Sequence
atgc intronic sequence ATGC exonic sequencegtagtacacactactagtttgcaaccgttttacgtaccagcgcattggcagcctgatcgctccaagaaaattctcagcttatttcgaagtgatcgattattgtgatttccatggtgtgaggagcagCAAGAAGAGCCAGCTGAAGAAGGTGGTGTACGAGGTGCCGGTGGCGGACGGCGGCGTCTCCTCCGACCTGTGGGCGTGGCGCAAGTACGGCCAAAAGCCC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g43550.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g43550.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G105140_T01 (Zea mays), 3'ss of exon 1
gtagtacacactactagtttgcaaccgttttacgtaccagcgcattggcagcctgatcgctccaagaaaattctcagcttatttcgaag-tgatcgattat---------tgtgatttccatggt-gtgagg-agcagCAAGAAGAGCCAGCTGAAGAAGGTGGTGTACGAGGTGCCGGTGGCGGACGGCGGC--GTC-TCCTCCGACCTGTGGGCGTGGCGCAAGTACGGCCAAAAGCCC
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-----gtaccgtaccggtcgtc--ccgtgcagcat---agaacggtagtagtagaaccagctgaagaaggtggtgcgatgatatgatggcttattgcttttctcttcttttttttcttccctggttgtggtatggcagCAAGAAGAGCCAGCTGAAGAAGGTGGTGCGGGAGATGCCGGCGGCCGACGGCGGCTCGTCGTCGTCGGACCCGTGGGCGTGGCGCAAGTATGGCCAAAAG---
upper sequence: LOC_Os01g43550.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G149683_T01 (Zea mays), 3'ss of exon 1
------------------------------------------------gtagtacacactacta-gtttgcaaccgttttacgtaccagcgcattggcagcctgatcgctccaagaaaattctcagcttatttcgaagtgatcgattattgtgatttccatggtgtgaggagcagCAAGAAGAGCCAGCTGAAGAAGGTGGTGTACGAGGTGCCGGTGGCGGACGGCGGC--GTCTCCTCCG-ACCTGTGGGCGTGGCGCAAGTACGGCCAAAAGCCC
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gtaccgtaaccgtagccgtaccgatgctgtgcgctcagctccatttatgcaagattcctttttttatttagacttgttttgcgcgc--gcgcatgatttggttaga-gaagaatgaagtgcgatggcttattgctttccgtttcctccctgcttgtcgtatgacatatga--cagCAAGAAGAGCCAGCTGAAGAAGGTGGTGCGCGAGATGCCGGTGGCCGACGGCAGCTCGTCGTCGCCGGACCCGTGGGCGTGGCGCAAGTATGGCCAAAAG--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctcagcttatttcgaagtgatcgattattgtgatttccatggtgtgaggagcagCAAGAAGAGCCAGCTGAAGAAGGTGGTGTACGAGGTGCCGGTGGCGGACGGCGGCGTCTCCTCCGACCTGTGGGCGTGGCGCAAGTACGGCCAAAAGCCC
attattgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagtacacactactagtttgcaaccgttttacgtaccagcgcattggcagcctgatcgctccaagaaaattctcagcttatttcgaagtgatcgattattgtgatttccatggtgtgaggagcagCAAGAAGAGCCAGCTGAAGAAGGTGGTGTACGAGGTGCCGGTGGCGGACGGCGGCGTCTCCTCCGACCTGTGGGCGTGGCGCAAGTACGGCCAAAAGCCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC