatacacatacacacaagctaatgtctgttattctatggaaatgaaattatataatctttccttaaatttttccttttgttgctaatgtctgctattctgtttcccctttccag

upper sequence: AT5G42020.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA05G36600.1 (Glycine max), 5'ss of exon 4
GTATTTGACCTTGGTGGTGGTACTTTTGATGTCAGTGTCTTGACCATTGATAACGGAGTGTTTGAGGTTCTCTCCACAAATGGTGACACTCACTTGGGAGgtaaaa--------tacttgtgaccacgaatgaattgttctgaattgcattaagaatgaattgttctg--aattgcattgtgttcaataacaaatgattgctgtgccaat-------------
|| ||||||||||| ||||| || |||||||| ||| ||||||| |||||||| || || |||||||||||  | |||||||| || |||||  | |||||| | |        |  || |||     ||| |   |  || | |      || |||  ||| ||||    |    ||| |  ||       |||| ||||| || |                
GTTTTTGACCTTGGGGGTGGAACATTTGATGTTAGTATCTTGACAATTGATAATGGTGTTTTTGAGGTTCTTGCTACAAATGGAGATACTCATCTTGGAGgtgagaattttttttttttatgagtcttaataagaagaacttattatgtagaaaaatatattattctttccaccaaattctcctctgatgttaatgcttgctatgtctccttcgccttgccag

upper sequence: AT5G42020.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv16s0098g01580.t01 (Vitis vinifera), 5'ss of exon 4
GTATTTGACCTTGGTGGTGGTACTTTTGATGTCAGTGTCTTGACCATTGATAACGGAGTGTTTGAGGTTCTCTCCACAAATGGTGACACTCACTTGGGAGgtaa--aatacttg--tgaccacgaatgaattgttctgaattgcat--taagaatgaattgttctgaattgcattgtgttcaataacaaatgattgctgtgccaat
|| ||||| |||||||||||||| |||||||||||| ||||||| || || || || || |||||||||||  |||| ||||| ||||||||  ||||||||||  | | |||   ||  | | |    ||| || || |||   |  |  | | || | |||  |  ||      | ||           ||   || |      
GTGTTTGATCTTGGTGGTGGTACATTTGATGTCAGTATCTTGACAATCGACAATGGTGTTTTTGAGGTTCTTGCCACTAATGGAGACACTCATCTGGGAGgtaagcattgcttccttggtccctaccttatttttgtgcattttttcctttgtaagattagttacggtttaaggattcttggtgtgttgtagagacctct------

upper sequence: AT5G42020.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 5'ss of exon 4
GTATTTGACCTTGGTGGTGGTACTTTTGATGTCAGTGTCTTGACCATTGATAACGGAGTGTTTGAGGTTCTCTCCACAAATGGTGACACTCACTTGGGAGgtaaa-atacttgtgaccacgaatga------attgttctgaattgcattaagaatgaattgttctgaattgcattgtgttcaataacaaatgattgctgtgccaat-----------
|| ||||||||||||||||| || || ||||||||  ||||||| ||||| || || || || ||||||||  | |||||||| |||||||| ||||||||| |  ||  || |  | ||  |||       ||  ||     |||||    ||| |||   ||  ||   | |   | ||  |      ||| |    || | | |           
GTTTTTGACCTTGGTGGTGGAACCTTCGATGTCAGCATCTTGACTATTGACAATGGTGTTTTCGAGGTTCTTGCTACAAATGGAGACACTCATTTGGGAGgtgaggatttttttctctactgatgctctttcatctttgctctttgcacattgaaagaaaatttacgagaggaaagttattatactgtggatgctcaaggttcaattctttcctgcag

upper sequence: AT5G42020.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: EFJ17607 (Selaginella moellendorffii), 5'ss of exon 4
GTATTTGACCTTGGTGGTGGTACTTTTGATGTCAGTGTCTTGACCATTGATAACGGAGTGTTTGAGGTTCTCTCCACAAATGGTGACACTCACTTGGGAGgtaaaatacttgtgaccacgaatgaattgttctgaattgcattaagaatgaattgttctgaattgcattgtgttcaataacaaatgattgctgtgccaat
|| ||||| || |||||||||||||| ||||||||| ||||||| || || |||||||||||||| ||  | || || || || ||||| ||  | |||||||   |  |     ||         |  |||| |      |  | | |||  | | |  |  ||||                                 
GTGTTTGATCTCGGTGGTGGTACTTTCGATGTCAGTATCTTGACGATCGACAACGGAGTGTTTGAAGTGTTGTCTACCAACGGAGACACCCATCTTGGAGgtactttgatcaaagccttctccttttctttctta--cagctcgaaactgacatctaccaa--tgcag--------------------------------

upper sequence: AT5G42020.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: EFJ29073 (Selaginella moellendorffii), 5'ss of exon 4
GTATTTGACCTTGGTGGTGGTACTTTTGATGTCAGTGTCTTGACCATTGATAACGGAGTGTTTGAGGTTCTCTCCACAAATGGTGACACTCACTTGGGAGgtaaaatacttgtgaccacgaatgaattgttctgaattgcattaagaatgaattgttctgaattgcattgtgttcaataacaaatgattgctgtgccaat
|| ||||| || |||||||||||||| ||||||||| ||||||| || || |||||||||||||| ||  | || || || || ||||| ||  | |||||||   |  |     ||     |    | ||||   || ||    |||   |   |     | ||||                                 
GTGTTTGATCTCGGTGGTGGTACTTTCGATGTCAGTATCTTGACGATCGACAACGGAGTGTTTGAAGTGTTGTCTACCAACGGAGACACCCATCTTGGAGgtactttgatcaaagcct----tctccttttctttcttacagctcgaaactaacatctaccaatgcag--------------------------------

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|124732881|gb|EH824283.1|EH824283
EST:     GGTTCTCTCCACAAATGGTGACACTCACTTGGGAG                         GTGAGGACTTTGACCACAGGATCATGGAGTACTTCATCAAGTTAATTAAGA
genomic: GGTTCTCTCCACAAATGGTGACACTCACTTGGGAGgtaaaatact ... atctgcgcagGTGAGGACTTTGACCACAGGATCATGGAGTACTTCATCAAGTTAATTAAGA
EST: gi|124719608|gb|EH811010.1|EH811010
EST:     AATGGTGACACTCACTTGGGAG                         GTGAGGACTTTGACCACAGGATCATGGAGTACTTCATCAAGTTAATTAAGA
genomic: AATGGTGACACTCACTTGGGAGgtaaaatact ... atctgcgcagGTGAGGACTTTGACCACAGGATCATGGAGTACTTCATCAAGTTAATTAAGA
EST: gi|125237725|gb|EL251810.1|EL251810
EST:     GGTTCTCTCCACAAATAGGTGACACTCACTTGGGAG                         GTGAGGACTTTGACCACAGGATCATGGAGTACTTCATCAAGTTAATTAAGA
genomic: GGTTCTCTCCACAAAT-GGTGACACTCACTTGGGAGgtaaaatact ... atctgcgcagGTGAGGACTTTGACCACAGGATCATGGAGTACTTCATCAAGTTAATTAAGA
EST: gi|124903498|gb|EH977578.1|EH977578
EST:     GGTTCTCTCCACAAATGGTGACACTCACTTTGGGAG                         GTGAGGACTTTGACCACAGGATCATGGAGTACTTCATCAAGTTAATTAAG
genomic: GGTTCTCTCCACAAATGGTGACACTCAC-TTGGGAGgtaaaatact ... atctgcgcagGTGAGGACTTTGACCACAGGATCATGGAGTACTTCATCAAGTTAATTAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATTTGACCTTGGTGGTGGTACTTTTGATGTCAGTGTCTTGACCATTGATAACGGAGTGTTTGAGGTTCTCTCCACAAATGGTGACACTCACTTGGGAGgtaaaatacttgtgaccacgaatgaattgttctgaattgcattaagaatgaattgttctgaattgcattgtgttcaataacaaatgattgctgtgccaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agaatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caataaca