Sequence
atgc intronic sequence ATGC exonic sequence...accaatatatgttcaaacccaccaagaaattcttgccttgaattaagttttgttcacttctcatatcttgaaaaaacaaatactaatgtctctcctgcagGCCACAAGCGGGAACCAGAACAACATGCTGATCCTCCAGGAGACGTGCACCGACTCATCGGGCTCCCTCGTCGTCTACGCTCCGGTGGACGTGCAGTCGA
Basic information
species | Oryza sativa |
transcript | LOC_Os09g35760.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g35760.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G116658_T01 (Zea mays), 3'ss of exon 8
accaatatatgttcaaacc-caccaagaaattcttgccttgaattaagttttgttcacttctcatatcttgaaaaaacaaatactaatgtc-tctcctgcagGCCACAAGCGGGAACCAGAACAACATGCTGATCCTCCAGGAGACGTGCACCGACTCATCGGGCTCCCTCGTCGTCTACGCTCCGGTGGACGTGCAGTCGA
|||||| | |||| || || | | | | | || | || || ||| || | || | || ||| | | ||||||| || || || ||||| ||||||||||| ||||| || ||||| ||||||||| | || ||||| || || || ||||| ||||||||||||||||| |
--ttatatatatctaaacaacatgcagtataaataagttcgcaatacatattttttactctcttcattacccctgatgaatttctgatgagatgtgttgcagGCAACTAGTGGCAACCAAAACAACATGCTCATCCTGCAAGAGACCTGCACCGACCCGTCAGGCTCTCTGGTGGTGTACGCCCCGGTGGACGTGCAGTCCA
upper sequence: LOC_Os09g35760.2 (Oryza sativa), 3'ss of exon 8
lower sequence: EFJ19972 (Selaginella moellendorffii), 3'ss of exon 10
accaatatatgttcaaacccaccaagaaattcttgccttgaattaagttttgttcacttctcatatcttgaaaaaacaaatactaatgtctctcctgc-agGCCACAAGCGGGAACCAGAACAACATGCTGATCCTCCAGGAGACGTGCACCGACTCATCGGGCTCCCTCGTCGTCTACGCTCCGGTGGACGTGCAGTCGA
| ||| | || ||| | | || ||| ||| | | | |||||||| | | || | | | || || | ||| ||||| ||||||||||||| ||||||||| |||||||| ||||| || ||||||||||||||| | | | |
-------------------------------gtaagctttcttggagcttt--cgatcttcgatctctagaactgaagcttcttcctgtctctctttccagACTCTCAACTCGACGCACAGCAATATGCTCATCCTCCAGGAGAGCTGCACCGACGACTCGGGCTCGCTCGTAGTTTACGCTCCGGTGGACATCCCAGCCA
upper sequence: LOC_Os09g35760.2 (Oryza sativa), 3'ss of exon 8
lower sequence: EFJ10492 (Selaginella moellendorffii), 3'ss of exon 10
accaatatatgttcaaacccaccaagaaattcttgccttgaattaagttttgttcacttctcatatcttgaaaaaacaaatactaatgtctctcctgc-agGCCACAAGCGGGAACCAGAACAACATGCTGATCCTCCAGGAGACGTGCACCGACTCATCGGGCTCCCTCGTCGTCTACGCTCCGGTGGACGTGCAGTCGA
| ||| | || ||| | | || ||| ||| | | || | |||||||| | | || | | | || || | ||| ||||| ||||||||||||| ||||||||| |||||||| ||||| || ||||||||||||||| | | | |
-------------------------------gtaagctttcttggagcttt--cgatcttcgatctctagaactgaaacttattcctgtctctctttccagACTCTCAACTCGACGCACAGCAATATGCTCATCCTCCAGGAGAGCTGCACCGACGACTCGGGCTCGCTCGTAGTTTACGCTCCGGTGGACATCCCAGCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttttgttcacttctcatatcttgaaaaaacaaatactaatgtctctcctgcagGCCACAAGCGGGAACCAGAACAACATGCTGATCCTCCAGGAGACGTGCACCGACTCATCGGGCTCCCTCGTCGTCTACGCTCCGGTGGACGTGCAGTCGA
tactaat putative branch site (score: 1)
tgtctctcct CT-rich tract
aaaaaacaaatactaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
accaatatatgttcaaacccaccaagaaattcttgccttgaattaagttttgttcacttctcatatcttgaaaaaacaaatactaatgtctctcctgcagGCCACAAGCGGGAACCAGAACAACATGCTGATCCTCCAGGAGACGTGCACCGACTCATCGGGCTCCCTCGTCGTCTACGCTCCGGTGGACGTGCAGTCGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA