RetrogeneDB ID:

retro_ptro_79

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:4:98237040..98238207(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPTRG00000016297
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:PDHA1
Ensembl ID:ENSPTRG00000021717
Aliases:None
Description:Pan troglodytes pyruvate dehydrogenase (lipoamide) alpha 1 (PDHA1), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001110813]


Retrocopy-Parental alignment summary:






>retro_ptro_79
ATGCTGGCCGCCTTCATCTCCCGCGTGTTGAGGCGCGTTGCCCAGAAATCAGCTCGCAGAGTGCTGGTGGCATCCCGTAA
GTCCTCAAATGACGCTACATTTGAAATTAAGAAATGTGATCTTTATCTGTTGGAAGAGGGTCCCCCTGTCACTACAGTGC
TCACTAGGGCGGAGGGGCTTAAATACTACAGGATGATGCTGACTGTTCGCCGCATGGAATTGAAGGCAGATCAGCTGTAC
AAACAGAAATTCATTCGCGGTTTCTGTCACCTGTGCGATGGTCAGGAAGCTTGTTGCGTGGGCCTTGAGGCCGGCATAAA
CCCCTCGGATCACGTCATTACATCCTATAGGGCTCATGGTGTGTGCTATACTCGGGGACTTTCTGTCCGATCCATTCTCG
CAGAGCTGACGGGAAGAAGAGGAGGTTGTGCTAAAGGAAAAGGAGGATCGATGCATATGTATACCAAGAACTTCTATGGG
GGCAATGGCATCGTCGGTGCACAGGGCCCCCTGGGCGCTGGCATTGCTCTGGCCTGTAAATATAAAGGAAACGATGAGAT
CTGTTTGACTTTATATGGGGATGGCGCTGCGAATCAGGGGCAGATAGCCGAAGCTTTCAATATGGCAGCTTTATGGAAAT
TACCTTGTGTTTTCATCTGTGAGAATAACCTATATGGAATGGGAACATCTACTGAGAGAGCAGCAGCCAGCCCTGATTAC
TACAAGAGGGGCAATTTTATCCCTGGGCTAAAGGTCGATGGAATGGATGTTCTGTGTGTTCGTGAGGCAACAAAATTTGC
AGCTAACTACTGTAGATCTGGAAAGGGGCCCATACTGATGGAGCTGCAAACCTACCGTTATCATGGACACAGTATGAGTG
ATCCTGGAGTCAGTTATCGTACACGAGAAGAAATTCAGGAAGTAAGAAGTAAGAGGGATCCTATAATAATTCTCCAAGAT
AGAATGGTAAACAGCAAGCTCGCCACTGTGGAAGAATTAAAGGAAATTGGGGCTGAGGTGAGGAAAGAAATTGATGATGC
TGCCCAGTTTGCTACCACTGATCCTGAGCCACATTTGGAAGAATTAGGCCATCACATCTACAGCAGTGATTCATCTTTTG
AAGTTCGTGGTGCAAATCCATGGATCAAGTTTAAGTCCGTCAGTTAA

