Sequence
atgc intronic sequence ATGC exonic sequence...ccatttcaggctatactgttattatgtttgaatttgtctaattattgtattagctctgttacttcaatatgaatatattgctgtggcttgtattttgcagCTACTGGGAAAGCAGCCGAATTTGGTCAACTAAAAGATGGCTATATGTTTGACACGTCTACTGGCTTGTCGCGGAT
Basic information
species | Oryza sativa |
transcript | LOC_Os01g66730.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g66730.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G173989_T01 (Zea mays), 3'ss of exon 7
---ccatttcaggctat--actgttattatgtttgaatttgtctaattattgtattagctctgttacttcaatatgaatatattgctgtggcttgtattttgcagCTACTGGGAAAGCAGCCGAATTTGGTCAACTAAAAGATGGCTATATGTTTGACACGTCTACTGGCTTGTCGCGGAT
| | |||| | | | || || | || || ||| | || | | ||| |||| | ||| | | | | ||||| || | | |||||| ||||||||||||||| ||||||||||| || || |||||||| |||||||| ||||| || |||||| |||| || ||
cgaacctctcagcttgtggaatgatactcagtctgg-cctgttttcttttggcttta--tctggttgttc--ttttactgtattgatgctgttcctattttcaagCTACTGGGAAAGCTGCCGAATTTGGACAGCTCAAAGATGGTTATATGTTCGACACATCAACTGGCATGTCACGAAT
upper sequence: LOC_Os01g66730.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G802854_T01 (Zea mays), 3'ss of exon 7
--ccatttcaggctat--actgttattatgtttgaatttgtctaattattgtattagct--ctgttacttcaatatgaatatattgctgtggcttgtattttgcagCTACTGGGAAAGCAGCCGAATTTGGTCAACTAAAAGATGGCTATATGTTTGACACGTCTACTGGCTTGTCGCGGAT
| | |||| | | | || || | ||| || ||| | || | | || || |||| || | | | || |||||||| | |||||| ||||||||||||||| ||| ||||||| || || |||||||| |||||||| ||||| || |||||| |||| || ||
gaacctctcagcttgtcgaatgatactctgtctgg-cctgttttcttttggctttgtctgattgttcttttactgt--attgattgctgt---tcctattttcaagCTACTGGGAAAGCTGCCAAATTTGGACAGCTGAAAGATGGTTATATGTTCGACACATCAACTGGCATGTCACGAAT
upper sequence: LOC_Os01g66730.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G540589_T01 (Zea mays), 3'ss of exon 5
-------------------------------------------------------------------ccatttcaggctatactg--ttattatgtttgaatttgt-ctaattattgtattagctctgttacttcaatatgaatata---ttgctgtg-gcttgtattttgca-gCTACTGGGAAAGCAGCCGAATTTGGTCAACTAAAAGATGGCTATATGTTTGACACGTCTACTGGCTTGTCGCGGAT
|| || ||| | ||| | ||| | | || | ||| | | || || || ||| | | || | || | | |||||| || |||||||||||||| || ||||||||||| || |||||||| |||||||||||||| || |||||| |||| | ||
gtaattttttagcttgcagctcagtgtctactttccttaattttctatcagaagtatggaataccaaatgttctagcatatgtaacctcattgcttgtgagatgatactcagtatggatcgtttgtttttggttttatctgattgttctttttccgtatgttcctatttttcaagCTACTGGGAAAGCTGCTGAATTTGGTCAGCTGAAAGATGGTTATATGTTTGACACATCAACTGGCATGTCAAGAAT
upper sequence: LOC_Os01g66730.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA01G06540.1 (Glycine max), 3'ss of exon 8
-----------------------------------------ccatttcaggctatactgttattat----gtttgaatttgtctaatt-attgtattagctctgttacttcaatatgaatatattgctgtggcttgtattttgcagCTACTGGGAAAGCAGCCGAATTTGGTCAACTAAAAGATGGCTATATGTTTGACACGTCTACTGGCTTGTCGCGGAT
||| || | | | || || | |||| ||||||| | || ||| | || || || | | | || ||| | ||| | | ||| ||| | ||||||||| || ||||||||| ||||||||||||||||||||||| | || || || ||||
gtaggtgttttatcttttttgtttttctgtgcctcttaacttaattatagattttttttttgttgtttacgtttaaatttgtttgttttatttttgcagacctaaccctgcctttt----attttgttttggtgtttgttt---agCCAGTGGGAAAGCTGCAGAATTTGGTGCCCTAAAAGATGGCTATATGTTTGAGTGTACAACAGGTCAATCAAGGAT
upper sequence: LOC_Os01g66730.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA02G12480.1 (Glycine max), 3'ss of exon 7
--------------------------------------------ccatttcaggctatactgttattat-gtttgaatttgtctaattattgtattagctctgttacttcaatatgaatatattgctgtggcttgtattttgcagCTACTGGGAAAGCAGCCGAATTTGGTCAACTAAAAGATGGCTATATGTTTGACACGTCTACTGGCTTGTCGCGGAT
| | ||| |||| || || | | || | || | ||| | | ||| | || | | | ||| ||| | || | | ||| ||| | |||||||||||| ||||||||| ||||||||||||||||||||||| | || || | || ||||
gtaggtgtttgttctcgacctcattttaagttcttattttctgtgcctatcaa-ttataggttttttgttggttaagttaaatttatttctattttatttttgctgacttgactcttttattttgtttcggtgtttgttt---agCCAGTGGGAAAGCAGCAGAATTTGGTGCCCTAAAAGATGGCTATATGTTTGAGTGTACAACGGGTCTCTCAAGGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtattagctctgttacttcaatatgaatatattgctgtggcttgtattttgcagCTACTGGGAAAGCAGCCGAATTTGGTCAACTAAAAGATGGCTATATGTTTGACACGTCTACTGGCTTGTCGCGGAT
ttacttcaatatgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccatttcaggctatactgttattatgtttgaatttgtctaattattgtattagctctgttacttcaatatgaatatattgctgtggcttgtattttgcagCTACTGGGAAAGCAGCCGAATTTGGTCAACTAAAAGATGGCTATATGTTTGACACGTCTACTGGCTTGTCGCGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG