top of page

mmu_circAlcam_597

Basic information of circular RNA
PanCircBase ID:

mmu_circAlcam_597

mm39_Chr. Position ID:

chr16|52109280|52117347|-

Gene name:

Alcam

Transcript:

ENSMUST00000023312.14

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

5

Exon/intron indexes:

8,7,6,5,4

Exon/intron offsets:

0,1959,6106,6745,8002

Genomic length:

8067

Exon/intron sizes in nt:

133,128,183,88,65

Flanking exon/introns:

chr16:52097263-52109280|chr16:52117347-52125921

Splice length:

597

Other database IDs:

circAtlas: mmu-Alcam_0011

Human Ortholog IDs:
Mature spliced Sequence:

AGCAACCATCTAAACCTGAAATTGTAAACAAAGCACCCTTTCTTGAAACAGATCAGCTGAAAAAGTTAGGTGACTGCATTTCAAGAGACAGTTACCCAGATGGCAACATCACATGGTACAGGAATGGCAAAGTGCTGCAACCTGTGGAAGGAGAGGTGGCCATACTTTTTAAAAAGGAAATTGATCCAGGAACTCAGTTGTATACCGTGACTTCCTCCTTGGAGTACAAGACAACCAGATCTGACATACAAATGCCATTCACCTGTTCTGTGACATATTATGGACCCTCCGGCCAGAAAACAATTTATTCCGAACAAGAAATCTTTGATATTTACTATCCTACAGAGCAGGTGACAATACAAGTGCTGCCACCAAAAAATGCCATCAAAGAAGGGGACAACATCACCCTTCAGTGTTTGGGGAATGGCAACCCACCTCCTGAGGAGTTCATGTTTTACTTACCAGGACAGCCTGAAGGCATAAGAAGCTCAAACACTTACACACTGACAGATGTGAGACGCAATGCCACAGGGGACTACAAATGCTCACTCATTGACAAAAGGAACATGGCGGCTTCAACGACCATCACAGTTCACT

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

AGATGTGAGACGCAATGCCA

60.04

TGTCTCTTGAAATGCAGTCACC

58.86

179

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

AGATGTGAGACGCAATGCCA

60.04

TGTCTCTTGAAATGCAGTCACCT

60.18

179

PCR template sequence:

TACACACTGACAGATGTGAGACGCAATGCCACAGGGGACTACAAATGCTCACTCATTGACAAAAGGAACATGGCGGCTTCAACGACCATCACAGTTCACTAGCAACCATCTAAACCTGAAATTGTAAACAAAGCACCCTTTCTTGAAACAGATCAGCTGAAAAAGTTAGGTGACTGCATTTCAAGAGACAGTTACCCAGA

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

4

Interacting miRNAs (#binding sites)

mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-200c-3p(1), mmu-miR-574-5p(1)

siRNAs for circular RNA silencing
Junction sequence

ATCACAGTTCACTAGCAACCATCTAA

siRNA sets

TAGATGGTTGCTAGTGAAC, TTAGATGGTTGCTAGTGAA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCALCAM_597_ORF_1

0.639

0.164588029

0.289352323

348

ORF sequence:

ATGCCATTCACCTGTTCTGTGACATATTATGGACCCTCCGGCCAGAAAACAATTTATTCCGAACAAGAAATCTTTGATATTTACTATCCTACAGAGCAGGTGACAATACAAGTGCTGCCACCAAAAAATGCCATCAAAGAAGGGGACAACATCACCCTTCAGTGTTTGGGGAATGGCAACCCACCTCCTGAGGAGTTCATGTTTTACTTACCAGGACAGCCTGAAGGCATAAGAAGCTCAAACACTTACACACTGACAGATGTGAGACGCAATGCCACAGGGGACTACAAATGCTCACTCATTGACAAAAGGAACATGGCGGCTTCAACGACCATCACAGTTCACTAG

Peptide sequence:

MPFTCSVTYYGPSGQKTIYSEQEIFDIYYPTEQVTIQVLPPKNAIKEGDNITLQCLGNGNPPPEEFMFYLPGQPEGIRSSNTYTLTDVRRNATGDYKCSLIDKRNMAASTTITVH

IRESfinder result

IRESfinder score

0.549226661

IRES/non IRES

IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

logo.png

Institute of Life sciences, Bhubaneswar, India

bottom of page