Sequence
atgc intronic sequence ATGC exonic sequence...aataatgtcctattaattgtttcatatttattctttatgggtctactgtttttacaagatgttgcaaacatgtaaaaaaatctcatggtttctttctcagGAATGAAAGCATATGTTACAGAAGAGCAGGAGTTGATAATGGAGCCATCTCTTAAGTGGGCAGCAAATCCGAATGTCACTGTTGTCGTAAAGGCTTATGG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g60350.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g60350.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G111737_T01 (Zea mays), 3'ss of exon 5
aataatgtcctattaattgtttcatatttattctttatgggtctactgtttttacaa--gatgttgcaaacatgta----aaaaaatctcatggtttctt-tctcagGAATGAAAGCATATGTTACAGAAGAGCAGGAGTTGATAATGGAGCCATCTCTTAAGTGGGCAGCAAATCCGAATGTCACTGTTGTCGTAAAGGCTTATGG
| | ||| || | || | | | ||||||||| | |||||||| || || || | ||||| || | || ||| ||||||| || | ||||| ||||| ||| |||||||||| ||||||||||| ||||| ||||| || ||| | |||||||| ||||| || |||||
-------ttccattcatgtaggagcctctagcactgagtctatcccaatttttacaactgcagttgcaaatatatattttgaagcaattcatgccttttcctcctagGGATGAAAGTCTACATCACAGAGGAGCAAGAGCTGATAATGGAACCATCTCTTAAATGGGCTGCAAACCCAAATATTACTGTTGTTGTAAAAGCCTATGG
upper sequence: LOC_Os01g60350.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G050193_T02 (Zea mays), 3'ss of exon 5
aataatgtcctattaattgtttcatatttattctttatgggt-ctactgtttttacaagatgttgcaaacatgtaaaaaaatc--tcatggtttctt-tctcagGAATGAAAGCATATGTTACAGAAGAGCAGGAGTTGATAATGGAGCCATCTCTTAAGTGGGCAGCAAATCCGAATGTCACTGTTGTCGTAAAGGCTTATGG
| | || || |||| | | | || | | |||| | || || | | | | | ||| | | ||| || | || |||| ||||||| ||||| ||||| ||||| ||| |||||||||| ||||||||||| ||||| ||||| || ||| | ||||||| ||||| || |||||
----gcctgtgttaggtttttctatatgtgatgctaatttttacaactgctgttgtaaataactaaatatgtattttgaaaccatttatgccttttcctcccagGGATGAAAGTCTATGTCACAGAGGAGCAAGAGCTGATAATGGAACCATCTCTTAAATGGGCTGCAAACCCAAATATTACTGTTGCTGTAAAAGCCTATGG
upper sequence: LOC_Os01g60350.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA11G11470.1 (Glycine max), 3'ss of exon 4
aataatgtcctattaattgtttcatatttattctttatggg-tctactgtttttacaa--gatgttgcaaacatgtaaaaaaatctcatggtttctttctcagGAATGAAAGCATATGTTACAGAAGAGCAGGAGTTGATAATGGAGCCATCTCTTAAGTGGGCAGCAAATCCGAATGTCACTGTTGTCGTAAAGGCTTATGG
||| |||| | || | ||| || | || |||||||| | || || | || | | | | | | || ||||||||||| ||||| || || ||| ||||||| || |||||||| ||| | || ||||| |||||||| |||||||||||| || ||||| | |||
cttaaatcaatattttctattataatgcatttccccataagatcctctgtttttgtcatgaatattcctaatacttct---tttgttaaatgcacatttatagGAATGAAAGTTTATGTGACTGATGAGAAGGAGTTAATTATGGAGCCTTCTGTAAAATGGGCTGCAAATCCTAATGTCACTGTTTCTGTTAAGGCATTTGG
upper sequence: LOC_Os01g60350.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv03s0038g02330.t01 (Vitis vinifera), 3'ss of exon 4
----------------aataatgtcctattaattgtttcatatttattctttatgggtctactgtttttacaagatgttgcaaacatgtaaaaaaatctcatggtttctttctcagGAATGAAAGCATATGTTACAGAAGAGCAGGAGTTGATAATGGAGCCATCTCTTAAGTGGGCAGCAAATCCGAATGTCACTGTTGTCGTAAAGGCTTATGG
|| ||| | || | | | | | ||| ||||| | || | | | || | | | | | | | | | ||||| || |||| ||| ||| || ||| |||||||||| |||||||||| | || |||||||||||||| ||||| ||||||| || || |||| |||
gttagtagatatgagaccccatttccattaaaatctcccctgcaactcattttgaagtctattcttgtgatatttgttttcgatttttttct----ttttcaactattctcatcagGGATAAAAGTCTATTCTACTGATGAGAAGGAGTTGATCATGGAGCCATGCTTGAAATGGGCAGCAAATCCAAATGTGACTGTTGCTGTTAAAGCTTTTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgtttttacaagatgttgcaaacatgtaaaaaaatctcatggtttctttctcagGAATGAAAGCATATGTTACAGAAGAGCAGGAGTTGATAATGGAGCCATCTCTTAAGTGGGCAGCAAATCCGAATGTCACTGTTGTCGTAAAGGCTTATGG
tttctttctc CT-rich tract
aaacatgtaaaaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aataatgtcctattaattgtttcatatttattctttatgggtctactgtttttacaagatgttgcaaacatgtaaaaaaatctcatggtttctttctcagGAATGAAAGCATATGTTACAGAAGAGCAGGAGTTGATAATGGAGCCATCTCTTAAGTGGGCAGCAAATCCGAATGTCACTGTTGTCGTAAAGGCTTATGG
- - - - - - - - -tgtttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catggtt