Sequence
atgc intronic sequence ATGC exonic sequencegtacttcttcttttttccaagaaacaagaacatgaaatggcatttacacattttgtttgaataatgcacaaccagattactgtattttgtagGCGTAGCGTCTCTAATCTTCTTCGTAGTGGCTTCCGAGAAAGTTTGGACCAGCTGATACAATCGTACGTTCGAAGACAAGAAGAGCATGATGATCCTCTT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g01720.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g01720.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G028870_T01 (Zea mays), 3'ss of exon 3
gtacttcttcttttttcc--aagaaacaagaacatgaaatggcatttacacattt-tgtttgaataatgcacaaccagat-tactgta---ttttgtagGCGTAGCGTCTCTAATCTTCTTCGTAGTGGCTTCCGAGAAAGTTTGGACCAGCTGATACAATCGTACGTTCGAAGACAAGAAGAGCATGATGATCCTCTT
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gtatttttccttatgtatgtatgcagtatgtatgtatgtatgtattcatgtatgtatgtatagttcatttatatatatatatattttaaatttttgtagGCGAAGCGTGTCAAATCTTCTCAGCAGTGGCTTCCGGGAAAGTCTTGACCAGCTCATTCGGTCTTATGTCCAGAGGCAAGAACATGAGTGGAATTTGGAG
upper sequence: LOC_Os03g01720.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA10G34240.1 (Glycine max), 3'ss of exon 6
-------------gtacttcttcttttttccaagaaacaagaacatgaaatggcatttacacattttgtttgaataatgcacaaccagattactgtattttgtagGCGTAGCGTCTCTAATCTTCTTCGTAGTGGCTTCCGAGAAAGTTTGGACCAGCTGATACAATCGTACGTTCGAAGACAAGAAGAGCATGATGATCCTCTT-
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aaaatctaaatgagtatgccatttatacttcatttattggc----tttcatttcttctagccaccaagcctta-tgattgttatggatttttattcatgtttcagGAGAAGTGTTTCTAACCTTCTTCGTAGTGGTTTCCGTGAAAGTCTGGACCAACTAATACAGTCATATGTGGAAAGGCAAGGTC-GTGCACCAATTGACTGG
upper sequence: LOC_Os03g01720.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA20G33300.1 (Glycine max), 3'ss of exon 5
---------gtactt--cttcttttttccaagaaacaagaacatgaaatggcatttacacattttgtttgaataatgcacaaccagattactgtattttgtagGCGTAGCGTCTCTAATCTTCTTCGTAGTGGCTTCCGAGAAAGTTTGGACCAGCTGATACAATCGTACGTTCGAAGACAAGAAGAGCATGATGATCCTCTT-
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gtcgagattgtactgaacatggttgatacttcatttattggctttcatttcttcttgc-caccaagccttattattgtatgg--atttttattcatgtttcagGAGAAGTGTTTCTAACCTTCTTCGTAGTGGTTTCCGTGAAAGTCTGGACCAATTAATACAGTCATATGTGGAAAGGCAAGGTC-GTGCACCAATTGACTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggcatttacacattttgtttgaataatgcacaaccagattactgtattttgtagGCGTAGCGTCTCTAATCTTCTTCGTAGTGGCTTCCGAGAAAGTTTGGACCAGCTGATACAATCGTACGTTCGAAGACAAGAAGAGCATGATGATCCTCTT
attttgtttgaataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacttcttcttttttccaagaaacaagaacatgaaatggcatttacacattttgtttgaataatgcacaaccagattactgtattttgtagGCGTAGCGTCTCTAATCTTCTTCGTAGTGGCTTCCGAGAAAGTTTGGACCAGCTGATACAATCGTACGTTCGAAGACAAGAAGAGCATGATGATCCTCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA