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mmu_circDnah9_1446
Basic information of circular RNA
PanCircBase ID:
mmu_circDnah9_1446
mm39_Chr. Position ID:
chr11|65838294|65872173|-
Gene name:
Dnah9
Transcript:
ENSMUST00000080665.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
49,48,47,46,45,44,43,42
Exon/intron offsets:
0,7348,7736,8172,18164,22497,28868,33717
Genomic length:
33879
Exon/intron sizes in nt:
2,61,23,41,62,14,31,24,00,00,00,000
Flanking exon/introns:
chr11:65818835-65838294|chr11:65872173-65880540
Splice length:
1446
Other database IDs:
circAtlas: mmu-Dnah9_0033
Human Ortholog IDs:
Mature spliced Sequence:
GGCATTCTTTTCTCCTCCGTGGAATGTGTAAAGTCCACACAGGACCTAGTGAAACTCTATCTGCACGAGTCAAGTCGGGTTTATCGGGATAAGATGGTGGAAGAAAAGGATTTCAATCTTTTTGACAAAATCCAAACAGAATTCCTCAAGAAAAATTTTGATGATAGTGAAGAGGTGCTGAAGCAGACCCAGAACCTGAACATGTATTGTCACTTTGCAAATGGCATTGGTGAGCCCAAGTACATGCCTGTGCAATCATGGGACCTTCTGAATCAGACTCTGGTGGAAGCCCTGGAGAGCCACAATGAAGTGAATGCTGTGATGGACCTAGTTCTCTTTGAGGATGCCATACGTCACATCTGTCACATCAACCGAATCCTGGAGTCCCCTCGAGGAAATGCCCTGCTAGTTGGTGTAGGTGGGAGTGGTAAGCAGAGTCTGACAAAGCTGGCAGCTTTTATCAGTTCCATGGATGTATTCCAGATCACCCTTCGCAAAGGCTACCAAATCCCTGACTTCAAGGTGGACCTGGCCAGCCTCTGTCTGAAAGCTGGGGTAAAAAATCTCAGTACAGTGTTCCTTATGACTGATGCCCATGTGGCTGACGAGAGGTTCCTGGTGCTCATCAATGACCTCCTGGCATCTGGTGAGATCCCAGATCTCTACTCTGATGAGGAAGAGGAGAACATCATAAACAATGTGAGAAATGAGGTCAAAAGCCAGGGACTCATGGACAGCAGGGAGAACTGCTGGAAATTCTTCATAGAGAGAGTCCAGCGACAACTTAAGGTGACTCTCTGTTTCTCCCCTGTGGGGAACAAGCTGAGAATTCGAAGCAGGAAGTTCCCAGCCATTGTGAACTGTACTGCTATCAACTGGTTCCATGAGTGGCCTCAGGAGGCCCTAGAGTCTGTGAGCCTCCGATTCTTGCAGAATACAAAGAACATTGAGCCTGCGGTGAAGCAGTCAATTAGCAAGTTCATGGCCTTTGTCCACATAAGTGTCAACAAGACATCCCAGTCATACCTGACCAATGAGCAGCGATACAACTACACAACACCCAAGTCCTTTCTGGAGTTCATCAGACTGTACCAGAGCTTGCTGGAGAGAAATGGAAAAGAGCTCCAGGCCAAGGTGGAGAGGCTGGAGAACGGGCTGTTGAAACTGCACAGCACCTCGGCCCAGGTGGATGATCTGAAAGCGAAGCTTGCCACCCAGGAAGTGGAGCTGAGGCACAAGAATGAAGATACAGACAAGCTGATTCAGGTGGTGGGTGTGGAGACCAGCAAAGTGAGCAGAGAGAAAGCCATTGCTGACGAGGAGGAGCAGAAGGTGGCCCTGATCATGCTGGAGGTGCAGCAGAAACAGAAAGACTGTGAAGAGGACCTGGCTAAGGCCGAGCCAGCCCTGACCGCAGCGCAGGCGGCCCTCAACACTCTCAACAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GACTGTGAAGAGGACCTGGC
60.04
CCGACTTGACTCGTGCAGAT
60.11
153
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGAGGTGCAGCAGAAACAGA
60.25
CCGACTTGACTCGTGCAGAT
60.11
175
PCR template sequence:
GCTGGAGGTGCAGCAGAAACAGAAAGACTGTGAAGAGGACCTGGCTAAGGCCGAGCCAGCCCTGACCGCAGCGCAGGCGGCCCTCAACACTCTCAACAAGGGCATTCTTTTCTCCTCCGTGGAATGTGTAAAGTCCACACAGGACCTAGTGAAACTCTATCTGCACGAGTCAAGTCGGGTTTATCGGGATAAGATGGTGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
21
Interacting miRNAs (#binding sites)
mmu-miR-1904(2), mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-103-3p(1), mmu-miR-135a-5p(1), mmu-miR-146a-5p(1), mmu-miR-23a-3p(1), mmu-miR-185-5p(1), mmu-miR-363-3p(1), mmu-miR-22-3p(1), mmu-miR-218-5p(1), mmu-miR-382-5p(1), mmu-miR-107-3p(1), mmu-miR-207(1), mmu-miR-673-5p(1), mmu-miR-335-3p(1), mmu-miR-484(1), mmu-miR-3105-3p(1), mmu-miR-146b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CACTCTCAACAAGGGCATTCTTTTCT
siRNA sets
AAAGAATGCCCTTGTTGAG, AAAAGAATGCCCTTGTTGA, AAGAATGCCCTTGTTGAGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCDNAH9_1446_ORF_1
1.256
0.418205476
0.999999994
2799
ORF sequence:
ATGGTGGAAGAAAAGGATTTCAATCTTTTTGACAAAATCCAAACAGAATTCCTCAAGAAAAATTTTGATGATAGTGAAGAGGTGCTGAAGCAGACCCAGAACCTGAACATGTATTGTCACTTTGCAAATGGCATTGGTGAGCCCAAGTACATGCCTGTGCAATCATGGGACCTTCTGAATCAGACTCTGGTGGAAGCCCTGGAGAGCCACAATGAAGTGAATGCTGTGATGGACCTAGTTCTCTTTGAGGATGCCATACGTCACATCTGTCACATCAACCGAATCCTGGAGTCCCCTCGAGGAAATGCCCTGCTAGTTGGTGTAGGTGGGAGTGGTAAGCAGAGTCTGACAAAGCTGGCAGCTTTTATCAGTTCCATGGATGTATTCCAGATCACCCTTCGCAAAGGCTACCAAATCCCTGACTTCAAGGTGGACCTGGCCAGCCTCTGTCTGAAAGCTGGGGTAAAAAATCTCAGTACAGTGTTCCTTATGACTGATGCCCATGTGGCTGACGAGAGGTTCCTGGTGCTCATCAATGACCTCCTGGCATCTGGTGAGATCCCAGATCTCTACTCTGATGAGGAAGAGGAGAACATCATAAACAATGTGAGAAATGAGGTCAAAAGCCAGGGACTCATGGACAGCAGGGAGAACTGCTGGAAATTCTTCATAGAGAGAGTCCAGCGACAACTTAAGGTGACTCTCTGTTTCTCCCCTGTGGGGAACAAGCTGAGAATTCGAAGCAGGAAGTTCCCAGCCATTGTGAACTGTACTGCTATCAACTGGTTCCATGAGTGGCCTCAGGAGGCCCTAGAGTCTGTGAGCCTCCGATTCTTGCAGAATACAAAGAACATTGAGCCTGCGGTGAAGCAGTCAATTAGCAAGTTCATGGCCTTTGTCCACATAAGTGTCAACAAGACATCCCAGTCATACCTGACCAATGAGCAGCGATACAACTACACAACACCCAAGTCCTTTCTGGAGTTCATCAGACTGTACCAGAGCTTGCTGGAGAGAAATGGAAAAGAGCTCCAGGCCAAGGTGGAGAGGCTGGAGAACGGGCTGTTGAAACTGCACAGCACCTCGGCCCAGGTGGATGATCTGAAAGCGAAGCTTGCCACCCAGGAAGTGGAGCTGAGGCACAAGAATGAAGATACAGACAAGCTGATTCAGGTGGTGGGTGTGGAGACCAGCAAAGTGAGCAGAGAGAAAGCCATTGCTGACGAGGAGGAGCAGAAGGTGGCCCTGATCATGCTGGAGGTGCAGCAGAAACAGAAAGACTGTGAAGAGGACCTGGCTAAGGCCGAGCCAGCCCTGACCGCAGCGCAGGCGGCCCTCAACACTCTCAACAAGGGCATTCTTTTCTCCTCCGTGGAATGTGTAAAGTCCACACAGGACCTAGTGAAACTCTATCTGCACGAGTCAAGTCGGGTTTATCGGGATAAGATGGTGGAAGAAAAGGATTTCAATCTTTTTGACAAAATCCAAACAGAATTCCTCAAGAAAAATTTTGATGATAGTGAAGAGGTGCTGAAGCAGACCCAGAACCTGAACATGTATTGTCACTTTGCAAATGGCATTGGTGAGCCCAAGTACATGCCTGTGCAATCATGGGACCTTCTGAATCAGACTCTGGTGGAAGCCCTGGAGAGCCACAATGAAGTGAATGCTGTGATGGACCTAGTTCTCTTTGAGGATGCCATACGTCACATCTGTCACATCAACCGAATCCTGGAGTCCCCTCGAGGAAATGCCCTGCTAGTTGGTGTAGGTGGGAGTGGTAAGCAGAGTCTGACAAAGCTGGCAGCTTTTATCAGTTCCATGGATGTATTCCAGATCACCCTTCGCAAAGGCTACCAAATCCCTGACTTCAAGGTGGACCTGGCCAGCCTCTGTCTGAAAGCTGGGGTAAAAAATCTCAGTACAGTGTTCCTTATGACTGATGCCCATGTGGCTGACGAGAGGTTCCTGGTGCTCATCAATGACCTCCTGGCATCTGGTGAGATCCCAGATCTCTACTCTGATGAGGAAGAGGAGAACATCATAAACAATGTGAGAAATGAGGTCAAAAGCCAGGGACTCATGGACAGCAGGGAGAACTGCTGGAAATTCTTCATAGAGAGAGTCCAGCGACAACTTAAGGTGACTCTCTGTTTCTCCCCTGTGGGGAACAAGCTGAGAATTCGAAGCAGGAAGTTCCCAGCCATTGTGAACTGTACTGCTATCAACTGGTTCCATGAGTGGCCTCAGGAGGCCCTAGAGTCTGTGAGCCTCCGATTCTTGCAGAATACAAAGAACATTGAGCCTGCGGTGAAGCAGTCAATTAGCAAGTTCATGGCCTTTGTCCACATAAGTGTCAACAAGACATCCCAGTCATACCTGACCAATGAGCAGCGATACAACTACACAACACCCAAGTCCTTTCTGGAGTTCATCAGACTGTACCAGAGCTTGCTGGAGAGAAATGGAAAAGAGCTCCAGGCCAAGGTGGAGAGGCTGGAGAACGGGCTGTTGAAACTGCACAGCACCTCGGCCCAGGTGGATGATCTGAAAGCGAAGCTTGCCACCCAGGAAGTGGAGCTGAGGCACAAGAATGAAGATACAGACAAGCTGATTCAGGTGGTGGGTGTGGAGACCAGCAAAGTGAGCAGAGAGAAAGCCATTGCTGACGAGGAGGAGCAGAAGGTGGCCCTGATCATGCTGGAGGTGCAGCAGAAACAGAAAGACTGTGAAGAGGACCTGGCTAAGGCCGAGCCAGCCCTGACCGCAGCGCAGGCGGCCCTCAACACTCTCAACAAG
Peptide sequence:
MVEEKDFNLFDKIQTEFLKKNFDDSEEVLKQTQNLNMYCHFANGIGEPKYMPVQSWDLLNQTLVEALESHNEVNAVMDLVLFEDAIRHICHINRILESPRGNALLVGVGGSGKQSLTKLAAFISSMDVFQITLRKGYQIPDFKVDLASLCLKAGVKNLSTVFLMTDAHVADERFLVLINDLLASGEIPDLYSDEEEENIINNVRNEVKSQGLMDSRENCWKFFIERVQRQLKVTLCFSPVGNKLRIRSRKFPAIVNCTAINWFHEWPQEALESVSLRFLQNTKNIEPAVKQSISKFMAFVHISVNKTSQSYLTNEQRYNYTTPKSFLEFIRLYQSLLERNGKELQAKVERLENGLLKLHSTSAQVDDLKAKLATQEVELRHKNEDTDKLIQVVGVETSKVSREKAIADEEEQKVALIMLEVQQKQKDCEEDLAKAEPALTAAQAALNTLNKGILFSSVECVKSTQDLVKLYLHESSRVYRDKMVEEKDFNLFDKIQTEFLKKNFDDSEEVLKQTQNLNMYCHFANGIGEPKYMPVQSWDLLNQTLVEALESHNEVNAVMDLVLFEDAIRHICHINRILESPRGNALLVGVGGSGKQSLTKLAAFISSMDVFQITLRKGYQIPDFKVDLASLCLKAGVKNLSTVFLMTDAHVADERFLVLINDLLASGEIPDLYSDEEEENIINNVRNEVKSQGLMDSRENCWKFFIERVQRQLKVTLCFSPVGNKLRIRSRKFPAIVNCTAINWFHEWPQEALESVSLRFLQNTKNIEPAVKQSISKFMAFVHISVNKTSQSYLTNEQRYNYTTPKSFLEFIRLYQSLLERNGKELQAKVERLENGLLKLHSTSAQVDDLKAKLATQEVELRHKNEDTDKLIQVVGVETSKVSREKAIADEEEQKVALIMLEVQQKQKDCEEDLAKAEPALTAAQAALNTLNK
IRESfinder result
IRESfinder score
0.456008442
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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