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mmu_circJak1_722
Basic information of circular RNA
PanCircBase ID:
mmu_circJak1_722
mm39_Chr. Position ID:
chr4|101038976|101051060|-
Gene name:
Jak1
Transcript:
ENSMUST00000102781.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
6,5,4,3,2
Exon/intron offsets:
0,2557,7299,9695,12003
Genomic length:
12084
Exon/intron sizes in nt:
164,154,124,199,81
Flanking exon/introns:
chr4:101036991-101038976|chr4:101051060-101122238
Splice length:
722
Other database IDs:
CIRCpedia: MMU_CIRCpedia_226550, circAtlas: mmu-Jak1_0001
circBase: hsa_circ_0012876, circAtlas: hsa-JAK1_0001, CIRCpedia: HSA_CIRCpedia_115908
Human Ortholog IDs:
Mature spliced Sequence:
ATCAGCTCTGAATGGGCTTTGGAAGGTAAAGAAGAAAATCCAGTCTGCTTTCAGGGACACTGGACAACCGAATAAATGCAGTATCTAAATATAAAAGAGGACTGCAATGCCATGGCGTTCTGTGCTAAAATGAGGAGCTTCAAGAAGACTGAGGTGAAGCAGGTGGTCCCTGAGCCTGGAGTGGAGGTGACTTTCTATCTGTTGGACAGGGAGCCCCTCCGCCTGGGCAGCGGAGAGTATACAGCCGAGGAGCTGTGCATCAGGGCCGCCCAGGAGTGCAGTATCTCTCCTCTCTGTCACAACCTCTTCGCCCTGTACGATGAGAGCACCAAGCTCTGGTACGCTCCGAACCGAATCATCACTGTGGATGACAAAACGTCTCTCCGGCTCCACTACCGCATGAGGTTCTACTTTACCAACTGGCACGGAACCAATGACAACGAACAGTCTGTATGGCGACATTCTCCAAAGAAGCAGAAAAACGGCTATGAGAAGAAAAGGGTTCCAGAAGCAACCCCACTCCTTGATGCCAGTTCACTGGAGTATCTGTTTGCACAGGGACAGTATGATTTGATCAAATGCCTGGCTCCCATTCGGGACCCCAAGACGGAGCAAGACGGACATGATATTGAAAATGAGTGCCTGGGCATGGCGGTCCTGGCCATCTCCCACTATGCCATGATGAAGAAGATGCAGTTGCCGGAACTTCCCAAAGACATCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCCTGGCCATCTCCCACTAT
59.73
ATTCGGTTGTCCAGTGTCCC
59.96
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GTCCTGGCCATCTCCCACTA
60.69
ATTCGGTTGTCCAGTGTCCC
59.96
141
PCR template sequence:
ATGATATTGAAAATGAGTGCCTGGGCATGGCGGTCCTGGCCATCTCCCACTATGCCATGATGAAGAAGATGCAGTTGCCGGAACTTCCCAAAGACATCAGATCAGCTCTGAATGGGCTTTGGAAGGTAAAGAAGAAAATCCAGTCTGCTTTCAGGGACACTGGACAACCGAATAAATGCAGTATCTAAATATAAAAGAGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-19b-3p(1), mmu-miR-19a-3p(1), mmu-miR-185-5p(1), mmu-miR-339-5p(1), mmu-miR-431-5p(1), mmu-miR-705(1), mmu-miR-484(1), mmu-miR-670-5p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
CCAAAGACATCAGATCAGCTCTGAAT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCJAK1_722_ORF_1
1.0931
0.361510899
0.971749121
735
ORF sequence:
ATGCAGTATCTAAATATAAAAGAGGACTGCAATGCCATGGCGTTCTGTGCTAAAATGAGGAGCTTCAAGAAGACTGAGGTGAAGCAGGTGGTCCCTGAGCCTGGAGTGGAGGTGACTTTCTATCTGTTGGACAGGGAGCCCCTCCGCCTGGGCAGCGGAGAGTATACAGCCGAGGAGCTGTGCATCAGGGCCGCCCAGGAGTGCAGTATCTCTCCTCTCTGTCACAACCTCTTCGCCCTGTACGATGAGAGCACCAAGCTCTGGTACGCTCCGAACCGAATCATCACTGTGGATGACAAAACGTCTCTCCGGCTCCACTACCGCATGAGGTTCTACTTTACCAACTGGCACGGAACCAATGACAACGAACAGTCTGTATGGCGACATTCTCCAAAGAAGCAGAAAAACGGCTATGAGAAGAAAAGGGTTCCAGAAGCAACCCCACTCCTTGATGCCAGTTCACTGGAGTATCTGTTTGCACAGGGACAGTATGATTTGATCAAATGCCTGGCTCCCATTCGGGACCCCAAGACGGAGCAAGACGGACATGATATTGAAAATGAGTGCCTGGGCATGGCGGTCCTGGCCATCTCCCACTATGCCATGATGAAGAAGATGCAGTTGCCGGAACTTCCCAAAGACATCAGATCAGCTCTGAATGGGCTTTGGAAGGTAAAGAAGAAAATCCAGTCTGCTTTCAGGGACACTGGACAACCGAATAAATGCAGTATCTAA
Peptide sequence:
MQYLNIKEDCNAMAFCAKMRSFKKTEVKQVVPEPGVEVTFYLLDREPLRLGSGEYTAEELCIRAAQECSISPLCHNLFALYDESTKLWYAPNRIITVDDKTSLRLHYRMRFYFTNWHGTNDNEQSVWRHSPKKQKNGYEKKRVPEATPLLDASSLEYLFAQGQYDLIKCLAPIRDPKTEQDGHDIENECLGMAVLAISHYAMMKKMQLPELPKDIRSALNGLWKVKKKIQSAFRDTGQPNKCSI
IRESfinder result
IRESfinder score
0.330810581
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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