Sequence
atgc intronic sequence ATGC exonic sequence...aaaaagaatggaatgttgcatgcggataatagtgtctagaaccatatttgttgaaattgtacttctcactgagtggatttccattgttttctccttttagGATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATGTTCTCTGCGACTGGGAGATGACCTTAAAACTTACTTTGGTATCCTCTTTTTTTTTTTGC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g40390.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g40390.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA15G13580.1 (Glycine max), 3'ss of exon 17
aaaaagaatggaatgttgcatgcggataatagtgtctagaaccatatttgttgaaattgtacttctcac--tgagtggatttc---cattgttttctccttttagGATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATGTTCTCTGCGACTGGGAGATGACCTTAAAACTTACTTTGGTATCCTCTTTTTTTTTTTGC
| |||| | | || || || ||| | | |||||||| || | || | ||| | || ||| | | ||| ||||||||||||||||||||||||| ||||| || || |||| |||| |||| |||||||||||| | |||
----ttctagttttgtttaacacttatgat-gtatcttgggatttttttgttgaggtttgatttacgatcatgataaaacatctgacataatatgtatcttgcagGATGTCTATTTTGATGATGAATCTGCAGAAGTTGTTATATCTTCTTTGCGGTTGGGAGATGACCATGAAAG-----------------------------
upper sequence: LOC_Os01g40390.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT1G30470.2 (Arabidopsis thaliana), 3'ss of exon 17
aaaaagaatggaatgttgcatgcggataatagtgtctaga-accatatttgttgaaattgtacttctcactgagtggatttccattgttttctccttttagGATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATGTTCTCTGCGACTGGGAGATGACCTTAAAACTTACTTTGGTATCCTCTTTTTTTTTTTGC
| | | | ||| | | | || | || | | | | || | | || | || |||||||||| |||||||||||||| ||||| ||||| |||| || |||| || |||||||||| | |
-actcgctcagcggctcctgtgcctgtttttataagcagccaatatggaagctttagtgatatggtagatatgaaaacctcttatgaagtctatgttgcagGATGTCTACTTTGATGATGAATCTGCAGAAGTCGTCATATCCTCCTTGCGCCTTGGAGATGACCAGGAGAG-----------------------------
upper sequence: LOC_Os01g40390.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv10s0003g04630.t01 (Vitis vinifera), 3'ss of exon 17
--aaaaagaatggaatgttg-catgcggataatagtgtctagaaccatatttgttgaaattgtacttctcactgagtggatttccattgttttctccttttagGATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATGTTCTCTGCGACTGGGAGATGACCTTAAAACTTACTTTGGTATCCTCTTTTTTTTTTTGC
| | || || | |||| |||| | | ||| || | | || | | | | || || | | || | |||||||||| |||||||||||||| || || || || |||| |||||||||| |||||||||| | | |
cattgtttagtcgactgctctcatgttcataa--gccattgctttgataccaaaacaagtattgtgtcaaatgaaatagcttcttatggagat-tcttggcagGATGTCTACTTTGATGATGAATCGGCTGAAGTTGTCATATCTTCTCTGCGATTGGGAGATGATCAGGAGAG----------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttgttgaaattgtacttctcactgagtggatttccattgttttctccttttagGATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATGTTCTCTGCGACTGGGAGATGACCTTAAAACTTACTTTGGTATCCTCTTTTTTTTTTTGC
ttctcac putative branch site (score: 2)
tttccattgttttctc putative PPT
ttgaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaaaagaatggaatgttgcatgcggataatagtgtctagaaccatatttgttgaaattgtacttctcactgagtggatttccattgttttctccttttagGATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATGTTCTCTGCGACTGGGAGATGACCTTAAAACTTACTTTGGTATCCTCTTTTTTTTTTTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
-aaaagaa
- - - - tggaatg
- - - - - - - - tgcatgc
- - - - - - - - - - - - - - - - - - - -aaccata
- - - - - - - - - - - - - - - - - - - - - - - - tgttgaa