Sequence
atgc intronic sequence ATGC exonic sequencegtatgatcataacaaatggaacaatatacaagatagttttaactcctgttagtttttgttatgttaattatgatttggatttagttattcagACCTGGTGAATGTGTTCGAGACATTTCTTCCGCAACTTCTTCTGTATCCGAATCCGTCAGATCCATTGAATGGTGAAGCAGCTGCATTGATGATGCGTGA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G63800.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G63800.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G150867_T02 (Zea mays), 3'ss of exon 4
--------------------------------------gtatgatcataacaaatg-gaacaatatacaagat---agttttaactcctgttagtttttgttat---gttaattatgatttggatttagttatt--cagACCTGGTGAATGTGTTCGAGACATTTCTTCCGCAACTTCTTCTGTATCCGAATCCGTCAGATCCATTGAATGGTGAAGCAGCTGCATTGATGATGCGTGA
| |||| || | || | | | || || | | ||| | || | | ||||| | | || | | | || |||| || || |||||||||||| || ||||| |||||||| | ||||| ||||| || |||||||| ||||| || |||||||| ||||||||||||||
gtaagattgatctttgcatttcattattaggatcgacaaccagttcattctctctgtgccttatctgtacagttaaagcttcatgttttgtactctgttataacagggttaacttgaacctgtgtgtgatattttgcagATCTTGTTAATGTGTTCGAGGTCTTCCTTCCACAACTTCTGTTATATCCTAATCCTTCTGATCCATTAAATGGAGATGCAGCTGCGTTGATGATGCGTGA
upper sequence: AT1G63800.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: AC149818.2_FGT006 (Zea mays), 3'ss of exon 4
--------------------------gtatgatcataacaaatggaacaatatacaag-atagttttaactcctgttagtttttgttat---gttaattatga---tttggatttagttattcagACCTGGTGAATGTGTTCGAGACATTTCTTCCGCAACTTCTTCTGTATCCGAATCCGTCAGATCCATTGAATGGTGAAGCAGCTGCATTGATGATGCGTGA
|| |||| | | | | ||||||| | | | | | ||| | || | | ||||| | ||| | || | || | |||| || || |||||||||||| || ||||| |||||||| | ||||| ||||| || |||||||| ||||| || |||||||| ||||||||||||||
gtaagattgatctttacatctcattattaggatctccgcgcctt-atctgtatacaattagcgctccatgttttgtactctgttataacagggttaactttgaacctatgtgtgatattttgcagATCTTGTCAATGTGTTCGAGGTCTTCCTTCCACAACTTCTGTTATATCCTAATCCTTCTGATCCATTAAATGGAGATGCAGCTGCGTTGATGATGCGTGA
upper sequence: AT1G63800.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G37650.1 (Glycine max), 3'ss of exon 4
----gtatgatcataacaaat-----ggaacaatatacaagatagttttaactcctgttagtttttgttatgttaat----tatgatttgg--atttagttat-----------tcagACCTGGTGAATGTGTTCGAGACATTTCTTCCGCAACTTCTTCTGTATCCGAATCCGTCAGATCCATTGAATGGTGAAGCAGCTGCATTGATGATGCGTGA
| | || ||| |||| ||| ||| || ||| | | | | ||| | || | | | |||||| ||| |||| | |||||||| || |||||||| ||| |||||||| |||||||||||||| || ||| | |||||||||||||||||||| || ||||| |||||||| || ||
gtaagcaacattttaaaaaatttattggatgcatacttgccatgcatttgatttagccttgctttgttactgccactacttaaaaatttggtaattcagttttcttattttctttcagACCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCAATGCATCAGATCCATTGAATGGTGATGCTGCTGCCTTGATGATTCGAGA
upper sequence: AT1G63800.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G01940.3 (Glycine max), 3'ss of exon 4
---------------------------gtatgatcataacaaatggaacaat---atacaagatagtttta--actcctgttagtttttgttatgttaattatgatttggatttagttattcagACCTGGTGAATGTGTTCGAGACATTTCTTCCGCAACTTCTTCTGTATCCGAATCCGTCAGATCCATTGAATGGTGAAGCAGCTGCATTGATGATGCGTGA
|| |||| | | || || ||| | | ||| ||| | || || || |||||||| | ||| || | ||||||||| || |||||||| ||| |||||||| |||||||||||||| || ||| | ||||||||||| |||||||| || ||||| |||||||| || ||
gtaagcagcaatatttaaagaattttattacatgcatacttgccatatccatttgattcaaccttgctttgttactgccactacttaaaatt-tgttaattcagttttctgatttcct-ttcagACCTTGTTAATGTGTTTGAGGTGTTTCTTCCTCAACTTCTTCTGTACCCCAATGCATCAGATCCATTAAATGGTGATGCTGCTGCCTTGATGATTCGAGA
upper sequence: AT1G63800.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S161_122V6.1 (Physcomitrella patens), 3'ss of exon 4
----gtatgatcataacaaatggaacaatatacaagatagttttaactcc--tgttagtttttgttatgttaattatgatttg--gatttagttattcagACCTGGTGAATGTGTTCGAGACATTTCTTCCGCAACTTCTTCTGTATCCGAATCCGTCAGATCCATTGAATGGTGAAGCAGCTGCATTGATGATGCGTGA
| | || ||||||| || | |||| | | | ||| | ||| | | | ||||| | || | | || ||||||| | ||||| ||||| || | || || || | || || || ||||| | ||||| |||||||||||||| ||||| ||||||||||| ||
tctaatcagtgaatgtgaaatggagttattgaactcttagtcatcttttgaacggtagggtaacttacagtgtgttttatttgtggcttgattcatgcagACCTCATCAATGTATTCGAAGTCTTCTTGCCTCAGCTCTTACTCTACCCTAATCCTACCGATCCTTTGAATGGTGAAGCTGCTGCGTTGATGATGCGAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttaactcctgttagtttttgttatgttaattatgatttggatttagttattcagACCTGGTGAATGTGTTCGAGACATTTCTTCCGCAACTTCTTCTGTATCCGAATCCGTCAGATCCATTGAATGGTGAAGCAGCTGCATTGATGATGCGTGA
ttagtttttgttatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgatcataacaaatggaacaatatacaagatagttttaactcctgttagtttttgttatgttaattatgatttggatttagttattcagACCTGGTGAATGTGTTCGAGACATTTCTTCCGCAACTTCTTCTGTATCCGAATCCGTCAGATCCATTGAATGGTGAAGCAGCTGCATTGATGATGCGTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC