Sequence
atgc intronic sequence ATGC exonic sequence...gtttattcccactgtcttagctactatttgatagttttgatttattgcttttgcctctagagttcagtctttgatgtgcccctcattgcttcttctgcagGTTGCTTTTAATCGGGATATTCGGACTCCAAGTGTCACACTTGAAGGTGACATTTTCCAGCCAAGTGGTCTTCTTACTGGTGGGAGTCGCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G62410.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G62410.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os01g67740.1 (Oryza sativa), 3'ss of exon 8
--------------------gtttattcccactgtcttagctactatttgatagttttgatttattgcttttgcctctagagttcagtct--ttgatgtgcccctcattgcttcttctgcagGTTGCTTTTAATCGGGATATTCGGACTCCAAGTGTCACACTTGAAGGTGACATTTTCCAGCCAAGTGGTCTTCTTACTGGTGGGAGTCGCAA
||| || | | || || || || | || || ||| | | | | | ||| || ||| | || | ||| ||||||| ||||| | || || | | | ||||||| || ||||||||||||||||| ||||| ||||| ||| | ||||| || |||||||
gtaatactgcattcaggaaatttttttgcttcagtttttactgagggctgtcaatt--gaagtatgatatatacgtaaaatgttggttcctattgttacatttgattctgttctttccatagGTTGCATTTAACAGAGAAGTTGGCAGTACAAGTGTGACCCTTGAAGGTGACATTTTTCAGCCCAGTGGCCTTTTGACTGGAGGTAGTCGCAG
upper sequence: AT5G62410.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA13G27210.1 (Glycine max), 3'ss of exon 8
gtttattcccactgtcttagctactatt-tgatagttttgatttattgcttttgcctctagagttcagtctttgatgtgcccctcattgcttcttctgcagGTTGCTTTTAATCGGGATATTCGGACTCCAAGTGTCACACTTGAAGGTGACATTTTCCAGCCAAGTGGTCTTCTTACTGGTGGGAGTCGCAA
| | | | | || | | || | ||| || | || | || || | | ||| | | || | ||| | | |||| || ||||||||||| |||| || |||||||||| |||||||| || || || ||||||||||||||||| |||||||| || |||||
atacttcatctattttttggttcttacaatcatacttgtctattctagcacatgatcatcttgctcaaattgtcttgcattttt-gttggatgtctaatagGTGGCATTTAATCGGGAGATTCACACCACAAGTGTCACTCTTGAAGGAGATATATTTCAGCCAAGTGGTCTTCTGACTGGTGGAAGCCGCAA
upper sequence: AT5G62410.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA12G36520.1 (Glycine max), 3'ss of exon 8
gtttattcccactg--tcttagctactatt-tgatagttttgatttattgcttttgcctctagagttcagtctttgatgtgcccctcattgcttcttctgcagGTTGCTTTTAATCGGGATATTCGGACTCCAAGTGTCACACTTGAAGGTGACATTTTCCAGCCAAGTGGTCTTCTTACTGGTGGGAGTCGCAA
|| | | || | || | | || | ||| || | || | | || | | ||| | | || | ||| | |||| || ||||||||||| |||| || |||||||||| |||||||| || || || ||||||||||||||||| || ||||| || |||||
--atacttcatctaatttttggtttttacaatcatacttgtctattctaccacatgatcatcttgctcaaattgtcttgcattttt-gttggatgcctaatagGTGGCATTTAATCGGGAGATTCACACCACAAGTGTCACTCTTGAAGGAGATATATTTCAGCCAAGTGGTCTTCTGACGGGTGGAAGCCGCAA
upper sequence: AT5G62410.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv16s0022g00060.t01 (Vitis vinifera), 3'ss of exon 8
gtttattcccactgtcttagctactatttgatagttttgatttattgcttttgcctctagagttcagtct---ttgatgtgcccctcattgcttcttctgcagGTTGCTTTTAATCGGGATATTCGGACTCCAAGTGTCACACTTGAAGGTGACATTTTCCAGCCAAGTGGTCTTCTTACTGGTGGGAGTCGCAA
|| || | | || | | | | || | | |||| | | || || | | || || | || | || |||||||||||||| ||||||| ||||||||||| || ||||| ||||| || || || |||||||||||||| |||||||| ||||||||
-ctttttatttaaatgcaaactggtcatagtgtgaattatatggtaaattttatttttga--tttagccaaagctaatttgtattgaaatgaatggtcgacagGTTGCTTTTAACAGGGATATCTCCACTCCAAGTGTTACTCTTGATGGTGATATATTTCAACCAAGTGGTCTTCTGACTGGTGGTAGTCGCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcttttgcctctagagttcagtctttgatgtgcccctcattgcttcttctgcagGTTGCTTTTAATCGGGATATTCGGACTCCAAGTGTCACACTTGAAGGTGACATTTTCCAGCCAAGTGGTCTTCTTACTGGTGGGAGTCGCAA
ctttgat putative branch site (score: 5)
cccctcattgcttctt putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttattcccactgtcttagctactatttgatagttttgatttattgcttttgcctctagagttcagtctttgatgtgcccctcattgcttcttctgcagGTTGCTTTTAATCGGGATATTCGGACTCCAAGTGTCACACTTGAAGGTGACATTTTCCAGCCAAGTGGTCTTCTTACTGGTGGGAGTCGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - -ttcccac
- - - - - - - - - - - - - - - - -gttttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctcat