RetrogeneDB ID:

retro_ptro_3162

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:X:121551331..121553005(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPTRG00000028207
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:GLUD2
Ensembl ID:ENSPTRG00000002711
Aliases:None
Description:Pan troglodytes glutamate dehydrogenase 2 (GLUD2), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001009004]


Retrocopy-Parental alignment summary:






>retro_ptro_3162
ATGTACCGCTACCTGGCCAAAGCGCTGCTGACGTCCCGGGCCGGGCCCGCTGCCCTGGGCTCCGCGGCCAACCACTCGGC
CGCGTTGCTGGGCCGGGGCCGCGGACAGCCCGCCGCCGCCTCGCAGCCGGGGCTCGCATTGGCCGCCCGGCGCCACTACA
GCGAGTTGGTGGCCGACCGCGAGGACGACCCCAACTTCTTCAAGATGGTGGAGGGCTTCTTCGATCGCGGCGCCAGCATC
GTGGAGGACAAGTTGGTGAAGGACCTGAGGACCCAGGAGAGCGAGGAGCAGAAGCGGAACCGGGTGCGCGGCATCCTGCG
GATCATCAAGCCCTGCAACCATGTGCTGAGTCTCTCCTTCCCCATCCGGCGCGACGACGGCTCCTGGGAGGTCATTGAAG
GCTACCGGGCCCAGCACAGCCAGCACCGCACGCCCTGCAAGGGAGGTATCCGTTACAGCACTGATGTAAGTGTAGATGAA
GTAAAAGCTTTGGCTTCTCTGATGACATACAAGTGTGCAGTGGTTGATGTGCCGTTTGGGGGTGCTAAAGCTGGTGTTAA
GATCAATCCCAAGAACTATACCGAAAATGAATTGGAAAAGATCACAAGGAGGTTCACCATGGAGCTAGCAAAGAAGGGCT
TTATTGGTCCTGGCGTTGATGTGCCTGCTCCAGACATGAACACAGGTGAGCGGGAGATGTCCTGGATTGCTGATACCTAT
GCCAGCACCATAGGGCACTATGATATTAATGCACACGCCTGTGTTACTGGTAAACCCATCAGCCAAGGGGGAATCCATGG
ACGCATCTCTGCTACTGGCCGTGGTGTCTTCCATGGGATTGAAAACTTCATCAATGAAGCTTCTTACATGAGCATTTTAG
GAATGACACCAGGGTTTAGAGATAAAACATTTGTTGTTCAGGGATTTGGTAATGTGGGCCTACACTCTATGAGATATTTA
CATCGTTTTGGTGCTAAATGTATTGCTGTTGGTGAGTCTGATGGGAGTATATGGAATCCAGATGGTATTGACCCAAAGGA
ACTGGAAGACTTCAGATTGCAACATGGGTCCCTTCTGGGCTTCCCCAAGGCAAAGCCCTATGAAGGAAGCATCTTGGAGA
TCGACTGTGACATACTGATCCCAGCTGCCACTGAGAAGCAGTTGACCAAATCCAACGCACCCAGAGTCAAAGCCAAGATC
ATTGCTGAAGGTGCCAATGGGCCAACAACTCCAGAAGCTGACAAGATCTTCCTGGAGAGAAACATTTTGGTTATTCCAGA
TCTCTACTTGAATGCTGGAGGAGTGACAGTATCTTACTTTGAGTGGCTGAAGAATCTAAATCATGTCAGCTATGGCCGTT
TGACCTTCAAATATGAAAGGGATTCTAACTACCACTTGCTCATGTCTGTTCAAGAGAGTTTAGAAAGAAAATTTGGAAAG
CATGGTGGAACTATTCCCATTGTACCCACGGCAGAGTTCCAAGACAGTATATCGGGTGCATCTGAGAAAGACATTGTGCA
CTCTGCCTTGGCATACACAATGGAGCGTTCTGCCAGGCAAATTATGCACACAGCCATGAAGTATAACCTGGGATTGGACC
TGAGAACAGCTGCCTATGTCAATGCCATTGAGAAAGTCTTCAAAGTGTACAGTGAAGCTGGTGTGACCTTCACA

