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mmu_circAftph_2414

Basic information of circular RNA
PanCircBase ID:

mmu_circAftph_2414

mm39_Chr. Position ID:

chr11|20653710|20677639|-

Gene name:

Aftph

Transcript:

ENSMUST00000035350.12

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

5

Exon/intron indexes:

6,5,4,3,2

Exon/intron offsets:

0,4970,5909,8453,21974

Genomic length:

23929

Exon/intron sizes in nt:

123,57,127,152,1955

Flanking exon/introns:

chr11:20648373-20653710|chr11:20677639-20691305

Splice length:

2414

Other database IDs:

circBase: mmu_circ_0000241, CIRCpedia: MMU_CIRCpedia_13031, circAtlas: mmu-Aftph_0013

circBase: hsa_circ_0054961, circAtlas: hsa-AFTPH_0018, CIRCpedia: HSA_CIRCpedia_42051

Human Ortholog IDs:
Mature spliced Sequence:

GCATAAACTAACTACTGGAAAGCTGCGGAATAATGGAGCCAGACATCATTCGAATGTACTCTTCCTCCCCCCCACCTCTAGACAACGGAGCAGAGGATGATGAGGAGGATGAGTTTGGGGAGTTTGGTGGGTTTTCGGAAGTCAGCCCTTCTGGTGTAGGGTTTGTTGATTTTGACACACCAGATTATACTCGTCCCAAGGAAGACTTTGTACCTTCAAACCACTTTATGCCAATTCATGAATATTCAGAAGATGTAGATAGCCTTACAAGCTTTAAGTCTGTTCAGAATGGTAATGATAAGGATATCACTGCTGAACTTTCTACTCCTGTGAAAAGTCAATCTGATGTTGTACTTTCTACCACCAGCAAAGAAATGATTCCATCTAAAACTTTGGATCCTTCCATCGATGGTATGGAAAGCCTGGAAGACTTAGATAAAGTAGTGGTGCAGGGACCAAGCACTGGGCAACTCAGAAGTTTCTCTCCTGGAGATTTTAGAACTGATAAGAACATTGTTCACCAAACCAAGCAGTTAGAGAGCTGCAACGGTGAAAAGCCTCCTTGTCTGGAAATTCTAACAAACGGGTTTGCAGGTTTGGAAACTGTAAATCCTCAGGGAACAGATGACCTGGACAATGTGGCAGATTCAAAGGGATCGAAGCCTCTTAACACTTGTGGCACCGAGTGCATTTTAGAGTCTGCAGCTAGTCATGCTACGGAATTTGCAGATTTTTCTACATTTTCCCAAACAGAAAGGACACAACTGGAAGAAATAGAATGTCCAGTTTTAAATGATGGTGATACACTGACCATTCAGGGAAACAGCAAAGGCCCCAGAGTCAAGGAACTAAACTGTGTGAAAGAAGTGACTTTGGATGGAAGCTTTGAGGATACGGGGAACACTGAAAGAGAACATCAGGTCTGCGTCTCAGAAATCCATGCCGTAGCTGACAGAGGGCTCAGTGTTGAAAAACAAGACCTTCAAACACTGCAACAGGATGAGTTTCTAAATTCAAGGATTCAGTCTGAGGCTTGGAGCTTGGTAGACTCAAGTGAAAATTCAGAAGCCATTACAAAGGAGCGGTGTAAAATGGAAAAAAATGACTTATTTGCCTCTAAGTGTGCTGACTTATCCATGGATTCTGTTAAAACTTCAGACGTTAATGAAATTGGTTCTTCCAAAGAAGAAAACAGAAAGCTGACTAATCCCAAAAGCCCAGACCCTGATCCCACAGGACAAAATGCTTTGGATGATTCTGCTGCAAGCATGAAAAATGGTGACAGTGGGAATGGCTTTGTGACTTGTCATGATACCAATGAGGATGATTTTGGTGACTTTGGTACAGCCAATGGCACCACTCCACCCTTTGTTACTAGTACTCAAGATTCAATGAGTGACGTCACTTTTGAAGACTCCTCAGAGCATTTTCTACATCTTAGTGAACCAGGTGATGATTTTGGAGAATTTGAGGATACAAATGCTGTTTCTTGTCAAGAGGAAATGAGATTTACTGAGTCAGACCTAAGACAGACTTCTGATGGCTTATCAGAGGAATGTCCATTGGCAGGAGAGTCTGGTGGAAAAGACAGTAAACCTGACTCAAAACTGAAAAATGGTCAAGACAGTGAATTTGGAGATTTTGATTCTGTGCCAAATACTCAAGGTAGTGCTTTTCAAGACTCGGATGATTTTGCAGACTTCAGTTCAGCAGGTCCTAGCCAAGCTGTAGATTGGAATGCTTTTGAGGATGAACAGAAAGATGGTTGTTCTTGGGCTGCCTTTGGGGATCAGCAGGAGACTGAGTCTCATCATCTAAAGGAAGTCTGGCAGTCACAGAGGACAGATGAAACTATGGGCACTCTGGGAACCCCTAAGATGCACAGTGTTTCTTCAGCAGCTTCCAAAGGAGCAGTTGCTAGTGGCCATTTGCAGGAACCAGGCACTTCAGTTCAGACAGCTTTACTCAACCGGTTGGAGAGAATTTTCGAAGCCTGTTTTCCGTCTGTGTTTGTCCCTGATGTGGAAGAGGAGGTTTCTTCCCTGAAGCACTTGCTGGAGACACACAGCTCGCCAGCAAAAACAAGAGAGGCCTTAGCTGACCGTGGTGAGTTGAGGGGTGTATGGACCGAACTGCAGGACATCCATGATGCACATGGTTTGCGGTACCAGTGGGGTGGCTCACATAGCAACAAGAAGCTTTTGTGCTCCTTGGGAATAGACACTCGAAACATTCTATTCACTGGCAATAAGAAGCAACCTGTTATAGTGCCCATGTATGCAGCAGGATTGGGAATGTTAGAGCCCACCAAGGAACCATTAAAACCACTATCTGCTGCAGAAAAAATTGCTTCTATTGGTCAGACAACCGTTATGACACCAGAAATAAACACGTGTACATCTGATCCATTCCAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

TCAGACAACCGTTATGACACCA

59.63

GCTCCGTTGTCTAGAGGTGG

59.83

146

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

TGGTCAGACAACCGTTATGACA

59.63

GCTCCGTTGTCTAGAGGTGG

59.83

149

PCR template sequence:

ACCATTAAAACCACTATCTGCTGCAGAAAAAATTGCTTCTATTGGTCAGACAACCGTTATGACACCAGAAATAAACACGTGTACATCTGATCCATTCCAGGCATAAACTAACTACTGGAAAGCTGCGGAATAATGGAGCCAGACATCATTCGAATGTACTCTTCCTCCCCCCCACCTCTAGACAACGGAGCAGAGGATGA

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

20

Interacting miRNAs (#binding sites)

mmu-miR-140-5p(2), mmu-miR-670-5p(2), mmu-miR-134-5p(1), mmu-miR-15a-5p(1), mmu-miR-93-5p(1), mmu-miR-135a-5p(1), mmu-miR-211-5p(1), mmu-miR-15b-5p(1), mmu-miR-326-3p(1), mmu-miR-138-5p(1), mmu-miR-185-5p(1), mmu-miR-149-5p(1), mmu-miR-136-5p(1), mmu-miR-351-5p(1), mmu-miR-370-3p(1), mmu-miR-362-5p(1), mmu-miR-224-5p(1), mmu-miR-129-5p(1), mmu-miR-335-3p(1), mmu-miR-350-3p(1)

siRNAs for circular RNA silencing
Junction sequence

TGATCCATTCCAGGCATAAACTAACT

siRNA sets

TAGTTTATGCCTGGAATGG, TTTATGCCTGGAATGGATC, AGTTTATGCCTGGAATGGA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCAFTPH_2414_ORF_1

1.094

0.115747072

0.999999434

2388

ORF sequence:

ATGGAGCCAGACATCATTCGAATGTACTCTTCCTCCCCCCCACCTCTAGACAACGGAGCAGAGGATGATGAGGAGGATGAGTTTGGGGAGTTTGGTGGGTTTTCGGAAGTCAGCCCTTCTGGTGTAGGGTTTGTTGATTTTGACACACCAGATTATACTCGTCCCAAGGAAGACTTTGTACCTTCAAACCACTTTATGCCAATTCATGAATATTCAGAAGATGTAGATAGCCTTACAAGCTTTAAGTCTGTTCAGAATGGTAATGATAAGGATATCACTGCTGAACTTTCTACTCCTGTGAAAAGTCAATCTGATGTTGTACTTTCTACCACCAGCAAAGAAATGATTCCATCTAAAACTTTGGATCCTTCCATCGATGGTATGGAAAGCCTGGAAGACTTAGATAAAGTAGTGGTGCAGGGACCAAGCACTGGGCAACTCAGAAGTTTCTCTCCTGGAGATTTTAGAACTGATAAGAACATTGTTCACCAAACCAAGCAGTTAGAGAGCTGCAACGGTGAAAAGCCTCCTTGTCTGGAAATTCTAACAAACGGGTTTGCAGGTTTGGAAACTGTAAATCCTCAGGGAACAGATGACCTGGACAATGTGGCAGATTCAAAGGGATCGAAGCCTCTTAACACTTGTGGCACCGAGTGCATTTTAGAGTCTGCAGCTAGTCATGCTACGGAATTTGCAGATTTTTCTACATTTTCCCAAACAGAAAGGACACAACTGGAAGAAATAGAATGTCCAGTTTTAAATGATGGTGATACACTGACCATTCAGGGAAACAGCAAAGGCCCCAGAGTCAAGGAACTAAACTGTGTGAAAGAAGTGACTTTGGATGGAAGCTTTGAGGATACGGGGAACACTGAAAGAGAACATCAGGTCTGCGTCTCAGAAATCCATGCCGTAGCTGACAGAGGGCTCAGTGTTGAAAAACAAGACCTTCAAACACTGCAACAGGATGAGTTTCTAAATTCAAGGATTCAGTCTGAGGCTTGGAGCTTGGTAGACTCAAGTGAAAATTCAGAAGCCATTACAAAGGAGCGGTGTAAAATGGAAAAAAATGACTTATTTGCCTCTAAGTGTGCTGACTTATCCATGGATTCTGTTAAAACTTCAGACGTTAATGAAATTGGTTCTTCCAAAGAAGAAAACAGAAAGCTGACTAATCCCAAAAGCCCAGACCCTGATCCCACAGGACAAAATGCTTTGGATGATTCTGCTGCAAGCATGAAAAATGGTGACAGTGGGAATGGCTTTGTGACTTGTCATGATACCAATGAGGATGATTTTGGTGACTTTGGTACAGCCAATGGCACCACTCCACCCTTTGTTACTAGTACTCAAGATTCAATGAGTGACGTCACTTTTGAAGACTCCTCAGAGCATTTTCTACATCTTAGTGAACCAGGTGATGATTTTGGAGAATTTGAGGATACAAATGCTGTTTCTTGTCAAGAGGAAATGAGATTTACTGAGTCAGACCTAAGACAGACTTCTGATGGCTTATCAGAGGAATGTCCATTGGCAGGAGAGTCTGGTGGAAAAGACAGTAAACCTGACTCAAAACTGAAAAATGGTCAAGACAGTGAATTTGGAGATTTTGATTCTGTGCCAAATACTCAAGGTAGTGCTTTTCAAGACTCGGATGATTTTGCAGACTTCAGTTCAGCAGGTCCTAGCCAAGCTGTAGATTGGAATGCTTTTGAGGATGAACAGAAAGATGGTTGTTCTTGGGCTGCCTTTGGGGATCAGCAGGAGACTGAGTCTCATCATCTAAAGGAAGTCTGGCAGTCACAGAGGACAGATGAAACTATGGGCACTCTGGGAACCCCTAAGATGCACAGTGTTTCTTCAGCAGCTTCCAAAGGAGCAGTTGCTAGTGGCCATTTGCAGGAACCAGGCACTTCAGTTCAGACAGCTTTACTCAACCGGTTGGAGAGAATTTTCGAAGCCTGTTTTCCGTCTGTGTTTGTCCCTGATGTGGAAGAGGAGGTTTCTTCCCTGAAGCACTTGCTGGAGACACACAGCTCGCCAGCAAAAACAAGAGAGGCCTTAGCTGACCGTGGTGAGTTGAGGGGTGTATGGACCGAACTGCAGGACATCCATGATGCACATGGTTTGCGGTACCAGTGGGGTGGCTCACATAGCAACAAGAAGCTTTTGTGCTCCTTGGGAATAGACACTCGAAACATTCTATTCACTGGCAATAAGAAGCAACCTGTTATAGTGCCCATGTATGCAGCAGGATTGGGAATGTTAGAGCCCACCAAGGAACCATTAAAACCACTATCTGCTGCAGAAAAAATTGCTTCTATTGGTCAGACAACCGTTATGACACCAGAAATAAACACGTGTACATCTGATCCATTCCAGGCATAA

Peptide sequence:

MEPDIIRMYSSSPPPLDNGAEDDEEDEFGEFGGFSEVSPSGVGFVDFDTPDYTRPKEDFVPSNHFMPIHEYSEDVDSLTSFKSVQNGNDKDITAELSTPVKSQSDVVLSTTSKEMIPSKTLDPSIDGMESLEDLDKVVVQGPSTGQLRSFSPGDFRTDKNIVHQTKQLESCNGEKPPCLEILTNGFAGLETVNPQGTDDLDNVADSKGSKPLNTCGTECILESAASHATEFADFSTFSQTERTQLEEIECPVLNDGDTLTIQGNSKGPRVKELNCVKEVTLDGSFEDTGNTEREHQVCVSEIHAVADRGLSVEKQDLQTLQQDEFLNSRIQSEAWSLVDSSENSEAITKERCKMEKNDLFASKCADLSMDSVKTSDVNEIGSSKEENRKLTNPKSPDPDPTGQNALDDSAASMKNGDSGNGFVTCHDTNEDDFGDFGTANGTTPPFVTSTQDSMSDVTFEDSSEHFLHLSEPGDDFGEFEDTNAVSCQEEMRFTESDLRQTSDGLSEECPLAGESGGKDSKPDSKLKNGQDSEFGDFDSVPNTQGSAFQDSDDFADFSSAGPSQAVDWNAFEDEQKDGCSWAAFGDQQETESHHLKEVWQSQRTDETMGTLGTPKMHSVSSAASKGAVASGHLQEPGTSVQTALLNRLERIFEACFPSVFVPDVEEEVSSLKHLLETHSSPAKTREALADRGELRGVWTELQDIHDAHGLRYQWGGSHSNKKLLCSLGIDTRNILFTGNKKQPVIVPMYAAGLGMLEPTKEPLKPLSAAEKIASIGQTTVMTPEINTCTSDPFQA

IRESfinder result

IRESfinder score

0.591287938

IRES/non IRES

IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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