Sequence
atgc intronic sequence ATGC exonic sequencegtaagcatgctatttgatttattttcatctcttaaataatactgtattggttactcatcttacgctcacaatggcatgctccttttttcagGAAGATGAAATCATTGTTCAGATGGTAAACAAACTTGGACCAAAGAAATGGTCAACCATTGCTCAAGCTTTGCCTGGACGTATAGGAAAGCAATGTCGAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g12860.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g12860.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G470307_T01 (Zea mays), 3'ss of exon 2
---------------------------------------------------------gtaagcatgct---atttgatttattttcatctcttaaataatactgtattggttactca-tcttacgctcacaatggcatgctccttttttcagGAAGATGAAATCATTGTTCAGATGGTAAACAAACTTGGACCAAAGAAATGGTCAACCATTGCTCAAGCTTTGCCTGGACGTATAGGAAAGCAATGTCGAG
|||| | | | || || | |||| ||||| ||||| || | | ||| ||| || | | || ||| ||||||| |||||||| |||||||||||||||||| || |||||||||||||| |||| |||||||||||||||||||| |||||||||||||| || |
gtaagcatcctattggattttctattttgtttttatttcttattaacatcaacaaaaaaaagcctaccccaacatgcttgggtaaggcatctt--ataatcacttattgaacacaaaatattaatatcaacctgttctctttctgtttatagGAAGACGAAATCATAGTTCAGATGGTAAACAAATACGGGCCAAAGAAATGGTCGGCCATCGCTCAAGCTTTGCCTGGACGCATAGGAAAGCAATGCCGGG
upper sequence: LOC_Os01g12860.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv11s0016g03750.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------------------------gtaagcatgctatttgatttattttcatctcttaaataatactgtattggttactcatcttacgctcacaatggcatgctcctttttt-----cagGAAGATGAAATCATTGTTCAGATGGTAAACAAACTTGGACCAAAGAAATGGTCAACCATTGCTCAAGCTTTGCCTGGACGTATAGGAAAGCAATGTCGAG
||| | | || ||| |||| ||| ||| | || ||| | || | | | | | || | || ||||| ||||| || || || || | || || || ||| |||||||| |||||||| ||||| ||||| || |||||||| || |||||||||||||| |
gtgaattcatttgtacatcagactgctttatagattccttgcctaaagtaccattatttcatgggcaattaatatcttgtaactaagttgctggtgtttattgatacaatggtataaccagttgattctaatattataaacagGAGGATGAGATAATAATTGAGTTAGTGAATAAGTATGGGCCAAAGAAGTGGTCAACTATTGCACAAGCATTACCTGGACGAATTGGAAAGCAATGTCGGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatactgtattggttactcatcttacgctcacaatggcatgctccttttttcagGAAGATGAAATCATTGTTCAGATGGTAAACAAACTTGGACCAAAGAAATGGTCAACCATTGCTCAAGCTTTGCCTGGACGTATAGGAAAGCAATGTCGAG
cgctcac putative branch site (score: 3)
catgctccttttttc putative PPT
ttttttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcatgctatttgatttattttcatctcttaaataatactgtattggttactcatcttacgctcacaatggcatgctccttttttcagGAAGATGAAATCATTGTTCAGATGGTAAACAAACTTGGACCAAAGAAATGGTCAACCATTGCTCAAGCTTTGCCTGGACGTATAGGAAAGCAATGTCGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA