Sequence
atgc intronic sequence ATGC exonic sequence...aacgttactgccatgtcctgtatggtggcctcatttaaaaatgttgatcttcatctgtgctctgtgggttggactggaatttaccataaaactttactagGAACAAGTGAGAAGTGGTGATGCAAGTGCTACTGAGTATTTTGAGCTGGGAGCAGTCATGCTACGGAGAAAATTTTACCCTGCCGCTATCAAATATCTAC
Basic information
species | Oryza sativa |
transcript | LOC_Os08g25890.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g25890.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G809292_T02 (Zea mays), 3'ss of exon 3
aacgttactgccatgtcctgtatggtggcctcatttaaaaatgttgatcttcat-ctgtgctctgtgggttggactggaatttacca----taaaactttactagGAACAAGTGAGAAGTGGTGATGCAAGTGCTACTGAGTATTTTGAGCTGGGAGCAGTCATGCTACGGAGAAAATTTTACCCTGCCGCTATCAAATATCTAC
| | || | || || | | | ||| | || | | | |||| ||| | ||| || | | ||| |||||||||||||||||| |||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| || || |||||||||||||| |
-----ggcagaagtgcctgtagtgatgattctgacagcacaattggatttatataccaatttacatatgttgacctgtattttgacaatttttattatttgctagGAACAAGTGAGAAGCGGTGATGCAAGTGCTACTGAGTATTTTGAGCTTGGAGCAGTCATGCTACGGAGAAAATTTTATCCAGCTGCTATCAAATATCTGC
upper sequence: LOC_Os08g25890.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA10G35950.3 (Glycine max), 3'ss of exon 4
--aacgttactgccatgtcctgtatggtggcctcatttaaaaatgttgatcttcatctgtgctctgtgggttggactggaatt-taccataaaactttactagGAACAAGTGAGAAGTGGTGATGCAAGTGCTACTGAGTATTTTGAGCTGGGAGCAGTCATGCTACGGAGAAAATTTTACCCTGCCGCTATCAAATATCTAC
| ||| || | | | | || || |||| | | | || ||| ||| | | | | | | | | | |||| ||||| |||||||||||||| |||| |||||| |||||| || || ||||| ||||| || || |||||||||||||| |||| ||| | | |
tagagcttatacacaagcacaactggacaagccagttggaactagttgttttatg---atcctttgtcagtttgtccttactcattttctgccattatctcagGAGCAAGTAAGAAGTGGTGATGCTGGTGCAACTGAGCTTTTTGAACTTGGTGCAGTGATGCTGCGCAGGAAATTTTACCCTGCTGCTACCAAGTTCTTGC
upper sequence: LOC_Os08g25890.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA20G31640.1 (Glycine max), 3'ss of exon 2
-aacgttactgccatgtcctgtatggtggcctcatttaaaaatg---ttgatcttcatctgtgctctgtgggttggactggaatttaccataaaactttactagGAACAAGTGAGAAGTGGTGATGCAAGTGCTACTGAGTATTTTGAGCTGGGAGCAGTCATGCTACGGAGAAAATTTTACCCTGCCGCTATCAAATATCTAC
|| ||| || | | | || || || | | | | | | || ||| ||| |||| | | | | |||| ||||| |||||||||||||| |||| |||||| |||||| || || ||||| ||||| || || |||||||||||||| |||| ||| | | |
aaagcttatacacaagcacaactgcacaagccagttggaacttggaactagttgttttttatcctttgtcatccttactc--attttctgcc--attatctcagGAGCAAGTAAGAAGTGGTGATGCTGGTGCAACTGAGCTTTTTGAACTTGGTGCAGTGATGCTGCGCAGGAAATTTTACCCTGCTGCTACCAAGTTCTTGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatcttcatctgtgctctgtgggttggactggaatttaccataaaactttactagGAACAAGTGAGAAGTGGTGATGCAAGTGCTACTGAGTATTTTGAGCTGGGAGCAGTCATGCTACGGAGAAAATTTTACCCTGCCGCTATCAAATATCTAC
tgttgat putative branch site (score: 4)
ctttact putative PPT
aatttaccataaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aacgttactgccatgtcctgtatggtggcctcatttaaaaatgttgatcttcatctgtgctctgtgggttggactggaatttaccataaaactttactagGAACAAGTGAGAAGTGGTGATGCAAGTGCTACTGAGTATTTTGAGCTGGGAGCAGTCATGCTACGGAGAAAATTTTACCCTGCCGCTATCAAATATCTAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - -tactgcc
- - - - - - - - -ctgtatg
- - - - - - - - - - - - - - - - - - - - atgttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - accataa