top of page

mmu_circAtrnl1_1488

Basic information of circular RNA
PanCircBase ID:

mmu_circAtrnl1_1488

mm39_Chr. Position ID:

chr19|57670802|57703155|+

Gene name:

Atrnl1

Transcript:

ENSMUST00000077282.7

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

9

Exon/intron indexes:

11,12,13,14,15,16,17,18,19

Exon/intron offsets:

0,3133,4288,9396,13803,17146,19617,24544,32215

Genomic length:

32353

Exon/intron sizes in nt:

8,52,09,11,91,33,18,22,00,00,00,00,000

Flanking exon/introns:

chr19:57661705-57670802|chr19:57703155-57719983

Splice length:

1488

Other database IDs:

circBase: mmu_circ_0007927, CIRCpedia: MMU_CIRCpedia_23909, circAtlas: mmu-Atrnl1_0021

circBase: hsa_circ_0092783, circAtlas: hsa-ATRNL1_0030, CIRCpedia: HSA_CIRCpedia_143530

Human Ortholog IDs:
Mature spliced Sequence:

CTTGTGACGAATGGAAGACATTGCCTAAACCAAATCTCCATAGAGATGTCAACCGATTTGGGCATTCTGCAGTCGTCATCAATGGGTCAATGTATATATTTGGTGGATTTTCTAGTGTACTCCTTAATGATATCCTTGTGTATAAACCCCCAAATTGCAAAGCTTTCCGAGATGAAGAACTGTGCAGAAACGCTGGTCCAGGGATAAAATGTGTTTGGAATAAGAATCACTGTGAATCTTGGGAGTCTGGGAATACAAATAATATTCTCAGAGCCAAGTGCCCTCCCAAGACAGCTGCTACCGATGACAGATGTTACAGATATGCTGACTGTGCCAGCTGCACAGCCAACACGAACGGGTGCCAGTGGTGTGACGACAAGAAATGCATCTCAGCCAGCAGCAACTGCAGCACGTCTGTCAGAAACTACACTAAATGTCATATAAGAAATGAGCAGATTTGTAACAAACTTACAAGCTGTAAAAGCTGTTCACTCAACTTGAATTGCCAGTGGGATCAGCGGCAGCAGGAATGTCAGGCTTTGCCAGCTCACCTTTGTGGAGAAGGCTGGAATCATGTTGGGGACGCTTGTCTTCGAATCAATTCCAGTCGAGAAAGCTATGATAATGCCAAACTTTATTGCTATAACCTCAGTGGAAATCTCGCCTCCCTGACCACGTCCAAGGAGGTGGAGTTTGTGTTGGATGAAATACAGAAGTTCACACAGCAGAAAGTGTCACCGTGGGTAGGCCTACGCAAGATCAACATATCCTACTGGGGATGGGAGGACATGTCTCCTTTCACAAATACAAGCCTGCAGTGGCTTCCTGGTGAGCCAAATGACTCTGGATTCTGTGCCTACTTAGAAAGGGCTGCAGTGGCAGGGTTAAAAGCAAACCCTTGCACATCCATGGCAGATGGACTCGTTTGTGAAAAGCCTGTAGTAAGCCCAAATCAGAACGCGAGGCCGTGCAAGAAGCCGTGCTCCCTGAGGACCTCCTGCGCCAACTGCACGAGCAGCGGCATGGAGTGCATGTGGTGCAGCAGCACGAAGCGCTGCGTGGACTCCAACGCTTACATCATCTCCTTTCCCTACGGACAGTGCCTGGAGTGGCAGACTGCCACCTGCTCGCCTCAAAATTGTTCTGGGTTAAGAACCTGTGGACAGTGCTTGGAGCAGCCTGGGTGTGGCTGGTGCAACGATCCTAGTAACACAGGAAGAGGCTATTGCATCGAAGGGTCTTCCCGGGGCCCAATGAAACTCGCGGGGGTCCACAACAGTGACGTGGTTCTTGACACCAGCCTCTGCCCCAAGGAGAAGAACTACGAGTGGTCTTTTATCCAGTGTCCAGCTTGCCAGTGTAATGGACACAGCACGTGCATCAACAACAACGTCTGTGAGCAGTGTAAGAATCTCACCACTGGGCGACAGTGTCAGGAATGCATGCCAGGGTACTATGGAGACCCAACCAACGGTGGGCAGTGCACAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

AAGAATCTCACCACTGGGCG

60.04

ACCCATTGATGACGACTGCA

59.68

169

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

AGTGTCAGGAATGCATGCCA

59.96

ACCCATTGATGACGACTGCA

59.68

147

PCR template sequence:

AACGTCTGTGAGCAGTGTAAGAATCTCACCACTGGGCGACAGTGTCAGGAATGCATGCCAGGGTACTATGGAGACCCAACCAACGGTGGGCAGTGCACAGCTTGTGACGAATGGAAGACATTGCCTAAACCAAATCTCCATAGAGATGTCAACCGATTTGGGCATTCTGCAGTCGTCATCAATGGGTCAATGTATATATT

Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs

12

Interacting miRNAs (#binding sites)

mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-7b-5p(1), mmu-miR-298-5p(1), mmu-miR-138-5p(1), mmu-miR-434-5p(1), mmu-miR-433-5p(1), mmu-miR-370-3p(1), mmu-miR-541-5p(1), mmu-miR-324-3p(1), mmu-miR-190b-5p(1), mmu-miR-129-5p(1)

siRNAs for circular RNA silencing
Junction sequence

GGGCAGTGCACAGCTTGTGACGAATG

siRNA sets

CATTCGTCACAAGCTGTGC,ATTCGTCACAAGCTGTGCA,TTCGTCACAAGCTGTGCAC

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCATRNL1_1488_ORF_1

0.8201

0.13160829

0.999999977

2886

ORF sequence:

ATGTATATATTTGGTGGATTTTCTAGTGTACTCCTTAATGATATCCTTGTGTATAAACCCCCAAATTGCAAAGCTTTCCGAGATGAAGAACTGTGCAGAAACGCTGGTCCAGGGATAAAATGTGTTTGGAATAAGAATCACTGTGAATCTTGGGAGTCTGGGAATACAAATAATATTCTCAGAGCCAAGTGCCCTCCCAAGACAGCTGCTACCGATGACAGATGTTACAGATATGCTGACTGTGCCAGCTGCACAGCCAACACGAACGGGTGCCAGTGGTGTGACGACAAGAAATGCATCTCAGCCAGCAGCAACTGCAGCACGTCTGTCAGAAACTACACTAAATGTCATATAAGAAATGAGCAGATTTGTAACAAACTTACAAGCTGTAAAAGCTGTTCACTCAACTTGAATTGCCAGTGGGATCAGCGGCAGCAGGAATGTCAGGCTTTGCCAGCTCACCTTTGTGGAGAAGGCTGGAATCATGTTGGGGACGCTTGTCTTCGAATCAATTCCAGTCGAGAAAGCTATGATAATGCCAAACTTTATTGCTATAACCTCAGTGGAAATCTCGCCTCCCTGACCACGTCCAAGGAGGTGGAGTTTGTGTTGGATGAAATACAGAAGTTCACACAGCAGAAAGTGTCACCGTGGGTAGGCCTACGCAAGATCAACATATCCTACTGGGGATGGGAGGACATGTCTCCTTTCACAAATACAAGCCTGCAGTGGCTTCCTGGTGAGCCAAATGACTCTGGATTCTGTGCCTACTTAGAAAGGGCTGCAGTGGCAGGGTTAAAAGCAAACCCTTGCACATCCATGGCAGATGGACTCGTTTGTGAAAAGCCTGTAGTAAGCCCAAATCAGAACGCGAGGCCGTGCAAGAAGCCGTGCTCCCTGAGGACCTCCTGCGCCAACTGCACGAGCAGCGGCATGGAGTGCATGTGGTGCAGCAGCACGAAGCGCTGCGTGGACTCCAACGCTTACATCATCTCCTTTCCCTACGGACAGTGCCTGGAGTGGCAGACTGCCACCTGCTCGCCTCAAAATTGTTCTGGGTTAAGAACCTGTGGACAGTGCTTGGAGCAGCCTGGGTGTGGCTGGTGCAACGATCCTAGTAACACAGGAAGAGGCTATTGCATCGAAGGGTCTTCCCGGGGCCCAATGAAACTCGCGGGGGTCCACAACAGTGACGTGGTTCTTGACACCAGCCTCTGCCCCAAGGAGAAGAACTACGAGTGGTCTTTTATCCAGTGTCCAGCTTGCCAGTGTAATGGACACAGCACGTGCATCAACAACAACGTCTGTGAGCAGTGTAAGAATCTCACCACTGGGCGACAGTGTCAGGAATGCATGCCAGGGTACTATGGAGACCCAACCAACGGTGGGCAGTGCACAGCTTGTGACGAATGGAAGACATTGCCTAAACCAAATCTCCATAGAGATGTCAACCGATTTGGGCATTCTGCAGTCGTCATCAATGGGTCAATGTATATATTTGGTGGATTTTCTAGTGTACTCCTTAATGATATCCTTGTGTATAAACCCCCAAATTGCAAAGCTTTCCGAGATGAAGAACTGTGCAGAAACGCTGGTCCAGGGATAAAATGTGTTTGGAATAAGAATCACTGTGAATCTTGGGAGTCTGGGAATACAAATAATATTCTCAGAGCCAAGTGCCCTCCCAAGACAGCTGCTACCGATGACAGATGTTACAGATATGCTGACTGTGCCAGCTGCACAGCCAACACGAACGGGTGCCAGTGGTGTGACGACAAGAAATGCATCTCAGCCAGCAGCAACTGCAGCACGTCTGTCAGAAACTACACTAAATGTCATATAAGAAATGAGCAGATTTGTAACAAACTTACAAGCTGTAAAAGCTGTTCACTCAACTTGAATTGCCAGTGGGATCAGCGGCAGCAGGAATGTCAGGCTTTGCCAGCTCACCTTTGTGGAGAAGGCTGGAATCATGTTGGGGACGCTTGTCTTCGAATCAATTCCAGTCGAGAAAGCTATGATAATGCCAAACTTTATTGCTATAACCTCAGTGGAAATCTCGCCTCCCTGACCACGTCCAAGGAGGTGGAGTTTGTGTTGGATGAAATACAGAAGTTCACACAGCAGAAAGTGTCACCGTGGGTAGGCCTACGCAAGATCAACATATCCTACTGGGGATGGGAGGACATGTCTCCTTTCACAAATACAAGCCTGCAGTGGCTTCCTGGTGAGCCAAATGACTCTGGATTCTGTGCCTACTTAGAAAGGGCTGCAGTGGCAGGGTTAAAAGCAAACCCTTGCACATCCATGGCAGATGGACTCGTTTGTGAAAAGCCTGTAGTAAGCCCAAATCAGAACGCGAGGCCGTGCAAGAAGCCGTGCTCCCTGAGGACCTCCTGCGCCAACTGCACGAGCAGCGGCATGGAGTGCATGTGGTGCAGCAGCACGAAGCGCTGCGTGGACTCCAACGCTTACATCATCTCCTTTCCCTACGGACAGTGCCTGGAGTGGCAGACTGCCACCTGCTCGCCTCAAAATTGTTCTGGGTTAAGAACCTGTGGACAGTGCTTGGAGCAGCCTGGGTGTGGCTGGTGCAACGATCCTAGTAACACAGGAAGAGGCTATTGCATCGAAGGGTCTTCCCGGGGCCCAATGAAACTCGCGGGGGTCCACAACAGTGACGTGGTTCTTGACACCAGCCTCTGCCCCAAGGAGAAGAACTACGAGTGGTCTTTTATCCAGTGTCCAGCTTGCCAGTGTAATGGACACAGCACGTGCATCAACAACAACGTCTGTGAGCAGTGTAAGAATCTCACCACTGGGCGACAGTGTCAGGAATGCATGCCAGGGTACTATGGAGACCCAACCAACGGTGGGCAGTGCACA

