Sequence
atgc intronic sequence ATGC exonic sequence...ttgagaaaactgtgctaccttaatgtttgtttaatatatattatgactactagcttgctcattattatatagattgtcaacactggtaaattgctttcagGCATATGTACTTGGTGCTGGTGGTGCAATTAGAAAGTTTTCTCCTGCTTTTGGGAAATTAAAATCCATGGAGCAACAGCTAGAAGGGGAATATCGGCAGG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g73530.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g73530.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G375807_T01 (Zea mays), 3'ss of exon 4
----------------------------------------------------------------------------ttgagaaaactgtgctaccttaatgtttgtttaatatatattatgact--actagct--tgctcattattatatagattgtcaacactggtaaattgctttcagGCATATGTACTTGGTGCTGGTGGTGCAATTAGAAAGTTTTCTCCTGCTTTTGGGAAATTAAAATCCATGGAGCAACAGCTAGAAGGGGAATATCGGCAGG
|||| | | |||| | |||| ||| | || | || || | | | || | | || || || ||| || ||| | |||| || ||||||||||||||||| | |||||||||||| |||||||||| ||||||||||||||||| || | || || | || ||||||||||| ||||||||||| ||
gtaattcttctttagatcaactgttgctctttattaactgcaaaaatgatgcagtacttactgttagaaaataaacttgacctagtt-tgct-tcataatttttttagaaaaaatgttcttattttacaaaatactgttccttcttagttacatttttaacatgtgtg---tgctttcagGCATATGTTATAGGTGCTGGTGGTACAATTAGAAAATTTTCTCCTGCTTTTGGCAAGCTGAAGTCTACAGAACAACAGCTAGAGGGGGAATATCGTCAAC
upper sequence: LOC_Os01g73530.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA18G02110.1 (Glycine max), 3'ss of exon 6
------------------------------------------------------ttgagaaaactgtgctaccttaatgtttgtttaatatatattatgactactagct--tgctc--attattatatagattgtcaac--actggtaaattgctttcagGCATATGTACTTGGTGCTGGTGGTGCAATTAGAAAGTTTTCTCCTGCTTTTGGGAAATTAAAATCCATGGAGCAACAGCTAGAAGGGGAATATCGGCAGG
|| || | || | || | || | | | ||| | | | || || | || | || || |||| |||| || | |||||||||||||||||||| ||||||| |||||| ||||| || |||||| | ||||| ||| | | || | ||||| || | ||||| || ||||| |||
gtatctgtgtaattgaactataatgttttataaatttctgattagcagcttatatttgcaattttttgagtttctgctgat-gtctggaagctgttagaagttagatctgatgttagaatcggtgcttatcttctcaatctactgttataaccttttcagGCATATGTACTTGGAGCTGGTGCTGCAATCAGAAACTTCTCTCCTTCATTTGGAAAACTTATGTCTAAAGAGCAGCAATTGGAAGGAGAGTATCGACAGC
upper sequence: LOC_Os01g73530.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA11G38160.1 (Glycine max), 3'ss of exon 5
------------------------------------------------------ttgagaaaactgtgctaccttaatgtttgtttaatatatattatgactactagcttgctc----attattatatagattgtcaac--actggtaaattgctttcagGCATATGTACTTGGTGCTGGTGGTGCAATTAGAAAGTTTTCTCCTGCTTTTGGGAAATTAAAATCCATGGAGCAACAGCTAGAAGGGGAATATCGGCAGG
|| || | || || || | || | | | ||| ||| | || | || | | || || |||| |||| || ||||||| |||||||||||| ||||||| |||||| ||||| ||||||||| | ||||| || | | |||| ||||| || | ||||| || ||||| |||
gtatctgtgtaattgaactgtactgttttataaatttctgattagcagcttatgtttgtaactttttgagtttttgctgat-gtctggaagttgttagaacttagatctggtgttagaatcagtgcttatcttctcaatctactgttatggccttttcagGTATATGTACTTGGAGCTGGTGCTGCAATCAGAAACTTTTCTCCTTCATTTGGAAAGCTTATGTCCAAAGAGCAGCAATTGGAAGGAGAGTATCGACAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actactagcttgctcattattatatagattgtcaacactggtaaattgctttcagGCATATGTACTTGGTGCTGGTGGTGCAATTAGAAAGTTTTCTCCTGCTTTTGGGAAATTAAAATCCATGGAGCAACAGCTAGAAGGGGAATATCGGCAGG
ttgctttc CT-rich tract
tcattattatatagat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgagaaaactgtgctaccttaatgtttgtttaatatatattatgactactagcttgctcattattatatagattgtcaacactggtaaattgctttcagGCATATGTACTTGGTGCTGGTGGTGCAATTAGAAAGTTTTCTCCTGCTTTTGGGAAATTAAAATCCATGGAGCAACAGCTAGAAGGGGAATATCGGCAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA