Sequence
atgc intronic sequence ATGC exonic sequencegtatggttcggcatatccatcatgttctccagtttgactaactttactactgtttttgggtagctgggaacgggtgctgtatagctgcagcagaagcagatcaattgttgatatatcttttttaactttgtgtaacagGAAGAAAAGGGGTGCAAGGTGCACAACCTGGTCCAGCACTTGATTGGATGCAACGAGTAAGAATAGCTGTTGATGCTGCCAAAGGACTTGAATATCTACA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g67340.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g67340.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G346132_T01 (Zea mays), 3'ss of exon 4
gtatggttcggcatatccatcatgttctccagtttg-actaactttactactgtttttgggtagctgggaacgggtgctgtatagctgcagcagaagcagatcaattgttgatatatcttttttaactttgtgt-aacagGAAGAAAAGGGGTGCAAGGTGCACAACCTGGTCCAGCACTTGATTGGATGCAACGAGTAAGAATAGCTGTTGATGCTGCCAAAGGACTTGAATATCTACA
| | |||| || || | | ||| | ||| | | || || ||| ||||||| | ||| | || || || ||||| | || ||| || |||||||||||| || |||||||| |||||||| | || |||||||||||||| ||||| ||| ||||||||||| || ||||||||||||||||| ||
-------------------------gtttgattttgcacatcctctgcaact--tgttgcacaaccccacactta-attgaata-ctgcagcttcaaatgataatttacaaat---tcgtttttgaattaatgtcaatagGAAGAAAAGGAGTTCAAGGTGCTCAACCTGGCCTGGCGCTTGATTGGATGCAGCGAGTGCAAATTGCTGTTGATGCGGCAAAAGGACTTGAATATCTTCA
upper sequence: LOC_Os01g67340.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA10G44210.1 (Glycine max), 3'ss of exon 5
gtatggttcggcatatccatcatgttctccagtttgactaactttactactgtttttgggtagctgggaacgggtgctgtatagctgcagcagaagcagatcaattgttgatatatcttttttaactttgtgtaacagGAAGAAAAGGGGTGCAAGGTGCACAACCTGGTCCAGCACTTGATTGGATGCAACGAGTAAGAATAGCTGTTGATGCTGCCAAAGGACTTGAATATCTACA
|| | | | | | | | |||| | || | | | ||| || || || || |||| ||||| ||||| || || |||||||| ||||| || ||| | ||||||||||| || ||||| ||||| || ||||||||||| ||| | |||||| ||||
---------------------------------------------------gtatgtagcttcttcttgtcctatctcgtat---ttcatatctattaagtt--ctgtcaatg-attttggttgtctttccactacagGTAGAAAGGGAGTTCAAGGTGCTCAACCAGGACCAACTCTTGATTGGATACAGCGAGTTAGAATTGCAGTTGATGCTGCTCGGGGATTGGAATATTTACA
upper sequence: LOC_Os01g67340.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA20G38980.1 (Glycine max), 3'ss of exon 5
gtatggttcggcatatccatcatgttctccagtttgactaactttactactgtttttgggtagctgggaacgggtgctgtatagctgcagcagaagcag-atcaattgttgatatatcttttttaactttgtgtaacagGAAGAAAAGGGGTGCAAGGTGCACAACCTGGTCCAGCACTTGATTGGATGCAACGAGTAAGAATAGCTGTTGATGCTGCCAAAGGACTTGAATATCTACA
||| | | || || || | | | | || | | || || || || || || |||| ||||| ||||| || || |||||||| |||||||| ||| | ||||||||||| || ||||| ||||| || |||||||| || | ||| | |||||| ||||
-----------------------------------------------------------gtatgtagcttcgtgtcctatcttg-tatttcatatctattatgttccgtcaatg-attttggttgtctttccactacagGTAGAAAGGGAGTTCAAGGTGCTCAACCTGGGCCAACTCTTGATTGGATACAGCGAGTTAGAATTGCAGTTGATGCAGCAAGGGGATTGGAATATTTACA
upper sequence: LOC_Os01g67340.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT2G43230.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatggttcggcatatccatcatgttctccagtttgactaactttactactgtttttgggtagctgggaacgggtgctgtatagctgcagcagaagcagatcaattgttgatatatcttttttaactttgtgt--aacagGAAGAAAAGGGGTGCAAGGTGCACAACCTGGTCCAGCACTTGATTGGATGCAACGAGTAAGAATAGCTGTTGATGCTGCCAAAGGACTTGAATATCTACA
| | | | | | | |||| | | || | ||| | || | ||||| || |||||| ||||| || |||||||| ||||||||||||||| ||||||| |||||||||||||| || | || |||||||| || |||||| | ||||| ||||
-------------------------------------------------------------------gtaagaaagatttctttctgctcaaacatcaatatggcttaggatggagattgataaacttgatgctaaacagGGAGAAAGGGAGTGCAAGGAGCACAACCTGGTCCAACACTTGAGTGGATGCAACGAGTCCGAGTTGCGGTTGATGCAGCTAAAGGATTAGAATACTTACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctgcagcagaagcagatcaattgttgatatatcttttttaactttgtgtaacagGAAGAAAAGGGGTGCAAGGTGCACAACCTGGTCCAGCACTTGATTGGATGCAACGAGTAAGAATAGCTGTTGATGCTGCCAAAGGACTTGAATATCTACA
ttttaac putative branch site (score: 2)
tcttttttaacttt CT-rich tract
aattgttgatatatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatggttcggcatatccatcatgttctccagtttgactaactttactactgtttttgggtagctgggaacgggtgctgtatagctgcagcagaagcagatcaattgttgatatatcttttttaactttgtgtaacagGAAGAAAAGGGGTGCAAGGTGCACAACCTGGTCCAGCACTTGATTGGATGCAACGAGTAAGAATAGCTGTTGATGCTGCCAAAGGACTTGAATATCTACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC