Sequence
atgc intronic sequence ATGC exonic sequencegtgaattttagagcgggatatcttcgcaatgcagcaatgcatggaaattaattttttgatctcaactctcaaattctcagGTGATAGTTGTATCTGGGGAGACTGGATGTGGTAAGACAACTCAGCTTCCACAATACATTTTGGAATCAGAGATAGAGTCTGGTCGGGGAGCATTCTGCA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G04895.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G04895.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G24630.1 (Glycine max), 3'ss of exon 8
------------------------gtgaattttagagcgggatatcttcgcaatgcagcaatgcatgga-aattaattttttgatctcaactctcaaattctcagGTGATAGTTGTATCTGGGGAGACTGGATGTGGTAAGACAACTCAGCTTCCACAATACATTTTGGAATCAGAGATAGAGTCTGGTCGGGGAGCATTCTGCA
|||||| | | | || ||| || | ||| || | |||| || || || | || ||||||||||| ||||||| |||||||| |||||||| || ||||| ||||| || || | || ||||||||| | ||||||||||| |||||||| || |
tgtgtatgtggttttccaatagaaatgaattgaatatcatgaactctgt----tggaattatgtatttataattgatacctt-attttggtgaataatgatctagGTGATAGTTATATCTGGAGAGACTGGCTGTGGTAAAACCACTCAACTTCCTCACTATGTATTAGAATCAGAGGTTGAGTCTGGTCGTGGAGCATTTTGTA
upper sequence: AT5G04895.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA15G29910.1 (Glycine max), 3'ss of exon 4
-------gtgaattttagagcgggatatctt---cgcaatg--------cagca--atgcatgga-aattaattttttgatctcaactctcaaattctcagGTGATAGTTGTATCTGGGGAGACTGGATGTGGTAAGACAACTCAGCTTCCACAATACATTTTGGAATCAGAGATAGAGTCTGGTCGGGGAGCATTCTGCA
||| ||| | | || | || | | |||| ||| || | |||| || || || | | || ||||||| ||||||||||| ||| |||| |||||||| | ||||| ||||| || || | || ||||||||||||||||||||||| |||||||| || |
attgtctgtggttttccaatagaaatgaactgaatgccacgaactctgttagcattatgtattcataattgatacctt-attttgatgaataatgatctagGTGATTGTTGTATCTGGAGAGGCTGGCTGTGGTAAAATCACTCAACTTCCTCAGTATGTATTAGAATCAGAGATAGAGTCTGGTCGTGGAGCATTTTGTA
upper sequence: AT5G04895.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ13473 (Selaginella moellendorffii), 3'ss of exon 5
gtgaattttagagcgggatatcttcgcaatgcagcaatgcatggaaattaattttttgatctcaactctca--aattct----cagGTGATAGTTGTATCTGGGGAGACTGGATGTGGTAAGACAACTCAGCTTCCACAATACATTTTGGAATCAGAGATAGAGTCTGGTCGGGGAGCATTCTGCA
||||| || |||| | | | | | |||||| ||||| | || | || || || || ||||||||||| |||||||||||||||||||| ||| |||| ||||||| ||| | || | || | ||| |
---------------------------------------gttggaagttctttttgttgttaaagtttcaagaaattcttctacagGTTGTGGTGATTTCAGGAGAAACAGGATGTGGTAAAACAACTCAGCTTCCACAATATATTCTGGAGGCAGAGATTGAGGCAGGCAGAGGCGGTAGCTGTA
upper sequence: AT5G04895.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ19043 (Selaginella moellendorffii), 3'ss of exon 5
gtgaattttagagcgggatatcttcgcaatgcagcaatgcatggaaattaattttttgatctcaactctcaaattctcagGTGATAGTTGTATCTGGGGAGACTGGATGTGGTAAGACAACTCAGCTTCCACAATACATTTTGGAATCAGAGATAGAGTCTGGTCGGGGAGCATTCTGCA
| | || | || | || | |||| | | ||||| | || | || || || || ||||||||||| |||||||||||||||||||| ||| |||| ||||||| ||| | || | || | ||| |
------------------------------gttggaagttctttttgttgttgttaaagtttcaagtaattcttctacagGTTGTGGTGATTTCAGGAGAAACAGGATGTGGTAAAACAACTCAGCTTCCACAATATATTCTGGAGGCAGAGATTGAGGCAGGCAGAGGCGGTAGCTGTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcaatgcagcaatgcatggaaattaattttttgatctcaactctcaaattctcagGTGATAGTTGTATCTGGGGAGACTGGATGTGGTAAGACAACTCAGCTTCCACAATACATTTTGGAATCAGAGATAGAGTCTGGTCGGGGAGCATTCTGCA
ttctc CT-rich tract
aaattaattttttgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaattttagagcgggatatcttcgcaatgcagcaatgcatggaaattaattttttgatctcaactctcaaattctcagGTGATAGTTGTATCTGGGGAGACTGGATGTGGTAAGACAACTCAGCTTCCACAATACATTTTGGAATCAGAGATAGAGTCTGGTCGGGGAGCATTCTGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA