Sequence
atgc intronic sequence ATGC exonic sequencegtacgccacgaatcccctcctcctcctcttgggccccgaatcggagctcggcgacatcgatttgattcgattgggagggatcgatgttgttcttgcagGAACCTGATGACGACGTCGGCGGACGAGGGGCAATTCCTGAACCTGCTGCTGAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGC
Basic information
species | Oryza sativa |
transcript | LOC_Os06g06980.3 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g06980.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G099363_T03 (Zea mays), 3'ss of exon 1
gtacgccacgaatcccctcctcctcctcttgggccccgaatcggagctcggcgacatc---gatttgattcgattggga---gggatcga---tgttgtt-cttgcagGAACCTGATGACGACGTCGGCGGACGAGGGGCAATTCCTGAACCTGCTGCTGAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGC
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gtatgtcccgctagcttttcgccctgtcgtacgtggtggattcgagtgtgtgggcctgctggacgtggacagaccgagatctgagaacgaacgtggcgtggcgtgcagGAACCTGATGACCACCTCCGCCGACGAGGGCCAGTTCCTCAACATGCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGC
upper sequence: LOC_Os06g06980.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G127948_T04 (Zea mays), 3'ss of exon 4
gtacgccacgaatcccctcctcctcctcttgggccccgaatcggagctcggcgacatcgatttgattcgattgggagggatcgatgttgttcttgcagGAACCTGATGACGACGTCGGCGGACGAGGGGCAATTCCTGAACCTGCTGCTGAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGC
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gtatgttccgctttcccgggccgatctctcgg-cggcgacctagctgctggacagatcga--------gatctgaaaaaatgg--------cgtgcagGAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGC
upper sequence: LOC_Os06g06980.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv03s0063g00140.t01 (Vitis vinifera), 3'ss of exon 2
gtacgccacgaatcccctcctcctcctcttgggccccgaatcggagctcggc-gacatcgatttgattcgattgggagggatcgatgttgttcttg--------cagGAACCTGATGACGACGTCGGCGGACGAGGGGCAATTCCTGAACCTGCTGCTGAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGC
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-----------gtgagcttttcttgattcggattctcaaatctttgaatacccgttgtctatttgatgcttgtttgtaacgttagtgttggtttgaaaacgaaacagGAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCTCAAGCTCATCAATGCCAAGAACACCATGGAGATAGGCGTCTACACTGGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gagctcggcgacatcgatttgattcgattgggagggatcgatgttgttcttgcagGAACCTGATGACGACGTCGGCGGACGAGGGGCAATTCCTGAACCTGCTGCTGAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGC
atttgat putative branch site (score: 5)
ttgttctt putative PPT
atttgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgccacgaatcccctcctcctcctcttgggccccgaatcggagctcggcgacatcgatttgattcgattgggagggatcgatgttgttcttgcagGAACCTGATGACGACGTCGGCGGACGAGGGGCAATTCCTGAACCTGCTGCTGAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC