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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gccctgtaccacctcttaatcgatagtgttcttattagatcatgaggaaagaaactagaggtacattgaagctaatgttgggtctgtgtatgatatgcagGTAGAAAGCATTGTGTTGAGTATCATATCGATGCTCTCAGGTCCCAACGATGAGTCACCAGCGAATGTGGAAGCTGCAAAGGAATGGAGAGACAACAGAG

Basic information

species Arabidopsis thaliana
transcript AT3G55380.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G55380.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ37995 (Selaginella moellendorffii), 3'ss of exon 4
gccctgtaccacctcttaatcgatagtgttcttattagatcatgaggaaagaaactagaggtacattgaagctaatgttgggtctgtgtatgatatgcagGTAGAAAGCATTGTGTTGAGTATCATATCGATGCTCTCAGGTCCCAACGATGAGTCACCAGCGAATGTGGAAGCTGCAAAGGAATGGAGAGACAACAGAG
                                         ||| |      | |  ||| |    | || ||  |     ||| |||| || |   |||||||||| |||| | |||||||| || |||||||||||  | ||||||||||| || ||||| ||  | || || ||                       
---------------------------------------gtatgcgtgcttgatcccgagct---ctcaaacttcttactcgtc-gtgtgtgcttctcagGTAGAAACCATTCTATTGAGTATAATCTCGATGCTCTCGAGCCCCAACGATGAATCGCCAGCCAACATCGATGCCGCG----------------------
















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|86066039|gb|DR361796.1|DR361796
EST:     ATCCTCATGGATACGAGCTTGCCTCTGAACGTTGGACCCCTGTCCATACG                         GTAGAAAGCATTGTGTTGAGTATCATATCGATGCTCTCAGGTCCCAACGAT
genomic: ATCCTCATGGATACGAGCTTGCCTCTGAACGTTGGACCCCTGTCCATACGgtatgttttt ... tgatatgcagGTAGAAAGCATTGTGTTGAGTATCATATCGATGCTCTCAGGTCCCAACGAT
EST: gi|124859179|gb|EH943616.1|EH943616
EST:     TGCCTCTGAACGTTGGACCCCTGTCCATACG                         GTAGAAAGCATTGTGTTGAGTATCATATCGATGCTCTCAGGTCCCAACGAT
genomic: TGCCTCTGAACGTTGGACCCCTGTCCATACGgtatgttttt ... tgatatgcagGTAGAAAGCATTGTGTTGAGTATCATATCGATGCTCTCAGGTCCCAACGAT
EST: gi|125201963|gb|EL216917.1|EL216917
EST:     ATCCTCATGGATACGAGCTTGCCTCTGAACGTTGGACCCCTGTCCATACG                         GTAGAAAGCATTGTGTTGAGTAT
genomic: ATCCTCATGGATACGAGCTTGCCTCTGAACGTTGGACCCCTGTCCATACGgtatgttttt ... tgatatgcagGTAGAAAGCATTGTGTTGAGTAT
EST: gi|125260703|gb|EL274788.1|EL274788
EST:     ATCCTCATGGGTACGAGCTTGCCTCTGAACGTTGGACCCCTGTCCATACG                         GTAGAAAGCATTGTGTTGAG
genomic: ATCCTCATGGATACGAGCTTGCCTCTGAACGTTGGACCCCTGTCCATACGgtatgttttt ... tgatatgcagGTAGAAAGCATTGTGTTGAG
EST: gi|86066040|gb|DR361797.1|DR361797
EST:     ATCCTCATGGATACGAGCTTGCCTCTGAACGTTGGACCCCTGTCCATACG                         GTAGAAAGCATTGTGTTGAGTATCATATCGATGCTCTCAGGTCCCAACGAT
genomic: ATCCTCATGGATACGAGCTTGCCTCTGAACGTTGGACCCCTGTCCATACGgtatgttttt ... tgatatgcagGTAGAAAGCATTGTGTTGAGTATCATATCGATGCTCTCAGGTCCCAACGAT
EST: gi|86066035|gb|DR361792.1|DR361792
EST:     ATCCTCATGGATACGAGCTTGCCTCTGAACGTTGGACCCCTGTCCATACG                         GTAGAAAGCATTGTGTTGAGTATCATATCGATGCTCTCAGGTCCCAACGAT
genomic: ATCCTCATGGATACGAGCTTGCCTCTGAACGTTGGACCCCTGTCCATACGgtatgttttt ... tgatatgcagGTAGAAAGCATTGTGTTGAGTATCATATCGATGCTCTCAGGTCCCAACGAT
EST: gi|86066038|gb|DR361795.1|DR361795
EST:     ATCCTCATGGATACGAGCTTGCCTCTGAACGTTGGACCCCTGTCCATACG                         GTAGAAAGCATTGTGTTGAGTATCATATCGATGCTCTCAGGTCCCAACGAT
genomic: ATCCTCATGGATACGAGCTTGCCTCTGAACGTTGGACCCCTGTCCATACGgtatgttttt ... tgatatgcagGTAGAAAGCATTGTGTTGAGTATCATATCGATGCTCTCAGGTCCCAACGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaaagaaactagaggtacattgaagctaatgttgggtctgtgtatgatatgcagGTAGAAAGCATTGTGTTGAGTATCATATCGATGCTCTCAGGTCCCAACGATGAGTCACCAGCGAATGTGGAAGCTGCAAAGGAATGGAGAGACAACAGAG
                        agctaat  putative branch site (score: 3)
                                           tatgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gccctgtaccacctcttaatcgatagtgttcttattagatcatgaggaaagaaactagaggtacattgaagctaatgttgggtctgtgtatgatatgcagGTAGAAAGCATTGTGTTGAGTATCATATCGATGCTCTCAGGTCCCAACGATGAGTCACCAGCGAATGTGGAAGCTGCAAAGGAATGGAGAGACAACAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - taccacc
- - - - - - - - - - - - - - - - - - - - - - - -aaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagctaa