Sequence
atgc intronic sequence ATGC exonic sequencegtgagtttttccttctctctttttacatgctagcttgtttgtgttaagcttattctgatgcattgcttttctttttagGTTAATGCCAGTGGTTTGTTCTGTGGCATGGCTGAGATGACTGGTCCAGTTTCTTTTGATAAAGACATGGATTTTTGGCAGCAAGACAAATGGAGTGGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G48110.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G48110.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g22630.1 (Oryza sativa), 3'ss of exon 5
gtgagtttttcc------ttctctctttttacatgctagcttgtttgtg-ttaagcttattctgatgcattgcttttctttttagGTTAATGCCAGTGGTTTGTTCTGTGGCATGGCTGAGATGACTGGTCCAGTTTCTTTTGATAAAGACATGGATTTTTGGCAGCAAGACAAATGGAGTGGAA
|| ||| || ||| || | || | |||| |||| |||| | | | || | || || | |||| |||| ||||| | ||||||||||||||||||||| |||||| ||| |||| |||| |||||||| |||||| || || ||||||| ||| |
gtaagtacctctaatgtattcaaactacatttattcagtgttgtctgtgattaaaatattaattctgggatttcttgtttatcagGTGAATGGTAGTGGGCTCTTCTGTGGCATGGCTGAGATGGTTGGTCCTGTTGATTTTCATAAGGACATGGACTTTTGGTGTCAGGATAAATGGACTGGCA
upper sequence: AT1G48110.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G36110.1 (Glycine max), 3'ss of exon 6
---------------------------------------------------gtgagtttttccttctctctttttacatgctagcttgtttgtgttaagcttattctgatgcattgcttttcttttt-------agGTTAATGCCAGTGGTTTGTTCTGTGGCATGGCTGAGATGACTGGTCCAGTTTCTTTTGATAAAGACATGGATTTTTGGCAGCAAGACAAATGGAGTGGAA
||| | | | | ||| | | | || | | || |||| || | ||||| |||||||||| |||||| || ||||| | |||||||||| ||| || ||| || |||| |||||||| |||||||||||||| ||||||||||| |
gtgagtttacattatgatgattcattcaatgagttttgattctgtattttactgatctgcatacctaaattatgtgcatctggaaatttcccttctatgatcatgctgacattttttcccttttttttcaatgtagGTTAATGCAAGTGGTCAATTTTGTGGGGTTGCTGAGATGATTGGACCTGTTGACTTCAATAAGGACATGGACTTTTGGCAGCAAGATAAATGGAGTGGGA
upper sequence: AT1G48110.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G04270.1 (Glycine max), 3'ss of exon 2
-----------------------------------------gtgagtttttccttctctctttttacatgctagcttgtttgtgttaag-------cttattctgat-------gcattgcttttcttttt--------agGTTAATGCCAGTGGTTTGTTCTGTGGCATGGCTGAGATGACTGGTCCAGTTTCTTTTGATAAAGACATGGATTTTTGGCAGCAAGACAAATGGAGTGGAA
|| ||||| || | | || | | | ||| | || | | | | | |||| ||||| ||| |||||| |||||||||| |||||| || ||||| | || ||||||| ||| || ||| || |||| |||||||| |||||||||||||| ||||||||||| |
gtgagtttacattatgatgatgctttcaatgagttttgattctgctttttttttttttaatcttcatacctaaacttatgtgcatctggaaatttcccttctatgatcatgctgacattgttttccttttttgcaatgtagGTTAATGCAAGTGGTCAATTTTGTGGGGTTGCAGAGATGATTGGACCTGTTGACTTCAATAAGGACATGGACTTTTGGCAGCAAGATAAATGGAGTGGGA
upper sequence: AT1G48110.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA15G14490.1 (Glycine max), 3'ss of exon 6
----------------------------------------------------------gtgagtttttccttctctctttt---tacatgctagcttgtttgtgttaagcttattctgatgcattgcttttctt-tttagGTTAATGCCAGTGGTTTGTTCTGTGGCATGGCTGAGATGACTGGTCCAGTTTCTTTTGATAAAGACATGGATTTTTGGCAGCAAGACAAATGGAGTGGAA
|| || || || ||| | || || |||| |||| | | | || || | |||||||| | |||||||||| ||||| ||||||||| | || |||||| |||| ||||| ||| || | ||||| |||||||||||||| |||||||||||||
gtgagtgttcattatcttgatacgatcaatgtgttttgatcctggttccttataatttgtatattatttctattctttattatctatatgcaagctaatcacgctgacttttcttttaccatgttgctttttaaatgcagGTTAATGCAAGTGGACAGTTCTGTGGGGTTGCAGAGATGGTTGGTACAGTTGACTTTAGCAAGAATATGGACTTTTGGCAGCAAGATAAATGGAGTGGAA
upper sequence: AT1G48110.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G03590.1 (Glycine max), 3'ss of exon 5
----------------------------------------------------------gtgagtttttcc-ttctctctt-tttacatgctagcttgtttgtgttaagcttattctgatgcattgcttttctt--tttagGTTAATGCCAGTGGTTTGTTCTGTGGCATGGCTGAGATGACTGGTCCAGTTTCTTTTGATAAAGACATGGATTTTTGGCAGCAAGACAAATGGAGTGGAA
| |||||| |||||| | || |||| |||| | | | || || || |||||||| | | |||||||||| ||||| ||||||||| | || |||||| |||| ||||| |||| | || | ||||| |||||||||||||| |||||||||||||
gtgagtgttcattatcaatgatatgttcaatgagttttgatcctggttctttataattttatatttttctattctctatcacctatatgcaagctaatcacactgacttttcttatgtaatgttgcttttttcaatgcagGTTAATGCAAGTGGGCAGTTCTGTGGGGTAGCAGAGATGGTTGGTACAGTTGATTTTAACAAGAATATGGACTTTTGGCAGCAAGATAAATGGAGTGGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacatgctagcttgtttgtgttaagcttattctgatgcattgcttttctttttagGTTAATGCCAGTGGTTTGTTCTGTGGCATGGCTGAGATGACTGGTCCAGTTTCTTTTGATAAAGACATGGATTTTTGGCAGCAAGACAAATGGAGTGGAA
ttctgat putative branch site (score: 3)
cattgcttttcttttt CT-rich tract
ttttcttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtttttccttctctctttttacatgctagcttgtttgtgttaagcttattctgatgcattgcttttctttttagGTTAATGCCAGTGGTTTGTTCTGTGGCATGGCTGAGATGACTGGTCCAGTTTCTTTTGATAAAGACATGGATTTTTGGCAGCAAGACAAATGGAGTGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA