Sequence
atgc intronic sequence ATGC exonic sequence...gactaggaccttctttcatgccaggacaagtattaaattgtgtgttgtgtcaatttattgttgcaattggtattgtctcaaatttattcccttatcacagGTACCTGTATGACATTCTGACAAAGGCAACTGTAGTGAAGAAGAGGATTCATGTTCTGATATTCTGCAACAAAACAGATAAAGTTACGGCTCACTCAAAA
Basic information
species | Oryza sativa |
transcript | LOC_Os06g27870.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g27870.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G091503_T04 (Zea mays), 3'ss of exon 5
gactaggaccttcttt--catgccaggacaagtattaaattg-tgtgttgtgtcaatttat-tgttgcaattggtattgtctcaaatttattcccttatcacagGTACCTGTATGACATTCTGACAAAGGCAACTGTAGTGAAGAAGAGGATTCATGTTCTGATATTCTGCAACAAAACAGATAAAGTTACGGCTCACTCAAAA
| ||||||| || || ||| ||| | |||| | ||| || | |||| | | | | ||| |||| ||| | ||||||||| ||||||||||||||||||||||||||||||||||| | | | | ||| || |||||||||||||| |||||||||||||| || ||||| ||
---aggaaccttctccactattcccaacattgtagagcattactctgttttatcatttcttacgttgttaacatt-tcataacaatattatcatctttttgcagGTACCTTTATGACATTCTGACAAAGGCAACTGTAGTGAAGAAAAAGGTCCCTGTGCTTATATTCTGCAACAAGACAGATAAAGTTACCGCCCACTCGAAG
upper sequence: LOC_Os06g27870.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G015642_T01 (Zea mays), 3'ss of exon 5
gactaggaccttctttcatgccaggacaagtattaaattg-tgtgttgtgtcaatttattgttgcaattggtattgtct--caaatttattcccttatcacagGTACCTGTATGACATTCTGACAAAGGCAACTGTAGTGAAGAAGAGGATTCATGTTCTGATATTCTGCAACAAAACAGATAAAGTTACGGCTCACTCAAAA
|||||| || | || | | ||| | |||| ||| |||||| || || ||| | ||| |||| | | | ||||||||| ||||||||||||||||| ||| ||||||| ||||| ||||| | ||| || |||||||||||||| || ||||||||||| || ||||| ||
--ctaggagatttcactgttcccaagattgcagagcattactctgtttcatca-tttattagtgttgttaacatttcataacaatattatcatccttttgcagGTACCTTTATGACATTCTGACAAAAGCATCTGTAGTTAAGAAAAGGATCCCTGTGCTTATATTCTGCAACAAGACGGATAAAGTTACCGCCCACTCGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgtcaatttattgttgcaattggtattgtctcaaatttattcccttatcacagGTACCTGTATGACATTCTGACAAAGGCAACTGTAGTGAAGAAGAGGATTCATGTTCTGATATTCTGCAACAAAACAGATAAAGTTACGGCTCACTCAAAA
tttattcccttatc CT-rich tract
aatttattgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gactaggaccttctttcatgccaggacaagtattaaattgtgtgttgtgtcaatttattgttgcaattggtattgtctcaaatttattcccttatcacagGTACCTGTATGACATTCTGACAAAGGCAACTGTAGTGAAGAAGAGGATTCATGTTCTGATATTCTGCAACAAAACAGATAAAGTTACGGCTCACTCAAAA
- - - - - - - ttcatgc
- - - - - - - - - - - - - - - - - - - - tgtgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgttgc