Sequence
atgc intronic sequence ATGC exonic sequence...atgatgggtaacattgccatgttttttaaatcattatctgggatgtaaatttctgcctaatttggacctactaacggatcgatatgttgtttcattgcagGAAAGAGTTCTATGGTTCCACAGTTCCTCCTGGAAGAAAACATGGAACCCATTCTATGCACGCAGCCAAGGAGGTTTGCAGTAGTAGCCATTGCTCAAAT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g15300.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g15300.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G146047_T01 (Zea mays), 3'ss of exon 1
atgatgggtaacattgccatgttttttaaatcattatctgggatgtaaatttct---gcctaatttggacctactaacggatcgata-tgttgtttcattgcagGAAAGAGTTCTATGGTTCCACAGTTCCTCCTGGAAGAAAACATGGAACCCATTCTATGCACGCAGCCAAGGAGGTTTGCAGTAGTAGCCATTGCTCAAAT
|| || | ||||| | | | | |||| || ||||| | ||| | | | || | | | | |||| ||||||| ||||||||| ||||||| ||||||||| | |||||||| ||||| || || || ||||| ||||| || ||||||||||| ||||||||||||| |
--aatttgt--cgttgccttactggatgcgcagtggagcaagatgcaattttcttgaaattcattggtttcatatgtttaattgccagtcctctttccttgcagGGAAGAGTTCTCTGGTTCCCCAGTTCCTCTTAGAAGAAAATATGGAGCCTATCCTGTGCACACAGCCTAGAAGGTTTGCAGTGGTAGCCATTGCTCGAGC
upper sequence: LOC_Os01g15300.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT2G47680.1 (Arabidopsis thaliana), 3'ss of exon 1
-----atgatgggtaacattgccatgttttttaaatcattatctgggatgtaaatttctgcctaatttggacctactaacggatcgatatgttgtttcattgcagGAAAGAGTTCTATGGTTCCACAGTTCCTCCTGGAAGAAAACATGGAACCCATTCTATGCACGCAGCCAAGGAGGTTTGCAGTAGTAGCCATTGCTCAAAT
|| | | || || || | ||| || |||| | | | | | | | | | || | | | | || | |||| |||||||| |||||||||||||| ||||||| |||||||| |||||| | || || ||||| ||||| ||||| || ||||| ||||| | ||
cttccctgcgcctttgaactgttgtgattgt--aatggatagctggattttcgactcatctcatacgtagtgtggttacttacttg---tccttctttgcttcagGGAAGAGTTCACAAGTTCCACAGTTCCTTCTGGAAGCAAACATGGCTCCCATTTTGTGTACACAGCCTAGGAGATTTGCGGTTGTAGCTGTTGCTAAGAT
upper sequence: LOC_Os01g15300.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv07s0005g00310.t01 (Vitis vinifera), 3'ss of exon 1
atgatgggtaacattgccatgttttttaaat--cattatctgggatgt--aaatttctgcctaatttggacctactaac--ggatcgatatgttgttt------cattgcagGAAAGAGTTCTATGGTTCCACAGTTCCTCCTGGAAGAAAACATGGAACCCATTCTATGCACGCAGCCAAGGAGGTTTGCAGTAGTAGCCATTGCTCAAAT
|| ||| | | | | || || ||| || | ||| | | ||| | || |||| | || | | || | || || ||| ||||| || ||||||||||| || |||||||||||||||| |||||| | ||||| || || ||||| ||||| || || || |||| |||
------------gctgtcatatcatacacgttgcaccatatggattgatagagttttttcttaactgagatgatttaacttgcattattttcatgctcatgtggcaatgaagGGAAGAGCTCACAAGTTCCACAGTTTCTTCTGGAAGAAAACATGGCACCCATATTGTGCACACAACCTAGGAGATTTGCTGTTGTTGCTGTTGCCAGAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaatttctgcctaatttggacctactaacggatcgatatgttgtttcattgcagGAAAGAGTTCTATGGTTCCACAGTTCCTCCTGGAAGAAAACATGGAACCCATTCTATGCACGCAGCCAAGGAGGTTTGCAGTAGTAGCCATTGCTCAAAT
tactaac putative branch site (score: 0)
ttgtttc putative PPT
taattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgatgggtaacattgccatgttttttaaatcattatctgggatgtaaatttctgcctaatttggacctactaacggatcgatatgttgtttcattgcagGAAAGAGTTCTATGGTTCCACAGTTCCTCCTGGAAGAAAACATGGAACCCATTCTATGCACGCAGCCAAGGAGGTTTGCAGTAGTAGCCATTGCTCAAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG