Sequence
atgc intronic sequence ATGC exonic sequence...taaacgttttgttgaaacaaatacgagcatgtgcatattcttttcttttatcatatcctgcttatataccaatgtcagctgattatcgtcgttattgcagATGGGAGTGCCTACTGACAGAGAACAATATATTCATCGACTTGGTAGAACTGGCCGCAGAGGAAACGAGGGGAGTGGAATCTTATTATTGGCACCGTGGG
Basic information
species | Oryza sativa |
transcript | LOC_Os06g33520.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g33520.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G041732_T01 (Zea mays), 3'ss of exon 8
-taaacgttttg---ttgaaacaaatacgagcatgtgcatattcttttcttttatcatatc-ctgcttatataccaatgtcagctgattatcgtcgttattgcagATGGGAGTGCCTACTGACAGAGAACAATATATTCATCGACTTGGTAGAACTGGCCGCAGAGGAAACGAGGGGAGTGGAATCTTATTATTGGCACCGTGGG
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ctagatagttggaagtctgaatttatattt-tgcatacttatctttttgccttaacatatttctaattacaaaccggagt--attaact--catgattatcacagTTGGGGGTGCCAACTGACAGAGAGCAATATATTCATCGACTTGGTAGAACTGGTCGCAGAGGCAATGAGGGGACAGGAATCTTACTATTGGCACCATGGG
upper sequence: LOC_Os06g33520.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT5G08620.1 (Arabidopsis thaliana), 3'ss of exon 8
-taaacgttttgttgaaacaaatacgagcatgtgcatattcttttcttttatcatatcctgcttatataccaatgtcagctgattat-cgtcgttattgcagATGGGAGTGCCTACTGACAGAGAACAATATATTCATCGACTTGGTAGAACTGGCCGCAGAGGAAACGAGGGGAGTGGAATCTTATTATTGGCACCGTGGG
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gtaaatcatgtagtagttttcaatcatggaattgaacagtatctacaaagttgattgtttttttttaccgaagttgttgttgtgtgtatgttgcttttgcagATGGGATTGCCATCAGACAGGGAACAATATATACATAGACTTGGCAGAACTGGGCGGAAAGGTAAGGAAGGAGAAGGTGTACTATTGTTGGCACCGTGGG
upper sequence: LOC_Os06g33520.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv15s0046g01010.t01 (Vitis vinifera), 3'ss of exon 9
-taaacgttttgttgaaacaaatacgagcatgtgcatattcttttcttttatcatatcctgcttatataccaatgtcagctgat-tatcgtcgttattgcagATGGGAGTGCCTACTGACAGAGAACAATATATTCATCGACTTGGTAGAACTGGCCGCAGAGGAAACGAGGGGAGTGGAATCTTATTATTGGCACCGTGGG
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ttgaacttgctttatactgtggatttagtataaagatttgagaatatttcttcagacc--gctatgggcttgaacctagaaaatatatttctgtaatttcagGTCGGTTTGCCATCTGATAAAGAACAGTATATACATCGACTTGGTAGAACTGGGCGTAAGGGTAAAGAAGGGCAAGGCATATTGTTACTGGCACCTTGGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttatcatatcctgcttatataccaatgtcagctgattatcgtcgttattgcagATGGGAGTGCCTACTGACAGAGAACAATATATTCATCGACTTGGTAGAACTGGCCGCAGAGGAAACGAGGGGAGTGGAATCTTATTATTGGCACCGTGGG
agctgat putative branch site (score: 4)
ttatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taaacgttttgttgaaacaaatacgagcatgtgcatattcttttcttttatcatatcctgcttatataccaatgtcagctgattatcgtcgttattgcagATGGGAGTGCCTACTGACAGAGAACAATATATTCATCGACTTGGTAGAACTGGCCGCAGAGGAAACGAGGGGAGTGGAATCTTATTATTGGCACCGTGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - -tgttgaa
- - - - - - - - acaaata
- - - - - - - - - - - - - - - gtgcata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - cctgctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgatt