Sequence
atgc intronic sequence ATGC exonic sequencegtacaattttttgcatggaaattaaacaagccttgcagaaatttaagcacaatgtgacatatttctctgattgttttcttgcagCAAATCAAGTTCATCCTAAGAATTGGTACCCTATTCCTCTCATATTTTGTCGGCCTTGGGGTAAACTTCCAGAAGATGTCCCGTGCCATCCAAAACTCGC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g19850.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g19850.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G401874_T01 (Zea mays), 3'ss of exon 7
----gtacaattttt-tgcatggaaattaaacaa-gccttgca-gaaatttaagcacaatgtgacatatttctctgattgttttcttgcagCAAATCAAGTTCATCCTAAGAATTGGTACCCTATTCCTCTCATATTTTGTCGGCCTTGGGGTAAACTTCCAGAAGATGTCCCGTGCCATCCAAAACTCGC
||| ||| | | || | || || ||||| | || |||| | || | | | ||| | || ||||||||| || ||||| ||||| |||||||| |||||||||||||| || || |||||||| || |||||||| | |||||||||||||| || |||||
gtacgtagaatatacatatatattatttcttcattatattgcatggaaattaaactttatttagagc--tagcttcattatcttggtgcagCAAACAGCGTACATCCAAAGAACTGGTACCCGATTCCTCTCATATTCTGCCGCCCTTGGGGCAAGCTTCCAGAGAACGTCCCGTGCCATCCGAAGCTCGC
upper sequence: LOC_Os01g19850.1 (Oryza sativa), 3'ss of exon 11
lower sequence: PP1S14_51V6.1 (Physcomitrella patens), 3'ss of exon 12
---------------------------------------gtacaattttttgcatggaaattaaacaagcctt----gcagaaatttaagcacaatgtgaca--------tatttctctgattgttttcttgcagCAAATCAAGTTCATCCTAAGAATTGGTACCCTATTCCTCTCATATTTTGTCGGCCTTGGGGTAAACTTCCAGAAGATGTCCCGTGCCATCCAAAACTCGC
| || || ||| || | | | || | || | | | | ||| | | || | | | | || |||||||| |||||| ||||| || |||||||| |||||||||||||| || || ||| ||||| | | || | || | || |||||||||||||| ||
gtgctactacagtgcatgacttgcttttttgaattacttattcagttcttta-atacaccccagatggctttttttagggtaactcttaatgccatggtagaaccagaactaatgcataaaatcattcgctgcagCAACTCAAGTACATCCAAAAAATTGGTATCCTATTCCTCTCATCTTCTGCAAGCCATGGGGGATCTTGCCGAATGACGCGCCTTGCCATCCAAAACTTGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gccttgcagaaatttaagcacaatgtgacatatttctctgattgttttcttgcagCAAATCAAGTTCATCCTAAGAATTGGTACCCTATTCCTCTCATATTTTGTCGGCCTTGGGGTAAACTTCCAGAAGATGTCCCGTGCCATCCAAAACTCGC
ctctgat putative branch site (score: 4)
ttgttttctt CT-rich tract
agaaatttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacaattttttgcatggaaattaaacaagccttgcagaaatttaagcacaatgtgacatatttctctgattgttttcttgcagCAAATCAAGTTCATCCTAAGAATTGGTACCCTATTCCTCTCATATTTTGTCGGCCTTGGGGTAAACTTCCAGAAGATGTCCCGTGCCATCCAAAACTCGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG