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mmu_circHdlbp_3212
Basic information of circular RNA
PanCircBase ID:
mmu_circHdlbp_3212
mm39_Chr. Position ID:
chr1|93340084|93366105|-
Gene name:
Hdlbp
Transcript:
ENSMUST00000170883.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
21
Exon/intron indexes:
24,23,22,21,20,19,18,17,16,15,14,13,12,11,10,9,8,7,6,5,4
Exon/intron offsets:
0,1128,1464,2449,4138,4809,5105,7706,8721,8980,10901,11407,12904,15195,15785,17015,17735,18592,18949,24731,25863
Genomic length:
26021
Exon/intron sizes in nt:
14,41,35,10,51,55,13,90,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,00,000
Flanking exon/introns:
chr1:93336858-93340084|chr1:93366105-93368401
Splice length:
3212
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
TTGCCACCTTAAATTCAGAAGAGGAAAATGACCCTCCAACCTACAAGGATGCCTTCCCTCCACTTCCTGAGAAAGCAGCTTGCTTGGAGAGTGCCCAAGAACCTGCCGGAGCCTGGAGTAACAAGATCCGGCCCATCAAGGCCTCTGTCATCACTCAGGTGTTTCATGTACCCCTGGAAGAGAGAAAATATAAGGACATGAACCAGTTTGGAGAGGGTGAACAAGCAAAAATCTGCCTTGAGATCATGCAGAGGACTGGTGCTCACCTGGAACTCTCTCTGGCTAAAGATCAAGGTCTCTCCATCATGGTCTCAGGGAAGCTGGATGCCGTCATGAAAGCCCGCAAAGACATTGTTGCTAGACTACAGACACAGGCCTCAGCAACTGTTCCCATTCCTAAAGAGCACCATCGCTTTGTTATTGGCAAAAACGGAGAGAAACTGCAAGACTTAGAACTAAAAACTGCAACCAAAATCCAGATCCCACGCCCAGATGACCCCAGTAATCAGATCAAGATCACTGGCACCAAAGAAGGCATCGAGAAAGCTCGCCATGAAGTCCTCCTAATCTCTGCTGAGCAGGACAAGCGTGCTGTAGAGAGGCTAGAAGTGGAGAAGGCTTTCCACCCCTTCATCGCTGGGCCGTACAACAGACTTGTGGGTGAAATCATGCAGGAGACAGGGACGCGAATCAACATCCCTCCACCCAGTGTTAACCGTACAGAAATCGTCTTCACTGGAGAGAAGGAGCAGCTGGCTCAGGCTGTGGCTCGCATTAAGAAGATTTATGAGGAAAAGAAGAAGAAGACTACAACCATTGCGGTAGAGGTGAAGAAGTCTCAGCACAAGTATGTTATTGGGCCAAAGGGCAATTCACTGCAAGAAATCCTGGAAAGAACTGGAGTTTCTGTTGAGATCCCACCCTCCGACAGCATCTCTGAGACTGTGATACTTAGAGGCGAACCTGAAAAGTTGGGACAGGCGTTGACTGAAGTCTATGCCAAGGCCAACAGTTTTACAGTCTCCTCAGTCTCTGCCCCTTCCTGGCTTCATCGTTTCATCATTGGTAAGAAAGGGCAGAACCTGGCCAAAATCACTCAGCAAATGCCAAAGGTTCACATTGAGTTCACAGAAGGTGAGGACAAGATCACCCTGGAGGGCCCCACAGAGGATGTGAATGTAGCCCAAGAACAGATTGAAGGAATGGTCAAAGACCTGATTAATAGGATGGACTATGTAGAGATCAACATTGACCATAAATTCCACAGACACCTCATTGGAAAGAGCGGAGCCAACATCAACAGAATCAAAGACCAGTACAAAGTGTCTGTGCGCATCCCCCCTGACAGTGAAAAGAGTAACCTGATCCGAATTGAGGGAGACCCACAGGGTGTTCAGCAGGCCAAGCGGGAGCTGCTGGAGCTTGCTTCTCGCATGGAAAATGAGCGCACCAAGGATCTAATCATCGAGCAAAGATTTCATCGCACAATCATTGGGCAGAAAGGTGAACGGATTCGAGAAATTCGTGACAAATTCCCAGAGGTTATCATCAACTTTCCAGACCCAGCACAAAAAAGTGATATTGTACAACTCAGAGGCCCCAAGAATGAGGTGGAGAAGTGCACTAAGTATATGCAGAAGATGGTCGCAGACCTGGTGGAAAATAGCTATTCAATTTCTGTACCAATCTTCAAACAGTTTCACAAGAATATCATCGGGAAAGGAGGCGCAAACATTAAAAAGATCCGTGAAGAGAGCAACACCAAGATTGACCTTCCTGCAGAGAACAGCAACTCTGAGACCATTATTATCACTGGCAAGCGAGCCAACTGTGAAGCTGCCCGCAGCCGGATTCTGTCTATCCAGAAAGATCTGGCCAACATAGCTGAAGTGGAGGTCTCAATTCCTGCCAAACTACACAACTCTCTCATTGGCACAAAGGGCCGTCTGATCCGCTCCATCATGGAGGAATGTGGTGGCGTCCATATTCACTTTCCTGTGGAAGGTTCTGGAAGCGACACTGTTGTCATCAGGGGTCCTTCCTCAGATGTAGAGAAGGCCAAGAAGCAGCTCCTGCACCTGGCTGAGGAGAAGCAAACCAAGAGTTTTACTGTGGACATCCGAGCCAAGCCAGAATACCACAAATTCCTCATTGGCAAAGGGGGAGGTAAAATCCGAAAGGTGCGTGACAGTACTGGAGCCCGCATCATATTTCCGGCTGCTGAAGATAAGGACCAGGACCTGATCACAATCATAGGAAAGGAGGATGCTGTCCGTGAGGCCCAAAAGGAGCTGGAAGCATTGATCCAGAACCTGGAGAATGTGGTTGAAGACTATATGCTGGTGGACCCCAAACACCACCGCCATTTTGTCATCCGAAGAGGACAAGTTTTACGAGAAATTGCTGAAGAGTATGGCGGGGTGATGGTCAGCTTCCCACGCTCTGGCACGCAGAGTGATAAAGTCACTCTCAAGGGTGCCAAGGACTGTGTGGAGGCAGCCAAGAAACGCATTCAGGAAATCATTGAGGATCTGGAAGCTCAAGTGACAGTGGAATGTGCTATACCCCAGAAGTTTCACCGATCGGTCATGGGTCCCAAAGGTTCAAGAATCCAGCAGATCACTCGGGACTACAATGTTCAAATCAAGTTCCCAGATAGAGAGGAAAATCCAGTTCACAGTGTAGAGCCTTCCATCCAGGAGAATGGAGATGAGGCTGGAGAGGGCAGAGAGGCCAAGGAGACCGACCCTGGCTCTCCCAGGAGGTGTGACATCATAATCATCTCTGGCCGGAAAGAGAAATGCGAGGCTGCCAAGGAAGCCCTGGAGGCACTGGTTCCAGTCACCATCGAGGTAGAGGTACCCTTTGATCTTCACCGCTACATCATTGGGCAAAAAGGAAGTGGAATCCGCAAGATGATGGATGAGTTTGAGGTGAACATCCATGTACCAGCCCCCGAGCTGCAGTCAGACACCATCGCCATCACTGGCCTTGCAGCAAATTTGGACAGGGCTAAGGCGGGGCTACTGGATCGAGTAAAGGAGCTGCAGGCTGAGCAGGAAGATCGGGCTTTAAGGAGTTTTAAGCTGAGTGTCACTGTAGACCCCAAATACCATCCCAAAATTATCGGGAGAAAAGGAGCAGTGATCACCCAGATCCGCTTGGAACATGAAGTGAACATCCAATTTCCTGATAAGGATGATGGGAACCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGGAGCAGTGATCACCCAGA
60.25
GGAAGTGGAGGGAAGGCATC
60.11
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGGGAGAAAAGGAGCAGTGA
59.68
GGAAGTGGAGGGAAGGCATC
60.11
152
PCR template sequence:
CCATCCCAAAATTATCGGGAGAAAAGGAGCAGTGATCACCCAGATCCGCTTGGAACATGAAGTGAACATCCAATTTCCTGATAAGGATGATGGGAACCAGTTGCCACCTTAAATTCAGAAGAGGAAAATGACCCTCCAACCTACAAGGATGCCTTCCCTCCACTTCCTGAGAAAGCAGCTTGCTTGGAGAGTGCCCAAGA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
22
Interacting miRNAs (#binding sites)
mmu-miR-139-5p(2), mmu-miR-207(2), mmu-miR-134-5p(1), mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-181a-5p(1), mmu-miR-221-3p(1), mmu-miR-125b-5p(1), mmu-miR-339-5p(1), mmu-miR-10a-5p(1), mmu-miR-181b-5p(1), mmu-miR-136-5p(1), mmu-miR-431-5p(1), mmu-miR-125a-5p(1), mmu-miR-383-5p(1), mmu-miR-1198-5p(1), mmu-miR-452-3p(1), mmu-miR-3470b(1), mmu-miR-670-5p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TGATGGGAACCAGTTGCCACCTTAAA
siRNA sets
TTAAGGTGGCAACTGGTTC, TAAGGTGGCAACTGGTTCC, TTTAAGGTGGCAACTGGTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCHDLBP_3212_ORF_1
1.2157
0.409804333
0.999999999
3027
ORF sequence:
ATGAACCAGTTTGGAGAGGGTGAACAAGCAAAAATCTGCCTTGAGATCATGCAGAGGACTGGTGCTCACCTGGAACTCTCTCTGGCTAAAGATCAAGGTCTCTCCATCATGGTCTCAGGGAAGCTGGATGCCGTCATGAAAGCCCGCAAAGACATTGTTGCTAGACTACAGACACAGGCCTCAGCAACTGTTCCCATTCCTAAAGAGCACCATCGCTTTGTTATTGGCAAAAACGGAGAGAAACTGCAAGACTTAGAACTAAAAACTGCAACCAAAATCCAGATCCCACGCCCAGATGACCCCAGTAATCAGATCAAGATCACTGGCACCAAAGAAGGCATCGAGAAAGCTCGCCATGAAGTCCTCCTAATCTCTGCTGAGCAGGACAAGCGTGCTGTAGAGAGGCTAGAAGTGGAGAAGGCTTTCCACCCCTTCATCGCTGGGCCGTACAACAGACTTGTGGGTGAAATCATGCAGGAGACAGGGACGCGAATCAACATCCCTCCACCCAGTGTTAACCGTACAGAAATCGTCTTCACTGGAGAGAAGGAGCAGCTGGCTCAGGCTGTGGCTCGCATTAAGAAGATTTATGAGGAAAAGAAGAAGAAGACTACAACCATTGCGGTAGAGGTGAAGAAGTCTCAGCACAAGTATGTTATTGGGCCAAAGGGCAATTCACTGCAAGAAATCCTGGAAAGAACTGGAGTTTCTGTTGAGATCCCACCCTCCGACAGCATCTCTGAGACTGTGATACTTAGAGGCGAACCTGAAAAGTTGGGACAGGCGTTGACTGAAGTCTATGCCAAGGCCAACAGTTTTACAGTCTCCTCAGTCTCTGCCCCTTCCTGGCTTCATCGTTTCATCATTGGTAAGAAAGGGCAGAACCTGGCCAAAATCACTCAGCAAATGCCAAAGGTTCACATTGAGTTCACAGAAGGTGAGGACAAGATCACCCTGGAGGGCCCCACAGAGGATGTGAATGTAGCCCAAGAACAGATTGAAGGAATGGTCAAAGACCTGATTAATAGGATGGACTATGTAGAGATCAACATTGACCATAAATTCCACAGACACCTCATTGGAAAGAGCGGAGCCAACATCAACAGAATCAAAGACCAGTACAAAGTGTCTGTGCGCATCCCCCCTGACAGTGAAAAGAGTAACCTGATCCGAATTGAGGGAGACCCACAGGGTGTTCAGCAGGCCAAGCGGGAGCTGCTGGAGCTTGCTTCTCGCATGGAAAATGAGCGCACCAAGGATCTAATCATCGAGCAAAGATTTCATCGCACAATCATTGGGCAGAAAGGTGAACGGATTCGAGAAATTCGTGACAAATTCCCAGAGGTTATCATCAACTTTCCAGACCCAGCACAAAAAAGTGATATTGTACAACTCAGAGGCCCCAAGAATGAGGTGGAGAAGTGCACTAAGTATATGCAGAAGATGGTCGCAGACCTGGTGGAAAATAGCTATTCAATTTCTGTACCAATCTTCAAACAGTTTCACAAGAATATCATCGGGAAAGGAGGCGCAAACATTAAAAAGATCCGTGAAGAGAGCAACACCAAGATTGACCTTCCTGCAGAGAACAGCAACTCTGAGACCATTATTATCACTGGCAAGCGAGCCAACTGTGAAGCTGCCCGCAGCCGGATTCTGTCTATCCAGAAAGATCTGGCCAACATAGCTGAAGTGGAGGTCTCAATTCCTGCCAAACTACACAACTCTCTCATTGGCACAAAGGGCCGTCTGATCCGCTCCATCATGGAGGAATGTGGTGGCGTCCATATTCACTTTCCTGTGGAAGGTTCTGGAAGCGACACTGTTGTCATCAGGGGTCCTTCCTCAGATGTAGAGAAGGCCAAGAAGCAGCTCCTGCACCTGGCTGAGGAGAAGCAAACCAAGAGTTTTACTGTGGACATCCGAGCCAAGCCAGAATACCACAAATTCCTCATTGGCAAAGGGGGAGGTAAAATCCGAAAGGTGCGTGACAGTACTGGAGCCCGCATCATATTTCCGGCTGCTGAAGATAAGGACCAGGACCTGATCACAATCATAGGAAAGGAGGATGCTGTCCGTGAGGCCCAAAAGGAGCTGGAAGCATTGATCCAGAACCTGGAGAATGTGGTTGAAGACTATATGCTGGTGGACCCCAAACACCACCGCCATTTTGTCATCCGAAGAGGACAAGTTTTACGAGAAATTGCTGAAGAGTATGGCGGGGTGATGGTCAGCTTCCCACGCTCTGGCACGCAGAGTGATAAAGTCACTCTCAAGGGTGCCAAGGACTGTGTGGAGGCAGCCAAGAAACGCATTCAGGAAATCATTGAGGATCTGGAAGCTCAAGTGACAGTGGAATGTGCTATACCCCAGAAGTTTCACCGATCGGTCATGGGTCCCAAAGGTTCAAGAATCCAGCAGATCACTCGGGACTACAATGTTCAAATCAAGTTCCCAGATAGAGAGGAAAATCCAGTTCACAGTGTAGAGCCTTCCATCCAGGAGAATGGAGATGAGGCTGGAGAGGGCAGAGAGGCCAAGGAGACCGACCCTGGCTCTCCCAGGAGGTGTGACATCATAATCATCTCTGGCCGGAAAGAGAAATGCGAGGCTGCCAAGGAAGCCCTGGAGGCACTGGTTCCAGTCACCATCGAGGTAGAGGTACCCTTTGATCTTCACCGCTACATCATTGGGCAAAAAGGAAGTGGAATCCGCAAGATGATGGATGAGTTTGAGGTGAACATCCATGTACCAGCCCCCGAGCTGCAGTCAGACACCATCGCCATCACTGGCCTTGCAGCAAATTTGGACAGGGCTAAGGCGGGGCTACTGGATCGAGTAAAGGAGCTGCAGGCTGAGCAGGAAGATCGGGCTTTAAGGAGTTTTAAGCTGAGTGTCACTGTAGACCCCAAATACCATCCCAAAATTATCGGGAGAAAAGGAGCAGTGATCACCCAGATCCGCTTGGAACATGAAGTGAACATCCAATTTCCTGATAAGGATGATGGGAACCAGTTGCCACCTTAA
Peptide sequence:
MNQFGEGEQAKICLEIMQRTGAHLELSLAKDQGLSIMVSGKLDAVMKARKDIVARLQTQASATVPIPKEHHRFVIGKNGEKLQDLELKTATKIQIPRPDDPSNQIKITGTKEGIEKARHEVLLISAEQDKRAVERLEVEKAFHPFIAGPYNRLVGEIMQETGTRINIPPPSVNRTEIVFTGEKEQLAQAVARIKKIYEEKKKKTTTIAVEVKKSQHKYVIGPKGNSLQEILERTGVSVEIPPSDSISETVILRGEPEKLGQALTEVYAKANSFTVSSVSAPSWLHRFIIGKKGQNLAKITQQMPKVHIEFTEGEDKITLEGPTEDVNVAQEQIEGMVKDLINRMDYVEINIDHKFHRHLIGKSGANINRIKDQYKVSVRIPPDSEKSNLIRIEGDPQGVQQAKRELLELASRMENERTKDLIIEQRFHRTIIGQKGERIREIRDKFPEVIINFPDPAQKSDIVQLRGPKNEVEKCTKYMQKMVADLVENSYSISVPIFKQFHKNIIGKGGANIKKIREESNTKIDLPAENSNSETIIITGKRANCEAARSRILSIQKDLANIAEVEVSIPAKLHNSLIGTKGRLIRSIMEECGGVHIHFPVEGSGSDTVVIRGPSSDVEKAKKQLLHLAEEKQTKSFTVDIRAKPEYHKFLIGKGGGKIRKVRDSTGARIIFPAAEDKDQDLITIIGKEDAVREAQKELEALIQNLENVVEDYMLVDPKHHRHFVIRRGQVLREIAEEYGGVMVSFPRSGTQSDKVTLKGAKDCVEAAKKRIQEIIEDLEAQVTVECAIPQKFHRSVMGPKGSRIQQITRDYNVQIKFPDREENPVHSVEPSIQENGDEAGEGREAKETDPGSPRRCDIIIISGRKEKCEAAKEALEALVPVTIEVEVPFDLHRYIIGQKGSGIRKMMDEFEVNIHVPAPELQSDTIAITGLAANLDRAKAGLLDRVKELQAEQEDRALRSFKLSVTVDPKYHPKIIGRKGAVITQIRLEHEVNIQFPDKDDGNQLPP
IRESfinder result
IRESfinder score
0.500770562
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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