Sequence
atgc intronic sequence ATGC exonic sequencegtatgtttgtttgttgatcacccttgttctaagcaaagttgcggatccaattcttatctttgggtcttttgcatgactataactcttaaatttgtgttgatttttttcagGAACAGCAAATGGTAATGCCTGGTCACCGAGACTCAAACCTTCAAAAGGAACTGAACCGATACATTCCCACGGCTGCAGCTTTTGGTGGTCTGTGTATCG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G78720.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G78720.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os09g17830.1 (Oryza sativa), 3'ss of exon 5
gtatgtttgtttgttgatcacccttgttctaagcaaagttgcggatccaattcttatctttgggtcttttgcatgactataactcttaaatttgtgttgatttttttcagGAACAGCAAATGGTAATGCCTGGTCACCGAGACTCAAACCTTCAAAAGGAACTGAACCGATACATTCCCACGGCTGCAGCTTTTGGTGGTCTGTGTATCG
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---tctatatatagtgggatatttagtgttgaggtgatctaatagtcta-----tattggtttactcaaaggccatctataaactccatttctatgtca--ctataacagGAACAGCAAATGGTGATGCCTGGCCATCGTGAGTCAAACTTGCAGAAGGAATTGAACAGATACATCCCCACTGCCGCTGCATTTGGTGGAGTGTGCATTG
upper sequence: AT1G78720.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G073498_T02 (Zea mays), 3'ss of exon 5
--gtatgtttgtttgttgatcacccttgttctaagcaaagttgcggatccaattcttatctttgggtcttttgcatgactataactcttaaatttgtgttgatttttttcagGAACAGCAAATGGTAATGCCTGGTCACCGAGACTCAAACCTTCAAAAGGAACTGAACCGATACATTCCCACGGCTGCAGCTTTTGGTGGTCTGTGTATCG
|||| | || | || || | || ||| | || || || | || | || | | | | || ||| || | |||||||| |||||||| ||||| || || || || |||||| | || |||||||||||||||||||| ||||| ||||| || |||||||| | || ||||
taacgtgttgagctactgttttatatttggctcactaattatgcaaactca--------ctatgcaacaattacctgtgatcatcctctgacactg----gatattctgcagGAACAACAAATGGTGATGCCAGGACATCGTGAGTCAAACTTGCAGAAGGAACTGAACCGATACATCCCCACTGCTGCTGCATTTGGTGGAGTATGCATCG
upper sequence: AT1G78720.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G130987_T04 (Zea mays), 3'ss of exon 5
gtatgtttgtttgttgatcacccttgttctaagcaaagttgcggatccaattcttatctttgggtcttttgcatgactataactcttaaatttgtgttgatttttttcagGAACAGCAAATGGTAATGCCTGGTCACCGAGACTCAAACCTTCAAAAGGAACTGAACCGATACATTCCCACGGCTGCAGCTTTTGGTGGTCTGTGTATCG
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-------tacaatataatcttaatgatttttcacatgcctatcagttgaagatttggtatggagcagtttgctaacctgtgatcctgacactggat---attatatgcagGAACAACAAATGGTGATGCCAGGCCATCGTGAGTCGAACTTGCAGAAGGAACTTAACCGATACATCCCCACTGCTGCTGCATTTGGTGGTGTATGCATTG
upper sequence: AT1G78720.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S323_56V6.1 (Physcomitrella patens), 3'ss of exon 6
gtatgtttgtttg-------ttgatcacc-cttgttctaagcaaagttgcggatccaattcttatctttgggtcttttgcatgactataactcttaaatttgtgttgattttttt--cagGAACAGCAAATGGTAATGCCTGGTCACCGAGACTCAAACCTTCAAAAGGAACTGAACCGATACATTCCCACGGCTGCAGCTTTTGGTGGTCTGTGTATCG
||| || |||| || || || | || | || ||| | | |||| || | || | ||| | || || | || || ||| |||||||| |||||| | |||||||| ||||| || || |||||||| | |||| ||||||| ||||||||||| || || |||||||| ||| ||||||| |
gta-attgatttgaaacgatttaattgccgcgtgattgtagttgggttagacagcaaattaggtctattatattgaaggccttgatattccactgaactcagtcgcttttggtttaacagGAACAACAAATGTTCATGCCTGGCCACCGTGAATCCAACCTTCAGAGGGAATTGAACCGGTACATTCCCACAGCAGCTGCTTTTGGAGGTATGTGTATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atctttgggtcttttgcatgactataactcttaaatttgtgttgatttttttcagGAACAGCAAATGGTAATGCCTGGTCACCGAGACTCAAACCTTCAAAAGGAACTGAACCGATACATTCCCACGGCTGCAGCTTTTGGTGGTCTGTGTATCG
tttttttc CT-rich tract
ttaaatttgtgttgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtttgtttgttgatcacccttgttctaagcaaagttgcggatccaattcttatctttgggtcttttgcatgactataactcttaaatttgtgttgatttttttcagGAACAGCAAATGGTAATGCCTGGTCACCGAGACTCAAACCTTCAAAAGGAACTGAACCGATACATTCCCACGGCTGCAGCTTTTGGTGGTCTGTGTATCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG