Sequence
atgc intronic sequence ATGC exonic sequencegtatgtggtttgtgttatgctctttaaactgttggtcttaaggttgttggataagttataaattttgactcgatttgcagGAGGAGGTTGGTGACGTTGTGATGTTAGCGAGACACAACAAAGGCTGTCACTGCAAGAAATCCGGATGTCTTAAGAAGTATTGTGAGTGCTTTCAAGCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G20110.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G20110.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os06g22670.1 (Oryza sativa), 3'ss of exon 4
-----------------------gtatgtggtttgtgttatgctctttaaactgttggtcttaaggttgttggataagttataaattttgactcgatttgcagGAGGAGGTTGGTGACGTTGTGATGTTAGCGAGACACAACAAAGGCTGTCACTGCAAGAAATCCGGATGTCTTAAGAAGTATTGTGAGTGCTTTCAAGCAA
| | |||| | |||| | | || || | | | || || | | || ||| || ||| | ||||| || | ||| | | | | | || || ||||| || || |||||||| || |||||||| |||||||| ||||| |||||||||||||
tcttttgaattttcaaactcattttgtttggtagat-ttatatacaacattctcttcatgt-gatatttttatgcatttgattaatcttaactgcacac-cagGATGATGCTGGAGCACCAGCCTCACTTCCAAAGCATAATAAAGGTTGCCATTGCAAGAAGTCAGGATGTCTCAAGAAGTACTGTGAATGCTTTCAAGCAA
upper sequence: AT2G20110.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g55580.2 (Oryza sativa), 3'ss of exon 3
-------------------gtatgtggtttgtgttatgctctttaaactgttggtcttaaggttgttggataagttataaattttgactcgatttgc-agGAGGAGGTTGGTGACGTTGTGATGTTAGCGAGACACAACAAAGGCTGTCACTGCAAGAAATCCGGATGTCTTAAGAAGTATTGTGAGTGCTTTCAAGCAA
| | | ||| ||| ||| ||| || | | | | | | | ||| | | || | |||| |||||| || |||||| || | | | || || || ||||| || ||||||||||| || || ||||| |||||||| ||||||||||| ||||| |
cgagtattttttggatgccatgtttcatttttgtacatctcattatctgatttgccctgctatgatgcgtgtacttaatgttagtccctgaaattgccagGAGGCGGCTGGTGATCTTCCATTAGTTGGGAAGCATAATAAAGGGTGCCACTGCAAGAAGTCAGGTTGTCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA
upper sequence: AT2G20110.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G059678_T01 (Zea mays), 3'ss of exon 3
--------------gtatgtggtttgtgttatgctctttaaactgttggtcttaaggttgttggataagttata--aattttgactcga-----tttgc-agGAGGAGGTTGGTGACGTTGTGATGTTAGCGAGACACAACAAAGGCTGTCACTGCAAGAAATCCGGATGTCTTAAGAAGTATTGTGAGTGCTTTCAAGCAA
||| | || || || ||| | | | | || | | | || | || | | |||| | | ||||| |||||| | | |||| | | ||| || || || ||||| || || |||||||| || |||||||| |||||||| ||||||||||| ||||| |
atcaattacaggcattatatcattattgc-atttcatttcggccat-gttattgtgctgccttgacacgtcacattaattctagtccatgaaattttgccagGAGGTGCCTAGTGATCTCCCTTTAGTAGGGAAGCATAATAAAGGGTGCCATTGCAAGAAGTCAGGATGTCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA
upper sequence: AT2G20110.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S10_254V6.2 (Physcomitrella patens), 3'ss of exon 5
---------gtatgtggttt----gtgttatgctctt-taaactgttggtcttaaggttgttggataagttataaattttg----actcgatt--tgcagGAGGAGGTTGGTGACGTTGTGATGTTAGCGAGACACAACAAAGGCTGTCACTGCAAGAAATCCGGATGTCTTAAGAAGTATTGTGAGTGCTTTCAAGCAA
| ||| || ||||| | || | || || || || | | | | || | | ||| ||| |||||||||| | ||| || | || | | |||||||||||| ||||| |||||||||||||| || || ||||||||||| || ||||| ||||| |
tcatgtattttctgtagtaccaaggtgttccttttttatggacatttcccctcaatctgggtcagtggatttcggaactaatagaactttattattgcagGAGGATGCTGGAGAGCATCCATTGGCGGGTAAACACAACAAAGGATGTCATTGCAAGAAATCCGGGTGCCTCAAGAAGTATTGCGAATGCTTCCAAGCTAMapped 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|116429112|gb|EG471704.1|EG471704EST: CGTTCAGGCCAAAGATTGCTGCTAGTCCACATGGTGGACGAGATAACAGG GAGGAGGTTGGTGACGTTGTGATGTTAGCGAGACACAACAAAGGCTGTCAC
genomic: CGTTCAGGCCAAAGATTGCTGCTAGTCCACATGGTGGACGAGATAACAGGgtatgtggtt ... cgatttgcagGAGGAGGTTGGTGACGTTGTGATGTTAGCGAGACACAACAAAGGCTGTCAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaactgttggtcttaaggttgttggataagttataaattttgactcgatttgcagGAGGAGGTTGGTGACGTTGTGATGTTAGCGAGACACAACAAAGGCTGTCACTGCAAGAAATCCGGATGTCTTAAGAAGTATTGTGAGTGCTTTCAAGCAA
ttttgac putative branch site (score: 3)
ataagttataaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtggtttgtgttatgctctttaaactgttggtcttaaggttgttggataagttataaattttgactcgatttgcagGAGGAGGTTGGTGACGTTGTGATGTTAGCGAGACACAACAAAGGCTGTCACTGCAAGAAATCCGGATGTCTTAAGAAGTATTGTGAGTGCTTTCAAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA