RetrogeneDB ID:

retro_pabe_39

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:X:23076025..23077912(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPPYG00000020185
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:DDX43
Ensembl ID:ENSPPYG00000016774
Aliases:None
Description:DEAD (Asp-Glu-Ala-Asp) box polypeptide 43 [Source:HGNC Symbol;Acc:18677]


Retrocopy-Parental alignment summary:






>retro_pabe_39
ATGTCCCACCAGGCCCCAGAGTGGAAGAGGGCGGAGGCTAATCCAAGAGACCTTGGGGCCAGCCGGGATGCCAGGGGCAG
CAGAGGCAGTGGCTGGAGTGGCCTCTTCGGCCATCAGGGACCGAGAGCAGCAGGCTCCCGTGAACCACCACTCTGCTTTA
AAATAAAGAACAATATGGTTGGTGCGGTCATTGGTTACAGTGGATCAAAAATACAAGATCTACAACATTCGACAAACACT
AAAATACAGATCATAAAGGGGGAATCTGAAGCAAAAGTCAGAATTTTTGGCAATAGGGAAATGAAGGCAAAGGCCAAAGC
GGCTATAGAAGCACTTACTAGAAAACAAGAAAGCTACAACTCAGAATCCAGTGTGGATAATGCTGCATCCCAATCCCCTA
TTGGAAGAAATCTAGGCAGAAATGACATTGATGGAGAAGCTCAGCCATTGTCCAATTGGGATCGCATTGGGGCAGCAGTC
GTGGAGTGCGAAAAGAGAAAATGGGCAGATCTACCACCAGTTAAGAAAAACTTTTACATAGAATCCAAAGCAACAAGCTG
CATGTCTGAAATGCAGGTGATTAACTGGAGAAAGGAAAATTTCAACATCATGTGTGATGACTTGAAAAGTGGTGAAAAGC
GTCTCATCCCAAAACCAACTTGTAGGTTTAAAGACGCTTTTCAGCAATACCCTGATCTTCTGAAAAGCATAACAAGGGTA
GGGATTGTAAAGCCAACACCAATTCAGTCACAGGCATGGCCAATTATTCTACAAGGAATAGATCTTATAGAAGTTGCACA
AACCGGAACAGGGAAAACATTGTCCTATTTAATGCCTGGGTTTATTCATCTTGATTCTCAACCAATATCTAGAGAGCAAA
GGAATGGGCCTGGGATGCTAGTCCTTACACCCACTAGAGAGTTGGCTCTTCAGGTGGAAGCTCAATGTTCAAAGTATTCA
TATAAAGGTCTCAAAAGCATTTGCATATATGGTGGTAGAAACAGAATTGGACAAATAGAAGACATTAGCAAAGGTGTAGA
TATCATTATTGCAACTCCTGGGAGGCTGAATGACCTACAAATGAATAACTCTGTCAACCTAAGAAGCATAACCTACTTGG
TTATAGATGAGGCAGATAAAATGCTGGATATGGAATTTGAACCCCAGATAATGAAGATTTTATTAGATGTGCGCCCAGAC
CGACAGACTGTTATGACAAGTGCAACTTGGCCAGATACTGTACGTCAACTAGCACTTTCTTATTTGAAAGATCCTATGAT
TGTTTATGTTGGTAATCTGAATCTAGTTGCTGTAAATACAGTGAAGCAAAATATAATTGTTACCACAGAAAAAGAAAAAC
GAGCTCTCACCCAAGAGTTCGTAGAGAACATGTCACCCAACGACAAAGTCATCATGTTTGTCAGCCAAAAACATACTGCT
GATGACTTGTCAAGCGACTTCAATATCCAAGGCATATCTGTAGAATCATTACATGGCAACACTGAACACAGTGATCAAGA
GCGAGCATTAGAGGACTTTAAAAGTGGAAACATAAAGATACTGATTACAACTGATTTCGTACCCCGAGGTCTTGATCTTA
ATGATGTCACACATGTATATAATTACGATTTCCCAAGGAATATTGAAGTATATGTACACAGAGTAGGGTACATTGGACGG
GCAGGAAAGACTGGCACATCAGTTACCCTCATCACTCAGAGAGATTCGAAAATGGCCGGTGAATTGATTAAAATTCTGGA
CAGAGCAAATCAGAGTGTTCCGGAAGATCTTGTAGTAATAGCTGAGCAATACAAGTTAAATCAACAAAAGAGGGACACAG
AAACACGATCAAGAAAACCTGGACAAAGACGCAAGGAGTTTTATTTT

ORF - retro_pabe_39 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.29 %
Parental protein coverage: 92.9 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalRGGRWRGPSRPPEAVAAGHEEPPLCFALKTQFVGAVIGRGGSKIKNIQSTTNTTIQIIQEQPESLVKIFG
RG..W.G........AAG..EPPLCF..K...VGAVIG..GSKI...Q..TNT.IQII....E..V.IFG
RetrocopyRGSGWSGLFGHQGPRAAGSREPPLCFKIKNNMVGAVIGYSGSKIQDLQHSTNTKIQIIKGESEAKVRIFG
ParentalSKAMQMKAKAVIDNFVKKLEENYNSECEVDTAFQPSVGKDGSTDSNVVAGDRPLIDWDQIREEGLKWQKT
...M..KAKA.I.....K..E.YNSE..VD.A...S................PL..WD.I........K.
RetrocopyNREMKAKAKAAIEALTRK-QESYNSESSVDNAASQSPIGRNLGRNDIDGEAQPLSNWDRIGAAVVECEKR
ParentalKWADLPPIKKNFYKESTATSTMSKVQADSWRKENFNITWDDLKDGEKRPIPNPACTFDDAFQCYPEVMEN
KWADLPP.KKNFY.ES.ATS.MS..Q...WRKENFNI..DDLK.GEKR.IP.P.C.F.DAFQ.YP.....
RetrocopyKWADLPPVKKNFYIESKATSCMSEMQVINWRKENFNIMCDDLKSGEKRLIPKPTCRFKDAFQQYPDLLKS
ParentalIKKAGFQKPTPIQSQAWPIVLQGIDLIGVAQTGTGKTLCYLMPGFIHLDLQPSLKGQRNRPGMLVLTPTR
I...G..KPTPIQSQAWPI.LQGIDLI.VAQTGTGKTL.YLMPGFIHLD.QP....QRN.PGMLVLTPTR
RetrocopyITRVGIVKPTPIQSQAWPIILQGIDLIEVAQTGTGKTLSYLMPGFIHLDSQPISREQRNGPGMLVLTPTR
ParentalELALQVEGECCKYSYKGLRSVCVYGGGNRDEQIEELRKGVDIIIATPGRLNDLQMNNFVNLKNITYLVLD
ELALQVE..C.KYSYKGL.S.C.YGG.NR..QIE...KGVDIIIATPGRLNDLQMNN.VNL..ITYLV.D
RetrocopyELALQVEAQCSKYSYKGLKSICIYGGRNRIGQIEDISKGVDIIIATPGRLNDLQMNNSVNLRSITYLVID
ParentalEADKMLDMGFEPQIMKILLDVRPDRQTVMTSATWPHSVHRLAQSYLKEPMIVYVGTLDLVAVSSVKQNII
EADKMLDM.FEPQIMKILLDVRPDRQTVMTSATWP..V..LA.SYLK.PMIVYVG.L.LVAV..VKQNII
RetrocopyEADKMLDMEFEPQIMKILLDVRPDRQTVMTSATWPDTVRQLALSYLKDPMIVYVGNLNLVAVNTVKQNII
ParentalVTTEEEKWSHMQTFLQNMSSTDKVIVFVSRKAVADHLSSDLILGNISIESLHGDREQRDREKALENFKTG
VTTE.EK....Q.F..NMS..DKVI.FVS.K..AD.LSSD.....IS.ESLHG..E..D.E.ALE.FK.G
RetrocopyVTTEKEKRALTQEFVENMSPNDKVIMFVSQKHTADDLSSDFNIQGISVESLHGNTEHSDQERALEDFKSG
ParentalKVRILIATDLASRGLDVHDVTHVYNFDFPRNIEEYVHRIGRTGRAGRTGVSITTLTRNDWRVASELITIL
...ILI.TD...RGLD..DVTHVYN.DFPRNIE.YVHR.G..GRAG.TG.S.T..T..D...A.ELI.IL
RetrocopyNIKILITTDFVPRGLDLNDVTHVYNYDFPRNIEVYVHRVGYIGRAGKTGTSVTLITQRDSKMAGELIKIL
ParentalERANQSIPEELVSMAERFKAHQQKREMERKMERPQGRPKKFH
.RANQS.PE.LV..AE..K..QQKR..E.....P..R.K.F.
RetrocopyDRANQSVPEDLVVIAEQYKLNQQKRDTETRSRKPGQRRKEFY

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






RNA-Seq - click to see more details

(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 0 .00 RPM
SRP007412_cerebellum 0 .00 RPM 0 .00 RPM
SRP007412_heart 0 .00 RPM 0 .00 RPM
SRP007412_kidney 0 .00 RPM 0 .00 RPM
SRP007412_liver 0 .00 RPM 0 .03 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_39 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_39 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_39 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_76
Pan troglodytes retro_ptro_35
Parental genes homology:
Parental genes homology involve 17 parental genes, and 21 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000078511 retrocopy
retro_amel_31,
Callithrix jacchus ENSCJAG000000099662 retrocopies
retro_cjac_3639, retro_cjac_3640,
Equus caballus ENSECAG000000179711 retrocopy
retro_ecab_7,
Felis catus ENSFCAG000000316311 retrocopy
retro_fcat_583,
Homo sapiens ENSG000000800071 retrocopy
retro_hsap_76,
Gorilla gorilla ENSGGOG000000160921 retrocopy
retro_ggor_2889,
Microcebus murinus ENSMICG000000171451 retrocopy
retro_mmur_1603,
Monodelphis domestica ENSMODG000000185461 retrocopy
retro_mdom_14,
Mustela putorius furoENSMPUG000000043421 retrocopy
retro_mputfur_47,
Nomascus leucogenys ENSNLEG000000012091 retrocopy
retro_nleu_1094,
Oryctolagus cuniculus ENSOCUG000000063382 retrocopies
retro_ocun_1061, retro_ocun_227,
Otolemur garnettii ENSOGAG000000136601 retrocopy
retro_ogar_227,
Procavia capensis ENSPCAG000000059621 retrocopy
retro_pcap_151,
Pongo abelii ENSPPYG000000023891 retrocopy
retro_pabe_3816,
Pongo abelii ENSPPYG000000023903 retrocopies
retro_pabe_2007, retro_pabe_2369, retro_pabe_2418,
Pongo abelii ENSPPYG00000016774 1 retrocopy
retro_pabe_39 ,
Pan troglodytes ENSPTRG000000183441 retrocopy
retro_ptro_35,


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