Sequence
atgc intronic sequence ATGC exonic sequence...acactataaatctgtaaataaatatctaggttatctatttcgtcagtggttctgattatatatctgtgaattttgatgtattttttgtacaaacttgcagTATGTTGGTAATGTCCATGGTGATGAACCTGTTGGAAGGGAGGTTCTTATAAAGCTTGCAAATTGGCTGTGTGATAACTATTTGAAGGATCCCTTG
Basic information
species | Oryza sativa |
transcript | LOC_Os06g05240.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g05240.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G127941_T01 (Zea mays), 3'ss of exon 4
acactataaatctgtaaataaatatctaggttatct---atttcgtcagtggttctgattatatatctgtgaattttga---tgtattttttgtacaaacttgcagTATGTTGGTAATGTCCATGGTGATGAACCTGTTGGAAGGGAGGTTCTTATAAAGCTTGCAAATTGGCTGTGTGATAACTATTTGAAGGATCCCTTG
||| | | || | | | || | | |||| | | | || | | || | | | | | | || || | | || |||||| |||| || || ||||||||||| ||||||| ||| ||||||||||| | ||||||||||||||||||||||||||| |||| ||| | ||
------cgtgcctgaaccttgatttgtggtttctgttgggtttcaactctagcctacatcaacttgcttgggactaaaagactttgttgttgttgtacacatgcagTTCATTGGAAACGTTCATGGTGATGAGCCTGTTGCAAGAGAGGTTCTTATGCATCTTGCAAATTGGCTGTGTGATAACTATCTGAAAGATTCACTG
upper sequence: LOC_Os06g05240.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G106683_T02 (Zea mays), 3'ss of exon 5
acactataaatctg--taaataaatatctaggttatctatttcgtcagtggtt--ctgattatatatctgtgaattttgatgtattttttgtacaaacttgcagTATGTTGGTAATGTCCATGGTGATGAACCTGTTGGAAGGGAGGTTCTTATAAAGCTTGCAAATTGGCTGTGTGATAACTATTTGAAGGATCCCTTG
| || || | | | | | || | || ||| | || | | | |||| ||| || ||||||| | |||||| |||| ||||| ||||||||||| ||||||||||| ||||||||||| | ||||||||||||||||||||||||||| |||| ||| | ||
--gcctgaaccttgatttgttgtttctgttgggtttcaattctagcctacaccaacttgcttgggactaaaagactttgttgttgttgttgtaca--catgcagTTCATTGGAAATGTTCATGGTGATGAGCCTGTTGGAAGAGAGGTTCTTATGCATCTTGCAAATTGGCTGTGTGATAACTATCTGAAAGATTCACTG
upper sequence: LOC_Os06g05240.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv18s0157g00050.t01 (Vitis vinifera), 3'ss of exon 5
----acactataaatctgtaaataaatatctaggttatctatttcgtcagtg-gttctgattatatatctgtgaattt-tgatgtattttttgtacaaacttgcagTATGTTGGTAATGTCCATGGTGATGAACCTGTTGGAAGGGAGGTTCTTATAAAGCTTGCAAATTGGCTGTGTGATAACTATTTGAAGGATCCCTTG
| || ||||| |||| | | | || || || | ||| | | |||| | | ||| |||| || | | ||||||| | |||| ||||| ||||| |||||||||||||| | ||| |||| || |||||||||||| | ||||||||| || ||||||||||||||
tttttctctctaaatg---aaatgcttccacaaatgtcctggggaatccatgcatgctggattagttcctgttagtccatgactgatttgctggata---ttgcagTTTATTGGAAATGTGCATGGAGATGAACCTGTTGGTCGTGAGCTTCTGTTACTCCTTGCAAATTGGTTATGTGATAACCATATGAAGGATCCCTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtggttctgattatatatctgtgaattttgatgtattttttgtacaaacttgcagTATGTTGGTAATGTCCATGGTGATGAACCTGTTGGAAGGGAGGTTCTTATAAAGCTTGCAAATTGGCTGTGTGATAACTATTTGAAGGATCCCTTG
aattttgatgtatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acactataaatctgtaaataaatatctaggttatctatttcgtcagtggttctgattatatatctgtgaattttgatgtattttttgtacaaacttgcagTATGTTGGTAATGTCCATGGTGATGAACCTGTTGGAAGGGAGGTTCTTATAAAGCTTGCAAATTGGCTGTGTGATAACTATTTGAAGGATCCCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - -aaataaa
- - - - - - - - - - - - - - - - - - - - - - - -ggttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttgatg