Sequence
atgc intronic sequence ATGC exonic sequencegtttgtgcttctttctttctctgattagtttttcttgttttagaacttctcgcaattctaatgtttctgggtaatgcagTACCGCAATATGACTACAGTATTGACAAGAGAATACCTCGATGTACGCCCTGATGGGTGGTTGGACTACGCAGCTATGAGAATTGCACAGTT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G08660.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G08660.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os11g36420.1 (Oryza sativa), 3'ss of exon 4
gtttgtgcttctttctttctctgattagtttttcttgttttagaacttctcgcaattctaatgtttctgggtaatgc-agTACCGCAATATGACTACAGTATTGACAAGAGAATACCTCGATGTACGCCCTGATGGGTGGTTGGACTACGCAGCTATGAGAATTGCACAGTT
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gttagtacatggtttatgaattatgaaatagcgtgtttattagaatatatacttatgtgttaatgctaatatgatgccagTACCGTAACATGACGACTGTGTTGACAAGGGAGTACTTAGATGTGCGACCTGATGGGTGGTTGGATTATGCAGCCAAAAGGATTGCACAGCT
upper sequence: AT1G08660.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G352941_T01 (Zea mays), 3'ss of exon 5
gtttgtgcttctttctttctctgattagtttttcttgttttagaacttctcgcaattctaatgtttctgggtaatgcagTACCGCAATATGACTACAGTATTGACAAGAGAATACCTCGATGTACGCCCTGATGGGTGGTTGGACTACGCAGCTATGAGAATTGCACAGTT
||| || | | |||| || || | | | | || ||| | ||| ||||| | ||| |||||||||||| ||||| || ||||||||||| |||||| | ||||| | || ||||| |||||||| || ||||||| || | |||||| |
gttagtacattcttcta-----gactaacatgtttgctcttgttactcgtgttaatactaatat-----ggt--cgcagTACCGCAACATGACAACTGTATTGACAAGGGAATACTTGGATGTGAGGCCGGATGGATGGTTGGATTATGCAGCTAAAAGGACCGCACAGCT
upper sequence: AT1G08660.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G119791_T07 (Zea mays), 3'ss of exon 4
gtttgtgcttctttctttctctgattagtttttcttgttttagaacttctcgcaattctaatgtttctgggtaatgcagTACCGCAATATGACTACAGTATTGACAAGAGAATACCTCGATGTACGCCCTGATGGGTGGTTGGACTACGCAGCTATGAGAATTGCACAGTT
||| || | | |||| || || | | | | || ||| | ||| ||||| | ||| |||||||||||| ||||| || ||||||||||| |||||| | ||||| | || ||||| |||||||| || ||||||| || || |||||| |
gttagtacattcttcta-----gactaacatgtttgctcttgttactcgtgttaatactaatat-----ggt--cgcagTACCGCAACATGACAACTGTATTGACAAGGGAATACTTGGATGTGAGGCCGGATGGATGGTTGGATTATGCAGCTAAAAGGATCGCACAGCT
upper sequence: AT1G08660.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G136098_T01 (Zea mays), 3'ss of exon 4
gtttgtgcttctttctttctctgattagtttttcttgttttagaacttctcgcaattctaatgtttctgggtaatgcagTACCGCAATATGACTACAGTATTGACAAGAGAATACCTCGATGTACGCCCTGATGGGTGGTTGGACTACGCAGCTATGAGAATTGCACAGTT
||| || | | |||| || || | | | || ||| | ||| ||||| | ||| |||||||||||| ||||| || ||||||||||| |||||| | ||||| | || ||||| |||||||| || ||||||| || || |||||| |
gttagtacattcttcta-----gactaacacgtttgctcttgttactcgtgttaatactaatat-----ggt--cgcagTACCGCAACATGACAACTGTATTGACAAGGGAATACTTGGATGTGAGGCCGGATGGATGGTTGGATTATGCAGCTAAAAGGATCGCACAGCT
upper sequence: AT1G08660.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv14s0068g01150.t01 (Vitis vinifera), 3'ss of exon 4
----gtttgtgcttctttctttctctgattagtttttcttgttttagaacttctcgcaattcta-atgtttctgggtaatgcagTACCGCAATATGACTACAGTATTGACAAGAGAATACCTCGATGTACGCCCTGATGGGTGGTTGGACTACGCAGCTATGAGAATTGCACAGTT
|| | || ||| ||| | | |||| | || | || | || |||| | | | | ||||||||| || || || || ||||| ||||||||||||||||| ||||| || || ||||| |||||| |||| || || | || || || || ||
gtaatattttatttatttatttattt-attattattattatttgtgagacaaggtaatattcaatgagatcattatgaatgcagTATCGTAACATCACGACAGTTTTGACAAGAGAATACCTAGATGTTCGGCCAGATGGATGGTTGAACTATGCTGCAAAAAGGATAGCTCAATT
upper sequence: AT1G08660.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S209_60V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------gtttgtgcttctttctttctctgattagt---ttttcttgttttagaacttctcgcaattc----taatgtttctgggt----aatgcagTACCGCAATATGACTACAGTATTGACAAGAGAATACCTCGATGTACGCCCTGATGGGTGGTTGGACTACGCAGCTATGAGAATTGCACAGTT
|| | | | | | |||| || || | || || | | | || ||| | |||||| |||||| |||||||| ||||||| |||||||||||||||| |||||| |||| ||| |||| ||||| | | ||||| | || ||
gtgggtaaccatcttctcctgtaatattggatagattaacaatgaaaaagtagtcgattcctacaagttggcacatcaaagactacacattagcattttctatttttgggtgcagTTCCGCAACATGACTACCATATTGACCAGAGAATACCTCGATGCACGCCCCAATGGCTGGCTGGAGTACGCCCCGACCCGAATTTCGCAATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttagtttttcttgttttagaacttctcgcaattctaatgtttctgggtaatgcagTACCGCAATATGACTACAGTATTGACAAGAGAATACCTCGATGTACGCCCTGATGGGTGGTTGGACTACGCAGCTATGAGAATTGCACAGTT
ttctaat putative branch site (score: 2)
aattctaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtgcttctttctttctctgattagtttttcttgttttagaacttctcgcaattctaatgtttctgggtaatgcagTACCGCAATATGACTACAGTATTGACAAGAGAATACCTCGATGTACGCCCTGATGGGTGGTTGGACTACGCAGCTATGAGAATTGCACAGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT