Sequence
atgc intronic sequence ATGC exonic sequence...tacattttttttaatcttgcagcaataaagttttttctttttgcatccatatgcccaaagggcaatatctacttgtttgatatcttggtcctgttctcagGTGGTGGCTATTGTCTATGCCATTATGACAACAAGAAATGAGCATATAACATGGGAAATGAGGGCAATCCGAGTGCTGCCGATGTTTGTCTTGCCTGCTG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g41990.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g41990.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G074436_T01 (Zea mays), 3'ss of exon 1
tacatttttt-ttaatcttgcagcaataaagttttttctttttgcatccatatgcccaaagggcaatatctacttgtttgatatcttggtcctgttctcagGTGGTGGCTATTGTCTATGCCATTATGACAACAAGAAATGAGCATATAACATGGGAAATGAGGGCAATCCGAGTGCTGCCGATGTTTGTCTTGCCTGCTG
||| ||| | || | | || | | ||| || | || | | ||||| || | | | | |||||| ||||||| | |||||||||||||||| | ||| |||| |||||||| ||||| |||||||||||| || |||| ||| ||||||||||||| |||||||| || ||||| | | |||||||
tacttttcatattgaacctgtactcttgtagtgacttatcttcac-tgcatatccctagcttgtagtttctactggtttgattgttcagtcctgttctcagGTGTTAGCTGTTGTTTATGCCATCATGACGACAAGAAATGAGGATCTAACTTGGCAAATGAGGGCAATACGAGTGCTACCTATGTTCATTCTTCCTGCTG
upper sequence: LOC_Os02g41990.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G153332_T01 (Zea mays), 3'ss of exon 1
-tacatttt--ttttaatcttgcagcaataaagttttttctttttgcatccatatgcccaaagggcaatatctacttgtttgatatcttggtcctgttctcagGTGGTGGCTATTGTCTATGCCATTATGACAACAAGAAATGAGCATATAACATGGGAAATGAGGGCAATCCGAGTGCTGCCGATGTTTGTCTTGCCTGCTG
| || ||| ||| || ||| | | | ||| || ||||| | | ||||| || | | | |||||| | || || | |||||||||||||||| | ||| |||| |||||||| |||| |||||||||||| || |||| ||| ||||||||||||| || ||||| || ||||| || | |||| ||
atgcagtttacctttcatattgaacc--tgtagtgacttatttttac-tgcatatccctacctttcggtttctactggcttaattgttcagtcctgttctcagGTGTTAGCTGTTGTTTATGCCATCATGATGACAAGAAATGAGGATCTAACTTGGCAAATGAGGGCAATACGGGTGCTACCTATGTTCGTTCTTCCTGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tccatatgcccaaagggcaatatctacttgtttgatatcttggtcctgttctcagGTGGTGGCTATTGTCTATGCCATTATGACAACAAGAAATGAGCATATAACATGGGAAATGAGGGCAATCCGAGTGCTGCCGATGTTTGTCTTGCCTGCTG
gtttgat putative branch site (score: 5)
tcctgttctc putative PPT
aatatcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tacattttttttaatcttgcagcaataaagttttttctttttgcatccatatgcccaaagggcaatatctacttgtttgatatcttggtcctgttctcagGTGGTGGCTATTGTCTATGCCATTATGACAACAAGAAATGAGCATATAACATGGGAAATGAGGGCAATCCGAGTGCTGCCGATGTTTGTCTTGCCTGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC