Sequence
atgc intronic sequence ATGC exonic sequence...ctaacctggttttttgtgacttctgtactttttaggtggtgcactgaagccaacaaatgttgataacttgtgggtacatgtgacatgtgcatggtttcagCCACAAGTTGCTTTTGCTAGTGATGAGCTGATGGAACCTGCTATTGGGATATTGAATATTACGCCTTTGCTATTCATGAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g46700.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g46700.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G170412_T01 (Zea mays), 3'ss of exon 12
---------------------------------------------------------------ctaa-cctggttttttgtgacttctgtactttt-taggtggtgcactgaagccaacaaatgttgataacttgtgggtacatgtgacatgtgcatggtttcagCCACAAGTTGCTTTTGCTAGTGATGAGCTGATGGAACCTGCTATTGGGATATTGAATATTACGCCTTTGCTATTCATGAAG
||| ||||| | |||| | || ||| || |||||||||| ||||||||||||||||||||||||||||||| || ||||||||||||||||||||| |||| ||||||||||||||||||||||| |||||
tcaattctggatttcaatatctgggtgcagtttgctctctttttattgagtattttttaatcattaatcctggcacctggtgaactttgaactattgtagGTGGTGCTTTGAAGCCAACAAATGTTGATAACTTGTGGGTTCACGTGACATGTGCATGGTTTCAGTCACAGGTTGCTTTTGCTAGTGATGAGCTCATGGA----------------------------------------------
upper sequence: LOC_Os01g46700.1 (Oryza sativa), 3'ss of exon 12
lower sequence: AT4G27910.1 (Arabidopsis thaliana), 3'ss of exon 12
--------------------------------------------------------ctaacctggttttttgtgacttctgtactttt--------taggtggtgcactgaagccaacaaatgttgataacttgtgggtacatgtgacatgtgcatggtttcagCCACAAGTTGCTTTTGCTAGTGATGAGCTGATGGAACCTGCTATTGGGATATTGAATATTACGCCTTTGCTATTCATGAAG
|||| | ||| | || | | | |||| |||||| |||||||||| |||| || | |||||||| |||||||||||||| ||||||||||| |||| |||||| ||||| || |||||
gtggctttataaagtatattcagctttttcacataaacatatggcaccactgcctattaactatatccattggctccgctatgttgtcactgatgatagGAGGTGCATTGAAGCCAACTGATGTGGAAACGTTGTGGGTTCATGTGACATGTGCTTGGTTTCAGCCTGAAGTATGTTTTGCAAGTGAGGAAAAAATGGA----------------------------------------------
upper sequence: LOC_Os01g46700.1 (Oryza sativa), 3'ss of exon 12
lower sequence: PP1S47_35V6.1 (Physcomitrella patens), 3'ss of exon 16
-----------------------------------------------------------------ctaacctggttttttgtgacttctgtactttttaggtggtgcactgaagccaacaaatgttgataacttgtgggtacatgtgacatgtgcatggtttcagCCACAAGTTGCTTTTGCTAGTGATGAGCTGATGGAACCTGCTATTGGGATATTGAATATTACGCCTTTGCTATTCATGAAG
| | || | | | ||| |||||| ||| |||| || | ||| || || ||||||||||||||||| |||||||||||| || |||| || | || |||||
gatttacttagaggttaaataatttagtactcagttacaagaaagtttatgtctcaagtcaggcaatgttatcaattaataaagagcttcttcttgccagGTGGGGCATTGAAACCGTCGAATACTGCAAATTTGTGGGTACATGTGACCTGTGCATGGTTTGTACCTGAAGTCAAGTTCAAAAACATTGTCAAAATGGA---------------------------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaagccaacaaatgttgataacttgtgggtacatgtgacatgtgcatggtttcagCCACAAGTTGCTTTTGCTAGTGATGAGCTGATGGAACCTGCTATTGGGATATTGAATATTACGCCTTTGCTATTCATGAAG
tgataac putative branch site (score: 2)
aacaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctaacctggttttttgtgacttctgtactttttaggtggtgcactgaagccaacaaatgttgataacttgtgggtacatgtgacatgtgcatggtttcagCCACAAGTTGCTTTTGCTAGTGATGAGCTGATGGAACCTGCTATTGGGATATTGAATATTACGCCTTTGCTATTCATGAAG
- - - - - - - - - acttctg
- - - - - - - - - - - - - - - - - -gtggtgc
- - - - - - - - - - - - - - - - - - - - - -ctgaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - atgttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgtgc