RetrogeneDB ID:

retro_pabe_1957

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:2a:59213222..59213658(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CCDC12
Ensembl ID:ENSPPYG00000013924
Aliases:None
Description:coiled-coil domain containing 12 [Source:HGNC Symbol;Acc:28332]


Retrocopy-Parental alignment summary:






>retro_pabe_1957
AAAGAACAGCTGAAGGCCCTAGAGAAAACCAGGTACAGGGACAAGGAAAATGGGGAGCCAAAGACCAAGCAGCTCAGAGA
AAAGGAGGAGGAAAGCAAGAAGCTCAGGGAATTCAGGCTGCAGAACCATGTCCCAGAGGATGAGGACCTGAAAAGGAGGA
GGGTTTCCAGGCCAAACCAGTTGCAGTGGAGGAGAAGATGAAGGAGAAGCTGTAGGCCGCCAAGGCACAGCCTGTCACTG
AGGAGATGGACCTGGCCAACCTTGTACTCTAGAAGCCTGATTGGGACCTAAGAGAGATGTGGGCAAGAACCTGGAGAAAC
TAAACAAAATGACTCAGAGGGCCATTGCAGAGGTGATCCATGGGAGGCTAAAAGGCCCAAATGACAGCCTAGTCTCTACA
GTGGAAGCCACCACTGAACAAGAGGCCTGTGACAAC

ORF - retro_pabe_1957 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.47 %
Parental protein coverage: 72.77 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalKERLKALREKTGRKDKEDGEPKTKHLREEEEEGEKHRELRLRNYVPEDEDLKKRRVP-QAKPVAVEEKVK
KE.LKAL.EKT...DKE.GEPKTK.LRE.EEE..K.RE.RL.N.VPEDEDLK.RRV..QAKPVAVEEK.K
RetrocopyKEQLKAL-EKTRYRDKENGEPKTKQLREKEEESKKLREFRLQNHVPEDEDLKRRRVS<QAKPVAVEEKMK
ParentalEQLEAAKPEPVIEEVDLANLAPRKPDWDL-KRDVAKKLEKLKKRTQRAIAELIRERLKGQEDNLASAVDA
E.L.AAK..PV.EE.DLANL...KPDWDL.KRDV.K.LEKL.K.TQRAIAE.I..RLKG..D.L.S.V.A
RetrocopyEKL*AAKAQPVTEEMDLANLVL*KPDWDL<KRDVGKNLEKLNKMTQRAIAEVIHGRLKGPNDSLVSTVEA
ParentalATEQKACDS
.TEQ.ACD.
RetrocopyTTEQEACDN

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain_prefrontal_cortex 0 .00 RPM 21 .01 RPM
SRP007412_cerebellum 0 .00 RPM 16 .90 RPM
SRP007412_heart 0 .00 RPM 11 .83 RPM
SRP007412_kidney 0 .00 RPM 24 .56 RPM
SRP007412_liver 0 .00 RPM 12 .24 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1957 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1957 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1957 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2257
Pan troglodytes retro_ptro_1597
Macaca mulatta retro_mmul_1025

Parental genes homology:
Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000022803 retrocopies
Dipodomys ordii ENSDORG000000165671 retrocopy
Echinops telfairi ENSETEG000000000302 retrocopies
Homo sapiens ENSG000001607991 retrocopy
Macaca mulatta ENSMMUG000000198101 retrocopy
Mus musculus ENSMUSG000000196591 retrocopy
Nomascus leucogenys ENSNLEG000000062191 retrocopy
Ochotona princeps ENSOPRG000000050861 retrocopy
Pongo abelii ENSPPYG00000013924 2 retrocopies
retro_pabe_1957 , retro_pabe_2033,
Pan troglodytes ENSPTRG000000148621 retrocopy
Sarcophilus harrisii ENSSHAG000000032651 retrocopy



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