ORF - retro_ptro_3162 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.34 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMYRYLGEALLLSRAGPAALGSASADSAALLGWARGQPAAAPQPGLALAARRHYSEAVADREDDPNFFKMV
MYRYL..ALL.SRAGPAALGSA...SAALLG..RGQPAAA.QPGLALAARRHYSE.VADREDDPNFFKMV
RetrocopyMYRYLAKALLTSRAGPAALGSAANHSAALLGRGRGQPAAASQPGLALAARRHYSELVADREDDPNFFKMV
ParentalEGFFDRGASIVEDKLVEDLRTRESEEQKRNRVRGILRIIKPCNHVLSLSFPIRRDDGSWEVIEGYRAQHS
EGFFDRGASIVEDKLV.DLRT.ESEEQKRNRVRGILRIIKPCNHVLSLSFPIRRDDGSWEVIEGYRAQHS
RetrocopyEGFFDRGASIVEDKLVKDLRTQESEEQKRNRVRGILRIIKPCNHVLSLSFPIRRDDGSWEVIEGYRAQHS
ParentalQHRTPCKGGIRYSTDVSVDEVKALASLMTYKCAVVDVPFGGAKAGVKINPKNYTDNELEKITRRFTMELA
QHRTPCKGGIRYSTDVSVDEVKALASLMTYKCAVVDVPFGGAKAGVKINPKNYT.NELEKITRRFTMELA
RetrocopyQHRTPCKGGIRYSTDVSVDEVKALASLMTYKCAVVDVPFGGAKAGVKINPKNYTENELEKITRRFTMELA
ParentalKKGFIGPGIDVPAPDMSTGEREMSWIADTYASTIGHYDINAHACVTGKPISQGGIHGRISATGRGVFHGI
KKGFIGPG.DVPAPDM.TGEREMSWIADTYASTIGHYDINAHACVTGKPISQGGIHGRISATGRGVFHGI
RetrocopyKKGFIGPGVDVPAPDMNTGEREMSWIADTYASTIGHYDINAHACVTGKPISQGGIHGRISATGRGVFHGI
ParentalENFINEASYMSILGMTPGFGDKTFVVQGFGNVGLHSMRYLHRFGAKCIAVGESEGSIWNPDGIDPKELED
ENFINEASYMSILGMTPGF.DKTFVVQGFGNVGLHSMRYLHRFGAKCIAVGES.GSIWNPDGIDPKELED
RetrocopyENFINEASYMSILGMTPGFRDKTFVVQGFGNVGLHSMRYLHRFGAKCIAVGESDGSIWNPDGIDPKELED
ParentalFKLQHGSILGFPKAKPYEGSILEADCDILIPAASEKQLTKSNAPRVKAKIIAEGANGPTTPEADKIFLER
F.LQHGS.LGFPKAKPYEGSILE.DCDILIPAA.EKQLTKSNAPRVKAKIIAEGANGPTTPEADKIFLER
RetrocopyFRLQHGSLLGFPKAKPYEGSILEIDCDILIPAATEKQLTKSNAPRVKAKIIAEGANGPTTPEADKIFLER
ParentalNIMVIPDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFKYERDSNYHLLMSVQESLERKFGKHGGTIPIVPT
NI.VIPDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFKYERDSNYHLLMSVQESLERKFGKHGGTIPIVPT
RetrocopyNILVIPDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFKYERDSNYHLLMSVQESLERKFGKHGGTIPIVPT
ParentalAEFQDRISGASEKDIVHSGLAYTMERSARQIMRTAMKYNLGLDLRTAAYVNAIEKVFKVYNEAGVTFT
AEFQD.ISGASEKDIVHS.LAYTMERSARQIM.TAMKYNLGLDLRTAAYVNAIEKVFKVY.EAGVTFT
RetrocopyAEFQDSISGASEKDIVHSALAYTMERSARQIMHTAMKYNLGLDLRTAAYVNAIEKVFKVYSEAGVTFT

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 2 .29 RPM 140 .90 RPM
SRP007412_cerebellum 0 .39 RPM 104 .43 RPM
SRP007412_heart 0 .58 RPM 109 .18 RPM
SRP007412_kidney 1 .54 RPM 315 .57 RPM
SRP007412_liver 1 .70 RPM 455 .56 RPM
SRP007412_testis 8 .11 RPM 31 .30 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_3162 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_3162 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_3162 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_31
Pongo abelii retro_pabe_79
Parental genes homology:
Parental genes homology involve 20 parental genes, and 28 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000075402 retrocopies
retro_btau_1413, retro_btau_1741,
Canis familiaris ENSCAFG000000160951 retrocopy
retro_cfam_747,
Choloepus hoffmanni ENSCHOG000000011011 retrocopy
retro_chof_2002,
Callithrix jacchus ENSCJAG000000116331 retrocopy
retro_cjac_2830,
Dipodomys ordii ENSDORG000000097671 retrocopy
retro_dord_400,
Equus caballus ENSECAG000000073712 retrocopies
retro_ecab_886, retro_ecab_919,
Echinops telfairi ENSETEG000000196382 retrocopies
retro_etel_141, retro_etel_2024,
Homo sapiens ENSG000001486721 retrocopy
retro_hsap_31,
Gorilla gorilla ENSGGOG000000157701 retrocopy
retro_ggor_2954,
Loxodonta africana ENSLAFG000000120591 retrocopy
retro_lafr_504,
Microcebus murinus ENSMICG000000165261 retrocopy
retro_mmur_524,
Monodelphis domestica ENSMODG000000027561 retrocopy
retro_mdom_124,
Nomascus leucogenys ENSNLEG000000116581 retrocopy
retro_nleu_36,
Otolemur garnettii ENSOGAG000000036411 retrocopy
retro_ogar_2757,
Procavia capensis ENSPCAG000000086621 retrocopy
retro_pcap_11,
Pongo abelii ENSPPYG000000028273 retrocopies
retro_pabe_3109, retro_pabe_3213, retro_pabe_79,
Pan troglodytes ENSPTRG00000002711 4 retrocopies
retro_ptro_3162 , retro_ptro_3283, retro_ptro_3285, retro_ptro_3290,
Ictidomys tridecemlineatus ENSSTOG000000128431 retrocopy
retro_itri_737,
Tarsius syrichta ENSTSYG000000015781 retrocopy
retro_tsyr_313,
Tursiops truncatus ENSTTRG000000081451 retrocopy
retro_ttru_950,


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