Peptide sequence:

MYIFGGFSSVLLNDILVYKPPNCKAFRDEELCRNAGPGIKCVWNKNHCESWESGNTNNILRAKCPPKTAATDDRCYRYADCASCTANTNGCQWCDDKKCISASSNCSTSVRNYTKCHIRNEQICNKLTSCKSCSLNLNCQWDQRQQECQALPAHLCGEGWNHVGDACLRINSSRESYDNAKLYCYNLSGNLASLTTSKEVEFVLDEIQKFTQQKVSPWVGLRKINISYWGWEDMSPFTNTSLQWLPGEPNDSGFCAYLERAAVAGLKANPCTSMADGLVCEKPVVSPNQNARPCKKPCSLRTSCANCTSSGMECMWCSSTKRCVDSNAYIISFPYGQCLEWQTATCSPQNCSGLRTCGQCLEQPGCGWCNDPSNTGRGYCIEGSSRGPMKLAGVHNSDVVLDTSLCPKEKNYEWSFIQCPACQCNGHSTCINNNVCEQCKNLTTGRQCQECMPGYYGDPTNGGQCTACDEWKTLPKPNLHRDVNRFGHSAVVINGSMYIFGGFSSVLLNDILVYKPPNCKAFRDEELCRNAGPGIKCVWNKNHCESWESGNTNNILRAKCPPKTAATDDRCYRYADCASCTANTNGCQWCDDKKCISASSNCSTSVRNYTKCHIRNEQICNKLTSCKSCSLNLNCQWDQRQQECQALPAHLCGEGWNHVGDACLRINSSRESYDNAKLYCYNLSGNLASLTTSKEVEFVLDEIQKFTQQKVSPWVGLRKINISYWGWEDMSPFTNTSLQWLPGEPNDSGFCAYLERAAVAGLKANPCTSMADGLVCEKPVVSPNQNARPCKKPCSLRTSCANCTSSGMECMWCSSTKRCVDSNAYIISFPYGQCLEWQTATCSPQNCSGLRTCGQCLEQPGCGWCNDPSNTGRGYCIEGSSRGPMKLAGVHNSDVVLDTSLCPKEKNYEWSFIQCPACQCNGHSTCINNNVCEQCKNLTTGRQCQECMPGYYGDPTNGGQCT

IRESfinder result

IRESfinder score

0.448303707

IRES/non IRES

non-IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

bottom of page