RetrogeneDB ID:

retro_ptro_1511

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:22:34598008..34599146(-)
Located in intron of:ENSPTRG00000014305
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:NDUFA9
Ensembl ID:ENSPTRG00000004557
Aliases:None
Description:Pan troglodytes NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 9, 39kDa (NDUFA9), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001079914]


Retrocopy-Parental alignment summary:






>retro_ptro_1511
ATGGCGGCCGCTGCACAATCCCGGGTTGTCTGGGCCCTGCCAATGTCACATTCTGCCATTACTGCAATAGCCACATCCAT
GTGTCACAGCCCACTCCATTGCCAGCTTCATCATGCCCTCATACCTCATGGGAAAGGTGGATGTTCCTCAAGTCAGTGGG
ATTGTGGCCACTGGGTTTGGAGCAACAGGATTCCTGGGCCGATGTGTTGTCAACCACCTTGGACGCGTGGGGTCACAGGT
GATCATACTCTATCGGTGTGATACATGTGACATCATGCACCTTCGTCCCATGGGAGACCTGGGCTAGCTTCTGTTTCTGG
AATGGGACGCGAGAGATAAAGATTCTATCCGACGAGTAGTGGAACACAGCAATGTGGTCATAAATCTTGTTGGATGAGAC
TGGGAAACCAAAAACTTTGATTTTGAGGATGTTTTTGTGAAGATTCCCCAAGCAATTGCTCAGGTGTCCAAGGAAGCTGA
AGTTGGAAAATTCATTCATGTTGCACATCTGAATGTGAATATTAAAAGCTCTTCTAGATATTTGAGAAAGAAGGCTGTTG
GAGAGAAAGCAGTGAGAGACACATTTCCAGAAGCCATTATCGTAAAGCTGTTGGACATCTTTGGAAGAGAGGATAGATTC
CTTAATTATTTTGAAAATATGTGTTGGTTTGGTGCTATACCCCTTGTTTCCTTGGGCTGGAAGGCAGTTAAACAACCAGT
GTATGTCGTAGATGTATCCAAAGGAATTGTTAATGCAGTTAAGGATCCTGATGCCAATGGGAAAACCTTTGCTTTCGTTG
GGCCAAATCGGTACCTCCTCTTTGACCTGGTGAAGTACATCTTTGCTGTGGCTCACAGCAAAGGGGTACTTCCTCCCGTA
CCCCTTGCCACCTTTTGCCTATCAGTGGGTAGCAAGAGACTTTGAAATAAGCCCACTTGAGTCCTGACAACAAGGGATAA
AGTGGAGCGTATTCACATCACAGACATGACCTTGTCTCACCTTCCCAGCTTAGAAGACCTTGGTATTCAGGCAACACCAC
TGGAACTCAAGGCCATTGAGGTGCTGCGGCTTCATCACACTTACTGCTGGCTGTCTGCTGAAATTGAGGATGTGAAGCCG
GCCAAGACCGTCAACATT

ORF - retro_ptro_1511 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.94 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMAAAAQSRVVRVLSMSRSAITAIATSVCHGPPCRQLHHALMPHGKGGRSS-VSGIVATVFGATGFLGRYV
MAAAAQSRVV..L.MS.SAITAIATS.CH.P...QLHHAL.PHGKGG.SS.VSGIVAT.FGATGFLGR.V
RetrocopyMAAAAQSRVVWALPMSHSAITAIATSMCHSPLHCQLHHALIPHGKGGCSS>VSGIVATGFGATGFLGRCV
ParentalVNHLGRMGSQVIIPYRCDKYDIMHLRPMGDLGQLLFLEWDARDKDSIRQVVQHSNVVINLIGRDWETKNY
VNHLGR.GSQVII.YRCD..DIMHLRPMGDLG.LLFLEWDARDKDSIR.VV.HSNVVINL.G.DWETKN.
RetrocopyVNHLGRVGSQVIILYRCDTCDIMHLRPMGDLG*LLFLEWDARDKDSIRRVVEHSNVVINLVG*DWETKNF
ParentalDFEDVFVKIPQAIAQLSKEAGVEKFIHVSHLNANIKSSSRYLRNKAVGEKVVRDAFPEAIIIKPSDIFGR
DFEDVFVKIPQAIAQ.SKEA.V.KFIHV.HLN.NIKSSSRYLR.KAVGEK.VRD.FPEAII.K..DIFGR
RetrocopyDFEDVFVKIPQAIAQVSKEAEVGKFIHVAHLNVNIKSSSRYLRKKAVGEKAVRDTFPEAIIVKLLDIFGR
ParentalEDRFLNSFASMHRFGPIPLGSLGWKTVKQPVYVVDVSKGIVNAVKDPDANGKSFAFVGPSRYLLFHLVKY
EDRFLN.F..M..FG.IPL.SLGWK.VKQPVYVVDVSKGIVNAVKDPDANGK.FAFVGP.RYLLF.LVKY
RetrocopyEDRFLNYFENMCWFGAIPLVSLGWKAVKQPVYVVDVSKGIVNAVKDPDANGKTFAFVGPNRYLLFDLVKY
ParentalIFAVAHR--LFLPFP-LPLFAYRWVARVFEISPFEP-WITRDKVERMHITDMKLPHLPGLEDLGIQATPL
IFAVAH......P.P.LP.FAY.WVAR.FEISP.E....TRDKVER.HITDM.L.HLP.LEDLGIQATPL
RetrocopyIFAVAHSKGVLPPVP>LPPFAYQWVARDFEISPLES<LTTRDKVERIHITDMTLSHLPSLEDLGIQATPL
ParentalELKAIEVLRRHRTYRWLSAEIEDVKPAKTVNI
ELKAIEVLR.H.TY.WLSAEIEDVKPAKTVNI
RetrocopyELKAIEVLRLHHTYCWLSAEIEDVKPAKTVNI

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 .55 RPM 51 .67 RPM
SRP007412_cerebellum 0 .07 RPM 41 .41 RPM
SRP007412_heart 0 .20 RPM 139 .49 RPM
SRP007412_kidney 0 .37 RPM 94 .38 RPM
SRP007412_liver 0 .20 RPM 50 .61 RPM
SRP007412_testis 0 .32 RPM 24 .34 RPM

ChIP-Seq - click to see more details

Pan troglodytes was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ptro_1511 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_1511 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1511 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2585
Gorilla gorilla retro_ggor_1618
Pongo abelii retro_pabe_1905
Macaca mulatta retro_mmul_648
Parental genes homology:
Parental genes homology involve 11 parental genes, and 11 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000095881 retrocopy
retro_acar_16,
Danio rerio ENSDARG000000707231 retrocopy
retro_drer_1,
Homo sapiens ENSG000001391801 retrocopy
retro_hsap_2585,
Gorilla gorilla ENSGGOG000000060761 retrocopy
retro_ggor_1618,
Macaca mulatta ENSMMUG000000208131 retrocopy
retro_mmul_648,
Monodelphis domestica ENSMODG000000182831 retrocopy
retro_mdom_209,
Nomascus leucogenys ENSNLEG000000032521 retrocopy
retro_nleu_1520,
Otolemur garnettii ENSOGAG000000052251 retrocopy
retro_ogar_2244,
Pongo abelii ENSPPYG000000041711 retrocopy
retro_pabe_1905,
Pan troglodytes ENSPTRG00000004557 1 retrocopy
retro_ptro_1511 ,
Ictidomys tridecemlineatus ENSSTOG000000065041 retrocopy
retro_itri_543,


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