Sequence
atgc intronic sequence ATGC exonic sequencegtgaagttcgtaaattgaatttaatgtttcataatcaagattcgtcttctaattggatttaatattttgcagATAGTAGCTGTTAAACAGCTTGATCGAAACGGTCTACAAGGAAACAGAGAGTTTCTTGTAGAGGTTCTTATGCTGAGCCTTCTGCATCATCCCAATCTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G18610.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G18610.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g15470.3 (Oryza sativa), 3'ss of exon 2
------------------gtgaagttcgtaaattgaatt-taatgtttcataatca------agattcgtcttctaatt---ggatttaatattttgcagATAGTAGCTGTTAAACAGCTTGATCGAAACGGTCTACAAGGAAACAGAGAGTTTCTTGTAGAGGTTCTTATGCTGAGCCTTCTGCATCATCCCAATCTTG
||| ||| | | | ||| | ||| | ||| | | ||| | | | || | |||| | | |||| | || || |||||||||||||||| ||| || || || ||||||||||| || ||||| |||||||| ||||| || || |||||||||| ||| | |
atgggaatgcttagactattgatgttaacagaaagtattgttatgctatataccctttgtataaatttctaatttggttccagcatttgctgcatcgcagGTTGTTGCAGTTAAACAGCTTGATCTAAATGGGCTTCAGGGAAACAGAGAATTCCTTGTGGAGGTTCTCATGCTCAGTCTCTTGCATCATCCTAATTTAG
upper sequence: AT5G18610.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G145709_T01 (Zea mays), 3'ss of exon 2
-------------------------------------------------------------------------------------------------gtgaagttcgtaaattgaatttaatgtttcataatcaagattcgtctt-----ctaattggatttaatattttgcagATAGTAGCTGTTAAACAGCTTGATCGAAACGGTCTACAAGGAAACAGAGAGTTTCTTGTAGAGGTTCTTATGCTGAGCCTTCTGCATCATCCCAATCTTG
| | | ||| | | | || || | | |||| ||| | |||| | ||| || || ||| || ||||| ||||| |||||||| || ||||| ||||||||||| || ||||| || |||||||| ||||| || || | ||||| | || || |
gtaagtatctcttaaacatgatgcatcgacattttatctgtgaagctaaatccttccaaatttggcttctgagttgaaacattaagtaaaatattggaaggaaatgctaacataacgattatacttaa-gccctggattagtcctggatactaacagagttt--tacttcccagGCTGTTGCTGTGAAACAACTTGATCGTAATGGTCTCCAAGGAAACAGGGAATTTCTGGTTGAGGTTCTCATGCTCAGTCTCTTACATCACACTAACCTGG
upper sequence: AT5G18610.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA13G28730.1 (Glycine max), 3'ss of exon 2
-----------------------------gtgaagttcgtaaattgaatttaatgtttcataatcaagattcgtcttctaattggatttaatattttgcagATAGTAGCTGTTAAACAGCTTGATCGAAACGGTCTACAAGGAAACAGAGAGTTTCTTGTAGAGGTTCTTATGCTGAGCCTTCTGCATCATCCCAATCTTG
||| | | | | | ||| | | | | | | | | | | || || |||||| |||| ||||| ||||||||||| ||||| ||||| |||||||| |||||||| | || || ||||||||||| || || |||||||||| |||||||
aagttatctgtctgctctcaattttcctgttgattattgctctgttactataactctgcctctttcataatt-tttaatgatgaaatcattctcgttgcagGTAGTTGCTGTAAAACAGCTTGACCGAAATGGTCTTCAAGGAAATCGAGAGTTTTTGGTGGAAGTTCTTATGCTCAGTCTCTTGCATCATCCAAATCTTG
upper sequence: AT5G18610.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G10360.1 (Glycine max), 3'ss of exon 2
---------------gtgaagttcgtaaattgaat-ttaatgtttcataatcaagattcgtcttc--taattggatttaata----------ttttgcagATAGTAGCTGTTAAACAGCTTGATCGAAACGGTCTACAAGGAAACAGAGAGTTTCTTGTAGAGGTTCTTATGCTGAGCCTTCTGCATCATCCCAATCTTG
||| || ||||| | || | | | | || | || | |||| |||| ||||| || |||| | || ||||| ||||||||||| ||||| ||||| |||||||| |||||||| | || || ||||||||||| || || |||||||||| |||||||
aagttatttgtctgctggaaattttcccattgattattgctctgttactataactatgcctctttcgtaatcttcattaatgaaatcattctcttcgcagGTGGTTGCTGTAAAACAGCTTGACCGAAATGGTCTTCAAGGAAATCGAGAGTTTTTGGTGGAAGTTCTTATGCTCAGTCTCTTGCATCATCCAAATCTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatttaatgtttcataatcaagattcgtcttctaattggatttaatattttgcagATAGTAGCTGTTAAACAGCTTGATCGAAACGGTCTACAAGGAAACAGAGAGTTTCTTGTAGAGGTTCTTATGCTGAGCCTTCTGCATCATCCCAATCTTG
ttctaattggatttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaagttcgtaaattgaatttaatgtttcataatcaagattcgtcttctaattggatttaatattttgcagATAGTAGCTGTTAAACAGCTTGATCGAAACGGTCTACAAGGAAACAGAGAGTTTCTTGTAGAGGTTCTTATGCTGAGCCTTCTGCATCATCCCAATCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG