Sequence
atgc intronic sequence ATGC exonic sequence...aattcatgctggagtcgagactgatcagtacatactgcctttaactcccataatccataattactcactggaacataatctgactagtcaacttatgcagGACCTTGTTGACGTTGATGTTTTTCTCGATGCAAAAAGAGTAATTGATTCTCTTCAGAACAAGGAAATCGCTCCTGCTTTAGCTTGGTGTGCAGAAAACA
Basic information
species | Oryza sativa |
transcript | LOC_Os05g06760.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g06760.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G177026_T02 (Zea mays), 3'ss of exon 2
--aattcatgctggagtcga---gactgatcagtacatactgcctttaact--cccataatccataattactcactggaacat-aatctgactagtcaact-----tatgcagGACCTTGTTGACGTTGATGTTTTTCTCGATGCAAAAAGAGTAATTGATTCTCTTCAGAACAAGGAAATCGCTCCTGCTTTAGCTTGGTGTGCAGAAAACA
|| | || ||| || | | || | | | ||| || || | | | | || | || | || || ||| | ||| | | |||||||||| ||||| ||||||| ||||||||||| |||||||||||||||||||||||||| || ||| | ||||||||||||||||||||||||||||||
gtaagtgtctgtgaagtggaatggcataatttttttttttttattttgtctaacctttcaacttcactttgatattgtgttgtcaagctaacttgccaattgttgatgtgcagGACCTCGTTGATATTGATGTCTTTCTCGATGCGAAAAGAGTAATTGATTCTCTTCAGAATAATGAAGTTTCTCCTGCTTTAGCTTGGTGTGCAGAAAACA
upper sequence: LOC_Os05g06760.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G177026_T01 (Zea mays), 3'ss of exon 2
aattcatgctgga-gtcgagactgatcagtacatactgcctttaactcccataatccataattactcactggaacataatctgactagtcaact-----tatgcagGACCTTGTTGACGTTGATGTTTTTCTCGATGCAAAAAGAGTAATTGATTCTCTTCAGAACAAGGAAATCGCTCCTGCTTTAGCTTGGTGTGCAGAAAACA
| | | | | | | | | | || | | |||| | | || | | || || || ||| | ||| | | |||||||||| ||||| ||||||| ||||||||||| |||||||||||||||||||||||||| || ||| | ||||||||||||||||||||||||||||||
-----aagtggaatggcataatttttttttttttattttgtctaacctttcaacttcactttgatattgtgttgt-caagctaacttgccaattgttgatgtgcagGACCTCGTTGATATTGATGTCTTTCTCGATGCGAAAAGAGTAATTGATTCTCTTCAGAATAATGAAGTTTCTCCTGCTTTAGCTTGGTGTGCAGAAAACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcccataatccataattactcactggaacataatctgactagtcaacttatgcagGACCTTGTTGACGTTGATGTTTTTCTCGATGCAAAAAGAGTAATTGATTCTCTTCAGAACAAGGAAATCGCTCCTGCTTTAGCTTGGTGTGCAGAAAACA
ataattact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aattcatgctggagtcgagactgatcagtacatactgcctttaactcccataatccataattactcactggaacataatctgactagtcaacttatgcagGACCTTGTTGACGTTGATGTTTTTCTCGATGCAAAAAGAGTAATTGATTCTCTTCAGAACAAGGAAATCGCTCCTGCTTTAGCTTGGTGTGCAGAAAACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA