RetrogeneDB ID:

retro_mmul_123

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:5:88796888..88798055(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMMUG00000021359
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:PDHA1
Ensembl ID:ENSMMUG00000017336
Aliases:None
Description:pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial [Source:RefSeq peptide;Acc:NP_001243768]


Retrocopy-Parental alignment summary:






>retro_mmul_123
ATGCTGGCCGTCTTCATCTCCCGCGTGTTGAGGCGAGTTGCCCAGAAGTCAGCTCGCAGAGTGCTGGTGGCATCCCGTAA
CTCCTCAAATGACGCTACATTTGAAATTGAGAAATGTGATCTTCACCTGTTGGAGGAGGGTCCCCCCGTCACTACAGTGC
TCACTAGGGCGGAGGGGCTTAAATACTACAGGATGATGCTGACTGTTCGCCGCATGGAATTGAAGGCAGATCAGCTGTAC
AAACAGAAATTCATTCGTGGTTTCTGTCACCTGTGCGATGGTCAGGAAGCTTGCTGCGTGGGCCTTGAGGCTGGAATAAA
CCCCTCGGATCACCTCATCACATCCTATAGGGCTCATGGTATGTGCTATACTCGGGGACTTTCTGTCCGATCCATTCTCA
CAGAGCTGACGGGAAGAAGAGGAGGTTGTGCTAAAGGAAAAGGAGGATCGATGCATATGTATACCAAGAACTTCTACGGG
GGCAATGGCATCGTCGGCGCGCAGGGCCCCCTGGGCGCTGGCATTGCTCTGGCCTGTAAATATAAGGGAAACAATGAGAT
CTGTTTGACTTTATATGGCGATGGCGCTGCGAATCAGGGGCAGATAGCCGAAGCTTTCAATATGGCAGCTTTATGGAAAT
TACCTTGTGTTTTCATCTGTGAGAATAACCTATATGCAATGGGAACATCTGCTGAGAGAGCAGCAGCCAGCACTGATTAC
TACAAGAGGGGCAATTTTATTCCTGGGCTAAAAGTCGATGGAATGGATGTTCTATGTGTTCGTGAGGCAACAAAATTTGC
AGCTGACTACTGTAGGTCTGGAAAGGGGCCCATACTGATGGAGCTGCAGACCTACCGTTATCATGGACACAGTATGAGTG
ATCCTGGAGTCAGTTATCGTACACGAGATGAAATTCAGGAAGTAAGAAGTAAGAGGGATCCTATAATGATTCTCCAAGAT
AGAATGGTAAACAGCAAGCTTGCCACTGTGGAAGAATTAAAGGAAATTGGGACTGAGGTGAAGAAAGAAATTGATGATGC
TGCCCAATTTGCTATCAGTGATCCTGAGCCACGTCTGGAAGAATTAGGCCATCACATCTACAGCAGTGATTCATCTTTTG
AAGTTCGTGGTGCAAATCCATGGATCAAGTTTAAGTCCGTCAGTTAA

ORF - retro_mmul_123 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.12 %
Parental protein coverage: 98.21 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalVSRVLSGASQKPASRVLVASRNFANDATFEIKKCDLHRLEEGPPVTTVLTREDGLKYYRMMQTVRRMELK
.SRVL....QK.A.RVLVASRN..NDATFEI.KCDLH.LEEGPPVTTVLTR..GLKYYRMM.TVRRMELK
RetrocopyISRVLRRVAQKSARRVLVASRNSSNDATFEIEKCDLHLLEEGPPVTTVLTRAEGLKYYRMMLTVRRMELK
ParentalADQLYKQKIIRGFCHLCDGQEACCVGLEAGINPTDHLITAYRAHGFTFTRGLSVREILAELTGRKGGCAK
ADQLYKQK.IRGFCHLCDGQEACCVGLEAGINP.DHLIT.YRAHG...TRGLSVR.IL.ELTGR.GGCAK
RetrocopyADQLYKQKFIRGFCHLCDGQEACCVGLEAGINPSDHLITSYRAHGMCYTRGLSVRSILTELTGRRGGCAK
ParentalGKGGSMHMYAKNFYGGNGIVGAQVPLGAGIALACKYNGKDEVCLTLYGDGAANQGQIFEAYNMAALWKLP
GKGGSMHMY.KNFYGGNGIVGAQ.PLGAGIALACKY.G..E.CLTLYGDGAANQGQI.EA.NMAALWKLP
RetrocopyGKGGSMHMYTKNFYGGNGIVGAQGPLGAGIALACKYKGNNEICLTLYGDGAANQGQIAEAFNMAALWKLP
ParentalCIFICENNRYGMGTSVERAAASTDYYKRGDFIPGLRVDGMDILCVREATRFAAAYCRSGKGPILMELQTY
C.FICENN.Y.MGTS.ERAAASTDYYKRG.FIPGL.VDGMD.LCVREAT.FAA.YCRSGKGPILMELQTY
RetrocopyCVFICENNLYAMGTSAERAAASTDYYKRGNFIPGLKVDGMDVLCVREATKFAADYCRSGKGPILMELQTY
ParentalRYHGHSMSDPGVSYRTREEIQEVRSKSDPIMLLKDRMVNSNLASVEELKEIDVEVRKEIEDAAQFATADP
RYHGHSMSDPGVSYRTR.EIQEVRSK.DPIM.L.DRMVNS.LA.VEELKEI..EV.KEI.DAAQFA..DP
RetrocopyRYHGHSMSDPGVSYRTRDEIQEVRSKRDPIMILQDRMVNSKLATVEELKEIGTEVKKEIDDAAQFAISDP
ParentalEPPLEELGYHIYSSDPPFEVRGANQWIKFKSVS
EP.LEELG.HIYSSD..FEVRGAN.WIKFKSVS
RetrocopyEPRLEELGHHIYSSDSSFEVRGANPWIKFKSVS

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 0 .00 RPM 41 .91 RPM
SRP007412_brain_prefrontal_cortex 0 .00 RPM 51 .17 RPM
SRP007412_cerebellum 0 .06 RPM 33 .84 RPM
SRP007412_heart 0 .00 RPM 126 .31 RPM
SRP007412_kidney 0 .12 RPM 51 .64 RPM
SRP007412_liver 0 .08 RPM 48 .37 RPM
SRP007412_testis 166 .30 RPM 5 .58 RPM

ChIP-Seq - click to see more details

Macaca mulatta was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_mmul_123 retrocopy.

TSS - click to see more details

Macaca mulatta was not studied using FANTOM5 data.

Lab - click to see more details

retro_mmul_123 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_123 has 9 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_41
Pan troglodytes retro_ptro_79
Gorilla gorilla retro_ggor_59
Pongo abelii retro_pabe_129
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 25 parental genes, and 30 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,
Echinops telfairi ENSETEG000000013921 retrocopy
retro_etel_1802,
Homo sapiens ENSG000001318281 retrocopy
retro_hsap_41,
Gorilla gorilla ENSGGOG000000135741 retrocopy
retro_ggor_59,
Loxodonta africana ENSLAFG000000094261 retrocopy
retro_lafr_91,
Myotis lucifugus ENSMLUG000000129322 retrocopies
retro_mluc_2363, retro_mluc_323,
Macaca mulatta ENSMMUG00000017336 1 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,
Procavia capensis ENSPCAG000000041961 retrocopy
retro_pcap_451,
Pongo abelii ENSPPYG000000201711 retrocopy
retro_pabe_129,
Pan troglodytes ENSPTRG000000217171 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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