Sequence
atgc intronic sequence ATGC exonic sequence...atgcccctactttgaacaaaaagaaaaaagaaaaaatacttcaattttttactttatacatattgcaagatggacactgactagtatgcctattttatagGTCGCCATCACCTTCTGCCCGTAGATCGAAATCTCGGTCAAGATCACCTATCAAGTACCGCCGGAGCAGGCGGTCTAGATCATACTCTCCGCCGGTTAGA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g01150.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g01150.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G132936_T03 (Zea mays), 3'ss of exon 2
atgcccctactttgaacaaaaagaaaaaagaaaaaatacttcaatt--ttttactttatacatattgcaagatggacactgactagtatgcctattttatagGTCGCCATCACCTTCTGCCCGTAGATCGAAATCTCGGTCAAGATCACCTATCAAGTACCGCCGGAGCAGGCGGTCTAGATCATACTCTCCGCCGGTTAGA
| || || | || | | || || | | | ||| |||| ||| ||| ||||| | || | |||| ||| | | |||| || || ||||| | || | |||||||| |||||||||||||||||||||||||||||||| ||||||| || || | || |||||||| || ||| ||
--gataaaacatttagggaagaaagtaactaagttagtcattgattgtttttccttcctacgtattgtgtgctgaagcctgatcagtttatatgatttacagATCACCATCTTCCCCTACTCGTAGATCAAAATCTCGGTCAAGATCACCTATCAAGTACCGTAGGAGCAGACGATCCCGCTCCTACTCTCCCCCAGTTGGA
upper sequence: LOC_Os01g01150.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G056145_T02 (Zea mays), 3'ss of exon 3
atgcccctactttgaacaaaaagaaaaaagaaaaaatacttcaat-tttttactttatacatattgcaagatggacactgactagtatgcctattttatagGTCGCCATCACCTTCTGCCCGTAGATCGAAATCTCGGTCAAGATCACCTATCAAGTACCGCCGGAGCAGGCGGTCTAGATCATACTCTCCGCCGGTTAGA
| || || || || || | || | || | | ||||| ||| || |||||| | || | ||||| ||| | || |||| || || ||||| || ||| | |||||||| ||||||||||| |||||||||||||| ||||| ||||||||||||| | || |||||||| || ||||||
-agataaaacattagggaagaaaggaactcaggaagtcattgattgtttttccttcctatatattgtgtgctgtagcctgaccagtttatataatttacagATCACCATCGCCCTCTACTCGTAGATCAAAATCTCGGTCGAGATCACCTATCAAATACCGTAGGAGCAGGCGGTCCCGCTCCTACTCTCCCCCAGTTAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttactttatacatattgcaagatggacactgactagtatgcctattttatagGTCGCCATCACCTTCTGCCCGTAGATCGAAATCTCGGTCAAGATCACCTATCAAGTACCGCCGGAGCAGGCGGTCTAGATCATACTCTCCGCCGGTTAGA
cactgac putative branch site (score: 2)
cctatttt putative PPT
actttatacatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgcccctactttgaacaaaaagaaaaaagaaaaaatacttcaattttttactttatacatattgcaagatggacactgactagtatgcctattttatagGTCGCCATCACCTTCTGCCCGTAGATCGAAATCTCGGTCAAGATCACCTATCAAGTACCGCCGGAGCAGGCGGTCTAGATCATACTCTCCGCCGGTTAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA