Sequence
atgc intronic sequence ATGC exonic sequence...gttttatagcgtgaccttattgacgccgaacaactttcatcttgtgtgcttgttggtcttggatttttgtttcatgtggtgtgtgcaatgttggttgcagAGGGTATGTGGCAGCAGATGACCATGAGCGGCAGTGGCGCTATGCAACCTGGACCATATCCTGAGCGGTCCGGAGAACCGGACTGCACTTACTACCTCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g68860.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g68860.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G087032_T04 (Zea mays), 3'ss of exon 1
-gttttatagcgtgaccttattgacgccgaacaactttcatcttgtgtgcttgttggtcttggatttttgtttcatgtggtgtgtgcaatgttggttgcagAGGGTATGTGGCAGCAGATGACCATGAGCGGCAGTGGCGCTATGCAACCTGGACCATATCCTGAGCGGTCCGGAGAACCGGACTGCACTTACTACCTCAG
||| | | | || || |||| | | | | ||| || | | | | | || || |||||||||||| |||||||||| |||||||| || ||| ||||| | || ||| | ||||||||||||| ||||||||||||| | || ||||| |||||||||||||| |||||
aatttcacactgc-acattgttgatattagtttgttataaattatagtggtttataattaagtaaagtagtaagtaagtgtatgtgcaatgttgattgcagAGGGGATGTGGCAACAAATGGCCATGGACAGCGGTGCCACTATGCAACCTGGGTCATATCCTGAGCGACCAGGTGAACCCGACTGCACTTACTATCTCAG
upper sequence: LOC_Os01g68860.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G107491_T03 (Zea mays), 3'ss of exon 1
-gttttatagcgtgaccttattgacgcc--gaacaactttcatcttgtgtgcttgttggtcttggatttttgtttcatgtggtgtgtgcaatgttggttgcagAGGGTATGTGGCAGCAGATGACCATGAGCGGCAGTGGCGCTATGCAACCTGGACCATATCCTGAGCGGTCCGGAGAACCGGACTGCACTTACTACCTCAG
| | || | ||| || | | || | | || | | || | | |||| ||| | | | | |||||||| |||||||| |||||| |||||| | || ||| | | ||||||||||| ||||||||||||| | || ||||||||||||||||||||||||||
tggtgtaaaatgtggatagtttcatctctcaaagaggagagacctaaagggaaaatttcgcactg-cacatgttgattgttataactttataatcaa--gcagAGGGGATGTGGCAACAGATGGCCATGAACAGCGGTGCCACAATGCAACCTGGGTCATATCCTGAGCGACCAGGTGAACCGGACTGCACTTACTACCTCAG
upper sequence: LOC_Os01g68860.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G107491_T02 (Zea mays), 3'ss of exon 1
gttttatagcgtgaccttattgacgccgaacaactttcatcttgtgtgcttgttggtcttggatttttgtttcatgtggtgtgtgcaatgttggttgcagAGGGTATGTGGCAGCAGATGACCATGAGCGGCAGTGGCGCTATGCAACCTGGACCATATCCTGAGCGGTCCGGAGAACCGGACTGCACTTACTACCTCAG-----------------
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-------agtttcatctc-tcaaagaggagagacctaaa----gggaaaatttcgcactgcacatgttgattgttataac-tttataatcaag----cagaggggatgtggcaacagATGGCCATGAACAGCGGTGCCACAATGCAACCTGGGTCATATCCTGAGCGACCAGGTGAACCGGACTGCACTTACTACCTCAGGACTGGATTGTGTCGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgcttgttggtcttggatttttgtttcatgtggtgtgtgcaatgttggttgcagAGGGTATGTGGCAGCAGATGACCATGAGCGGCAGTGGCGCTATGCAACCTGGACCATATCCTGAGCGGTCCGGAGAACCGGACTGCACTTACTACCTCAG
atttttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttatagcgtgaccttattgacgccgaacaactttcatcttgtgtgcttgttggtcttggatttttgtttcatgtggtgtgtgcaatgttggttgcagAGGGTATGTGGCAGCAGATGACCATGAGCGGCAGTGGCGCTATGCAACCTGGACCATATCCTGAGCGGTCCGGAGAACCGGACTGCACTTACTACCTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA