Sequence
atgc intronic sequence ATGC exonic sequencegtgagctcatgttctttctattctgttttgttttgctagtctacacattttgtaatttcttatctgaaacctagcaatgcccttgcagGTCTCCTATTTTCAGTTCTTATCACGGCGGTAATAACTGATGCCATTAAAGATGGGGTTGGTCGACCGCGTCCAGATTTCTTTTGGCGCTGTTTTCCTGA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g49820.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g49820.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G077187_T01 (Zea mays), 3'ss of exon 3
gtgagctcatgttctttctattctgttttgttttgctagtctacacattttgtaatttcttatctgaaacctagcaatgcccttgcagGTCTCCTATTTTCAGTTCTTATCACGGCGGTAATAACTGATGCCATTAAAGATGGGGTTGGTCGACCGCGTCCAGATTTCTTTTGGCGCTGTTTTCCTGA
| ||| |||||| | | || | | ||| | || || || | || || |||||| ||| | || ||| |||||||||||||||||||| ||||| || || || |||||||||| || || ||||| ||||| ||||| ||||| |||||||| ||||| || || |||||
----gtacattcactttctcgccagattcactattctactttatcaatatt---acttatt--ctgaaatctaact-tgtcctggcagGTCTCCTATTTTCAGTACTTATTACTGCTGTTTTAACTGATGCGATAAAGGATGGTGTTGGGCGACCACGTCCTGATTTCTTCTGGCGTTGCTTCCCTGA
upper sequence: LOC_Os01g49820.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G18450.2 (Glycine max), 3'ss of exon 3
gtgagctcatgttctttctattctgttttgttttgctagtctacacat---tttgtaatttcttatctgaaacctagc--aatgcccttgcagGTCTCCTATTTTCAGTTCTTATCACGGCGGTAATAACTGATGCCATTAAAGATGGGGTTGGTCGACCGCGTCCAGATTTCTTTTGGCGCTGTTTTCCTGA
|| | ||| ||| | || ||| | || | | || || |||| || | || | | | || ||||| | |||| || ||||||| || || || || ||||| ||||| ||||| || |||||||| ||||| || || || ||||||||||| ||||| ||||| |||||
gtacttttctgtcttttagaaact-tttcctaaccttattttgcatatcactttgctatagcctaacctatgtattgccaaatgcatattcagGCCTTTTATTTTCTGTACTCATTACTGCGGTGATAACGGATGCTATCAAAGATGGTGTTGGACGGCCACGCCCAGATTTCTTCTGGCGTTGTTTCCCTGA
upper sequence: LOC_Os01g49820.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G15080.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgagctcatgttctttctattctgttttgttttgctagt-ctacacattttgtaatttcttatctgaaacctagcaatgcccttgcagGTCTCCTATTTTCAGTTCTTATCACGGCGGTAATAACTGATGCCATTAAAGATGGGGTTGGTCGACCGCGTCCAGATTTCTTTTGGCGCTGTTTTCCTGA
|| | ||||| | ||| ||||| | || | | | || | | | |||| | | || || | | |||| || | || || || ||||| || | || ||||| ||||| || || || | ||||||||||| ||||| |||||||||||||| ||||| |||||
gtacctctttcttcttccaattgtgtttcatgtttcgaattctctgtagctcttgattt-tgaggtgtgttctcttgggtcttcttcagGGCTTTTGTTCTCTGTACTTATAACCGGTGTCATAACCGATGCTATAAAGGACGCTGTTGGTCGACCTCGTCCTGATTTCTTTTGGCGTTGTTTCCCTGA
upper sequence: LOC_Os01g49820.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv01s0011g04180.t01 (Vitis vinifera), 3'ss of exon 2
gtga-gctcatgttctttctattctgttttgtttt-gctagtctacacattttgtaatttcttatctga-aacctagcaatgcccttgcagGTCTCCTATTTTCAGTTCTTATCACGGCGGTAATAACTGATGCCATTAAAGATGGGGTTGGTCGACCGCGTCCAGATTTCTTTTGGCGCTGTTTTCCTGA
|| || | ||| ||| | |||| | | || | | |||| | || | | || ||| | ||| || ||||| || || || |||||||| || ||||||||||| |||||||||| ||||| ||||| |||||||| ||||||||||| ||||| ||| |
gtatcactttttcccttcctagatttctttgagtcaggtactgttgtttccttgtggtgcattgcttaatggattatgtgtgcatgtttagGCCTTCTATTCTCTGTACTGATCACGGCAGTTATAACTGATGCAATTAAAGATGCTGTTGGCCGACCTCGTCCAGACTTCTTTTGGCGTTGTTTCCCTAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgctagtctacacattttgtaatttcttatctgaaacctagcaatgcccttgcagGTCTCCTATTTTCAGTTCTTATCACGGCGGTAATAACTGATGCCATTAAAGATGGGGTTGGTCGACCGCGTCCAGATTTCTTTTGGCGCTGTTTTCCTGA
tgccctt CT-rich tract
attttgtaatttctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagctcatgttctttctattctgttttgttttgctagtctacacattttgtaatttcttatctgaaacctagcaatgcccttgcagGTCTCCTATTTTCAGTTCTTATCACGGCGGTAATAACTGATGCCATTAAAGATGGGGTTGGTCGACCGCGTCCAGATTTCTTTTGGCGCTGTTTTCCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT