RetrogeneDB ID:

retro_ptro_3229

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:X:67812663..67813491(-)
Located in intron of:ENSPTRG00000021979
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PGK1
Ensembl ID:ENSPTRG00000022052
Aliases:None
Description:Pan troglodytes phosphoglycerate kinase 1 (PGK1), mRNA. [Source:RefSeq mRNA;Acc:NM_001135738]


Retrocopy-Parental alignment summary:






>retro_ptro_3229
AGTGAGCCCGCCAAAATAGAAGCTTTCCGAGCTTCACTTTCCACGCTAGGGAATGTGTATGTCAATGGTGCTTTTGGCAC
TGCTCACAGAGCCCACAGCTCCATGGTAGGAGTCAGTCTGCCACAGAAGGCTGGTGGTTTTTTGATGAAGAAGGAGCTGA
ACTACTTTGTGAAGGTCTTGGAGAGCCCATAGCGACCCTTCCTGGCCATTCTGGGTGGAGCTAAATTTGCAGACAAGATC
CACCTGATCAATAATATGCTGGACAAAGTCAATGAGATGATTATTGGTGGTGGAACGGCTTTTACCTTCCTTAAGGTGCT
CAACAACATGGAGACTGGCACTTCTCTGTTTGATGAAGAGGGAGCCAAGATTGTCAAAGACCTAATGTCCCAAGCTGAGA
AGAATGGTGTGAAGATTACCTTGCCTATTGACTTTGTCACTGCTGAGAAATTTGATGAGAATGCCAAGACTGGCCAAGCC
ACTGTGGCTTCTGGCATACCTGCTGGCTGAATGGGCTTGGACTGTGGTCCTGAAAGCAGCAAGAAGTATGCTGAGACTGT
CACTTGGGCTAAGCAGATTGTGTGGAATGGTCCTGTGGGGGTATTTGAATGGGAAGCTTTTGCCCAGGGAACCAAAGCCC
TCATGGACGAGGTGGTGAAAGCCACTTCTAGGGGCTGCACTACCATCATAGGTGGTGGAAACACTGCCACTTGTTGTGCC
AAATGGAACACAGAGGATAAAATCAGACATGTGAGCACTAGGGGTGGTGCCAGTTTAGAGCTCCTGGACGGTAAAGTCCT
TCCTGGGGTGGATGCTCTCGGCAATATT

ORF - retro_ptro_3229 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.58 %
Parental protein coverage: 99.28 %
Number of stop codons detected: 2
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalAEPAKIEAFRASLS-LGDVYVNDAFGTAHRAHSSMVGVNLPQKAGGFLMKKELNYFAKALESPERPFLAI
.EPAKIEAFRASLS.LG.VYVN.AFGTAHRAHSSMVGV.LPQKAGGFLMKKELNYF.K.LESP.RPFLAI
RetrocopySEPAKIEAFRASLSTLGNVYVNGAFGTAHRAHSSMVGVSLPQKAGGFLMKKELNYFVKVLESP*RPFLAI
ParentalLGGAKVADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNNMEIGTSLFDEEGAKIVKDLMSKAEKNGVKIT
LGGAK.ADKI.LINNMLDKVNEMIIGGG.AFTFLKVLNNME.GTSLFDEEGAKIVKDLMS.AEKNGVKIT
RetrocopyLGGAKFADKIHLINNMLDKVNEMIIGGGTAFTFLKVLNNMETGTSLFDEEGAKIVKDLMSQAEKNGVKIT
ParentalLPVDFVTADKFDENAKTGQATVASGIPAGWMGLDCGPESSKKYAEAVTRAKQIVWNGPVGVFEWEAFARG
LP.DFVTA.KFDENAKTGQATVASGIPAG.MGLDCGPESSKKYAE.VT.AKQIVWNGPVGVFEWEAFA.G
RetrocopyLPIDFVTAEKFDENAKTGQATVASGIPAG*MGLDCGPESSKKYAETVTWAKQIVWNGPVGVFEWEAFAQG
ParentalTKALMDEVVKATSRGCITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGKVLPGVDALSNI
TKALMDEVVKATSRGC.TIIGGG.TATCCAKWNTEDK..HVST.GGASLELL.GKVLPGVDAL.NI
RetrocopyTKALMDEVVKATSRGCTTIIGGGNTATCCAKWNTEDKIRHVSTRGGASLELLDGKVLPGVDALGNI

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 .32 RPM 170 .83 RPM
SRP007412_cerebellum 0 .07 RPM 138 .09 RPM
SRP007412_heart 0 .09 RPM 182 .98 RPM
SRP007412_kidney 0 .16 RPM 194 .91 RPM
SRP007412_liver 0 .10 RPM 151 .59 RPM
SRP007412_testis 0 .00 RPM 31 .40 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_3229 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_3229 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_3229 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_4850
Gorilla gorilla retro_ggor_3026
Pongo abelii retro_pabe_3770
Parental genes homology:
Parental genes homology involve 29 parental genes, and 52 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000176191 retrocopy
retro_amel_117,
Bos taurus ENSBTAG000000008941 retrocopy
retro_btau_1021,
Canis familiaris ENSCAFG000000172702 retrocopies
retro_cfam_1194, retro_cfam_510,
Callithrix jacchus ENSCJAG000000210823 retrocopies
retro_cjac_1367, retro_cjac_137, retro_cjac_4171,
Cavia porcellus ENSCPOG000000237851 retrocopy
retro_cpor_102,
Equus caballus ENSECAG000000149841 retrocopy
retro_ecab_557,
Felis catus ENSFCAG000000132092 retrocopies
retro_fcat_123, retro_fcat_316,
Homo sapiens ENSG000001021442 retrocopies
retro_hsap_1966, retro_hsap_90,
Gorilla gorilla ENSGGOG000000171113 retrocopies
retro_ggor_1429, retro_ggor_2420, retro_ggor_3026,
Loxodonta africana ENSLAFG000000119541 retrocopy
retro_lafr_13,
Macropus eugenii ENSMEUG000000047793 retrocopies
retro_meug_11, retro_meug_1649, retro_meug_400,
Myotis lucifugus ENSMLUG000000177912 retrocopies
retro_mluc_1657, retro_mluc_2159,
Macaca mulatta ENSMMUG000000128741 retrocopy
retro_mmul_144,
Monodelphis domestica ENSMODG000000040552 retrocopies
retro_mdom_140, retro_mdom_170,
Mus musculus ENSMUSG000000620702 retrocopies
retro_mmus_29, retro_mmus_9,
Nomascus leucogenys ENSNLEG000000014233 retrocopies
retro_nleu_2372, retro_nleu_2610, retro_nleu_79,
Oryctolagus cuniculus ENSOCUG000000147261 retrocopy
retro_ocun_171,
Otolemur garnettii ENSOGAG000000111041 retrocopy
retro_ogar_73,
Procavia capensis ENSPCAG000000021171 retrocopy
retro_pcap_17,
Pongo abelii ENSPPYG000000204963 retrocopies
retro_pabe_134, retro_pabe_1624, retro_pabe_3770,
Pan troglodytes ENSPTRG00000022052 2 retrocopies
retro_ptro_2, retro_ptro_3229 ,
Rattus norvegicus ENSRNOG000000024677 retrocopies
retro_rnor_1526, retro_rnor_1527, retro_rnor_2603, retro_rnor_3, retro_rnor_462, retro_rnor_590, retro_rnor_611,
Sorex araneus ENSSARG000000039561 retrocopy
retro_sara_14,
Sarcophilus harrisii ENSSHAG000000018531 retrocopy
retro_shar_11,
Sus scrofa ENSSSCG000000124401 retrocopy
retro_sscr_933,
Ictidomys tridecemlineatus ENSSTOG000000019721 retrocopy
retro_itri_65,
Tupaia belangeri ENSTBEG000000103091 retrocopy
retro_tbel_35,
Tarsius syrichta ENSTSYG000000079171 retrocopy
retro_tsyr_40,
Vicugna pacos ENSVPAG000000012081 retrocopy
retro_vpac_21,


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