RetrogeneDB ID:

retro_pabe_1624

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:19:12759033..12760054(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PGK1
Ensembl ID:ENSPPYG00000020496
Aliases:None
Description:Phosphoglycerate kinase 1 [Source:UniProtKB/Swiss-Prot;Acc:Q5NVB5]


Retrocopy-Parental alignment summary:






>retro_pabe_1624
ATGTCACTTTCTAACAAGCTGATGCTGGACAAGCTGGACGTGAAAGGGAAGCGGGTCGTTATGAGAGTCGACTTCAATTT
TCCTATGAAGAACAACCAGATAACAAACAACCGGAGGATTAAGGCTGCTGTCCCAAGCATCAAATTCTGCTTGGACAATG
GATCCAAGTCAGTAGTCCTTATAAGCCACCTAGGCTGGCCTGATGGTGTCCCTATGCCTGAGAAGTACTCCTCAGAGCCA
GCTGCTGTAGAACTCAAATCTCTGCTGGGCAAGGATGTTCTGTTCTTGAAGGACTGTGTAGGCCCAGAAATGGAGAAAGC
CTGTACCAACCCAGCTGATGGGTCTGTCATCCTGCTGGAGAACCTCCGCTTTCATGTGGAGGAAGAGGGAAGGGAAAAGT
TGCTTCTGGGAACAAGGCTAACGCTGAGCCAGCCAAATTAGAAGCTTCCAAGCTTCACTTCCCAAGCTAGGGGATGTCTA
CGTCAACGATGCTTTTGGCACTGCTCACAGAGCCCACAGCTCCATGGCAGAAGTCAATCTGCCACAGAAGGCTGGTGGTT
TTTTGATGAAGAAGGAGCTGAACTACTTTGCCGAGGCCTTGGAGAGCCCAGAGTGACACTTCCTGGCCATCCTGGGAAGA
GCTAAAGTTGCAGACAAGATCCAGCTGATCAAGAATATGCTGGGCAAAGTCAATGAGATGATTATTGGTGGTGGAATGGC
TTGTACCTTCCTTAAGGTGCTCAGCAACATGGAGACTGGCACTTCTCTGTTTGATGAAGAGGGAGCCAAGATTGTCAAAG
ACCTAATGTCCAAAGCTGAGAAGAATGGTGTGAAGATTATCTTGCCTGTTGACTTTGTCACTGCTGGCAAGTTTGATGAG
AATGCCAAGACTGGCCAAGCCACTGTGGCTTCTGGCATACCTGCTGGCTGGCTGGGCTTGGACTGTGGTCCTGAAAGCAG
CAAGAAGTATGCTGAGGCTGTCACTCAGGCTAAGCAGATTGTGTGGAATGGTCCTGTGGGG

ORF - retro_pabe_1624 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.8 %
Parental protein coverage: 81.77 %
Number of stop codons detected: 1
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalMSLSNKLTLDKLDVKGKRVVMRVDFNVPMKNNQITNNQRIKAAVPSIKFCLDNGAKSVVLMSHLGRPDGV
MSLSNKL.LDKLDVKGKRVVMRVDFN.PMKNNQITNN.RIKAAVPSIKFCLDNG.KSVVL.SHLG.PDGV
RetrocopyMSLSNKLMLDKLDVKGKRVVMRVDFNFPMKNNQITNNRRIKAAVPSIKFCLDNGSKSVVLISHLGWPDGV
ParentalPMPDKYSLEPVAVELKSLLGKDVLFLKDCVGPEVEKACANPAAGSVILLENLRFHVEEEG-KGKDASGNK
PMP.KYS.EP.AVELKSLLGKDVLFLKDCVGPE.EKAC.NPA.GSVILLENLRFHVEEEG.KGK.ASGNK
RetrocopyPMPEKYSSEPAAVELKSLLGKDVLFLKDCVGPEMEKACTNPADGSVILLENLRFHVEEEG<KGKVASGNK
ParentalVKAEPAKIEA-FRASLSKLGDVYVNDAFGTAHRAHSSMVGVNLPQKAGGFLMKKELNYFAKALESPERPF
..AEPAK.EA.F.ASL.KLGDVYVNDAFGTAHRAHSSM..VNLPQKAGGFLMKKELNYFA.ALESPE..F
RetrocopyANAEPAKLEA<FQASLPKLGDVYVNDAFGTAHRAHSSMAEVNLPQKAGGFLMKKELNYFAEALESPE*HF
ParentalLAILGGAKVADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNNMEIGTSLFDEEGAKIVKDLMSKAEKNGV
LAILG.AKVADKIQLI.NML.KVNEMIIGGGMA.TFLKVL.NME.GTSLFDEEGAKIVKDLMSKAEKNGV
RetrocopyLAILGRAKVADKIQLIKNMLGKVNEMIIGGGMACTFLKVLSNMETGTSLFDEEGAKIVKDLMSKAEKNGV
ParentalKITLPVDFVTADKFDENAKTGQATVASGIPAGWMGLDCGPESSKKYAEAVTRAKQIVWNGPVG
KI.LPVDFVTA.KFDENAKTGQATVASGIPAGW.GLDCGPESSKKYAEAVT.AKQIVWNGPVG
RetrocopyKIILPVDFVTAGKFDENAKTGQATVASGIPAGWLGLDCGPESSKKYAEAVTQAKQIVWNGPVG

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 .11 RPM 354 .91 RPM
SRP007412_cerebellum 0 .12 RPM 266 .43 RPM
SRP007412_heart 0 .12 RPM 171 .08 RPM
SRP007412_kidney 0 .17 RPM 230 .30 RPM
SRP007412_liver 0 .03 RPM 136 .88 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_1624 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_1624 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1624 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1966
Gorilla gorilla retro_ggor_1429
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 ENSPPYG00000020496 3 retrocopies
retro_pabe_134, retro_pabe_1624 , retro_pabe_3770,
Pan troglodytes ENSPTRG000000220522 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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