Sequence
atgc intronic sequence ATGC exonic sequence...agctgtcattccaaccagtaggaattcagctccatgtacatggatgagttgattgaatgatcaatttacagcaatcctttttcataattaatgcttgcagATATACACCTGGTGTTTATCCGCTTCCAAATGAGAAAGATTCTGCAAACTTCTATAAGATAGCTTCGAAACGTCTTTCTGAAGCAGGATATAACCATTAT
Basic information
species | Oryza sativa |
transcript | LOC_Os12g17070.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g17070.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G105436_T01 (Zea mays), 3'ss of exon 1
agctgtcattccaaccagtaggaattcagctccatgtacatggatgagttgattgaatgatcaatttacagcaatcctttttcataattaa-tgcttgcagATATACACCTGGTGTTTATCCGCTTCCAAATGAGAAAGATTCTGCAAACTTCTATAAGATAGCTTCGAAACGTCTTTCTGAAGCAGGATATAACCATTAT
||| | | | || || | ||| | | | ||||| || | | | ||| || ||| | |||||| ||||| |||||||| | ||| || || | ||| | || |||||||||||||| | ||| |||||||| || |||||||||||||| |||||||| |||
-tgtgtgtgtacgtttgggccttgttaagaccattgtgcttcagttgaagagacgaatggacactgattcttatattatattcgtatgtaactttttgcagGTATACTCCTGGTGTCTTTCCTCTGCCGAGTGACACCGAATCTGCAAACTTCTACAGGATTGCTTCGAAGCGACTTTCTGAAGCAGGTTATAACCACTAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gagttgattgaatgatcaatttacagcaatcctttttcataattaatgcttgcagATATACACCTGGTGTTTATCCGCTTCCAAATGAGAAAGATTCTGCAAACTTCTATAAGATAGCTTCGAAACGTCTTTCTGAAGCAGGATATAACCATTAT
aattaat putative branch site (score: 3)
tttttcataattaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agctgtcattccaaccagtaggaattcagctccatgtacatggatgagttgattgaatgatcaatttacagcaatcctttttcataattaatgcttgcagATATACACCTGGTGTTTATCCGCTTCCAAATGAGAAAGATTCTGCAAACTTCTATAAGATAGCTTCGAAACGTCTTTCTGAAGCAGGATATAACCATTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
-gctgtca
- - - - - - - - - - - - ttcagct
- - - - - - - - - - - - - - - - catgtac
- - - - - - - - - - - - - - - - - - - -atggatg
- - - - - - - - - - - - - - - - - - - - - - - - - - ttgaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tacagca