ORF - retro_ptro_79 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.57 %
Parental protein coverage: 99.23 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMLAA-VSRVLSGASQKPASRVLVASRNFANDATFEIKKCDLHRLEEGPPVTTVLTREDGLKYYRMMQTVR
MLAA..SRVL....QK.A.RVLVASR...NDATFEIKKCDL..LEEGPPVTTVLTR..GLKYYRMM.TVR
RetrocopyMLAAFISRVLRRVAQKSARRVLVASRKSSNDATFEIKKCDLYLLEEGPPVTTVLTRAEGLKYYRMMLTVR
ParentalRMELKADQLYKQKIIRGFCHLCDGQEACCVGLEAGINPTDHLITAYRAHGFTFTRGLSVREILAELTGRK
RMELKADQLYKQK.IRGFCHLCDGQEACCVGLEAGINP.DH.IT.YRAHG...TRGLSVR.ILAELTGR.
RetrocopyRMELKADQLYKQKFIRGFCHLCDGQEACCVGLEAGINPSDHVITSYRAHGVCYTRGLSVRSILAELTGRR
ParentalGGCAKGKGGSMHMYAKNFYGGNGIVGAQVPLGAGIALACKYNGKDEVCLTLYGDGAANQGQIFEAYNMAA
GGCAKGKGGSMHMY.KNFYGGNGIVGAQ.PLGAGIALACKY.G.DE.CLTLYGDGAANQGQI.EA.NMAA
RetrocopyGGCAKGKGGSMHMYTKNFYGGNGIVGAQGPLGAGIALACKYKGNDEICLTLYGDGAANQGQIAEAFNMAA
ParentalLWKLPCIFICENNRYGMGTSVERAAASTDYYKRGDFIPGLRVDGMDILCVREATRFAAAYCRSGKGPILM
LWKLPC.FICENN.YGMGTS.ERAAAS.DYYKRG.FIPGL.VDGMD.LCVREAT.FAA.YCRSGKGPILM
RetrocopyLWKLPCVFICENNLYGMGTSTERAAASPDYYKRGNFIPGLKVDGMDVLCVREATKFAANYCRSGKGPILM
ParentalELQTYRYHGHSMSDPGVSYRTREEIQEVRSKSDPIMLLKDRMVNSNLASVEELKEIDVEVRKEIEDAAQF
ELQTYRYHGHSMSDPGVSYRTREEIQEVRSK.DPI..L.DRMVNS.LA.VEELKEI..EVRKEI.DAAQF
RetrocopyELQTYRYHGHSMSDPGVSYRTREEIQEVRSKRDPIIILQDRMVNSKLATVEELKEIGAEVRKEIDDAAQF
ParentalATADPEPPLEELGYHIYSSDPPFEVRGANQWIKFKSVS
AT.DPEP.LEELG.HIYSSD..FEVRGAN.WIKFKSVS
RetrocopyATTDPEPHLEELGHHIYSSDSSFEVRGANPWIKFKSVS

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 34 .71 RPM
SRP007412_cerebellum 0 .04 RPM 32 .01 RPM
SRP007412_heart 0 .17 RPM 123 .43 RPM
SRP007412_kidney 0 .16 RPM 67 .21 RPM
SRP007412_liver 0 .00 RPM 25 .27 RPM
SRP007412_testis 510 .90 RPM 7 .90 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_79 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_79 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_79 has 9 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_41
Gorilla gorilla retro_ggor_59
Pongo abelii retro_pabe_129
Macaca mulatta retro_mmul_123
Callithrix jacchus retro_cjac_27
Mus musculus retro_mmus_63
Oryctolagus cuniculus retro_ocun_264
Bos taurus retro_btau_100
Equus caballus retro_ecab_21
Parental genes homology:
Parental genes homology involve 22 parental genes, and 27 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000167301 retrocopy
retro_amel_400,
Bos taurus ENSBTAG000000198522 retrocopies
retro_btau_100, retro_btau_1807,
Callithrix jacchus ENSCJAG000000054962 retrocopies
retro_cjac_2414, retro_cjac_27,
Dipodomys ordii ENSDORG000000118481 retrocopy
retro_dord_35,
Equus caballus ENSECAG000000019641 retrocopy
retro_ecab_21,
Erinaceus europaeus ENSEEUG000000054851 retrocopy
retro_eeur_580,
Homo sapiens ENSG000001318281 retrocopy
retro_hsap_41,
Gorilla gorilla ENSGGOG000000135741 retrocopy
retro_ggor_59,
Myotis lucifugus ENSMLUG000000129322 retrocopies
retro_mluc_2363, retro_mluc_323,
Macaca mulatta ENSMMUG000000173361 retrocopy
retro_mmul_123,
Mustela putorius furoENSMPUG000000032691 retrocopy
retro_mputfur_812,
Mus musculus ENSMUSG000000312992 retrocopies
retro_mmus_63, retro_mmus_631,
Nomascus leucogenys ENSNLEG000000098051 retrocopy
retro_nleu_74,
Oryctolagus cuniculus ENSOCUG000000147481 retrocopy
retro_ocun_264,
Pongo abelii ENSPPYG000000201711 retrocopy
retro_pabe_129,
Pan troglodytes ENSPTRG00000021717 1 retrocopy
retro_ptro_79 ,
Pteropus vampyrus ENSPVAG000000054201 retrocopy
retro_pvam_1306,
Sarcophilus harrisii ENSSHAG000000153751 retrocopy
retro_shar_84,
Sus scrofa ENSSSCG000000236432 retrocopies
retro_sscr_1015, retro_sscr_281,
Ictidomys tridecemlineatus ENSSTOG000000154331 retrocopy
retro_itri_1529,
Tupaia belangeri ENSTBEG000000143131 retrocopy
retro_tbel_3327,
Tursiops truncatus ENSTTRG000000006601 retrocopy
retro_ttru_1427,


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