RetrogeneDB ID:

retro_rnor_3

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:9:22956394..22957648(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSRNOG00000013600
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Pgk1
Ensembl ID:ENSRNOG00000002467
Aliases:Pgk1, Pgk
Description:Phosphoglycerate kinase 1 [Source:UniProtKB/Swiss-Prot;Acc:P16617]


Retrocopy-Parental alignment summary:






>retro_rnor_3
ATGGCTCTTTCTAGTAAGTTGACTCTGGACAAAGTGGATGTTAAGGAAAAAAGAGTCATCATGAGAGTAGATTTCAACGT
TCCCATGAAGAATAACCAAATTACAAACAACCAGAGAATCAAGGCTGCCATCCCAAGCATCAAATACTGTCTGGACAATG
GAGCCACGTCCGTAGTTCTCATGAGTCACCTCGGCCGGCCTGATGGTATCCCCATGCCGGACAAATACTCATTACAGCCT
GTTGCTGCTGAGCTCAAGTCCCTACTGAACAAGGACGTTATATTCTTAAAGGACTGTGTGGGCTCTGAAATAGAGAAAGC
CTGTGCCAACCCAGGTAAAGGCTCTGTAATCCTTCTGGAGAACCTGCGCTTTCATGTGGAGGAAGAAGGGAAGGGTAAAG
ATGCTTCTGGACAAAAGATTACCGCTGAGCCTGATAAAGTGGAAGCCTTCCGAGCTTCACTGTCCAAACTCGGTGATGTC
TACGTCAACGATGCTTTTGGCACTGCACATCGGGCTCACAGTTCCATGGTGGGAATAAATTTGCCCCAGAAGGCATCTGG
GTTCCTCATGAAGAAGGAGCTAGATTATTTTTCCAAGGTCTTAGAAAAGCCAGAGAGGCCCTTCCTGGCTATTCTTGGTG
GAGCCAAAGTGACAGACAAGATCCAACTTATCAAAAATATGTTAGACAAAGTCAATTTCATGATTATTGGTGGTGCGATG
GCTTTCACCTTCCTGAAAGAACTCAAGAACATGAAGATTGGTGCTTCCTTGTTTGATGAAGACGGAGCCAAGATCGTCAA
AGAGATCATGGACAAGGCAGAAAAGAATGGCGTAAAGATAACCTTTCCTGTTGACTTTGTTACCGGTGACAAGTTTGATG
AGCATGCTAAAGTTGGACAAGCCACTGTAGAATCTGGTATACCATCTGGCTGGATGGGTTTGGATTGCGGCCCTGAGAGC
ATTAAAAACAATGCTCAAATTGTGGCCCAAGCAAAGCTGATTGTTTGGAATGGACCTCTGGGGGTATTTGAATGGGATGG
CTTTGCTAAGGGAACCAAAGCCCTCATGGATGAAGTTGTAAAGGCCACCTCCAATGGCTGTATCACCATCATAGGAGGCG
GGGACACTGCTACTTGCTGTGCCAAATGGAACACTGAAGACAAGGTCAGCCATGTGAGCACAGGAGGCGGGGCAAGTCTT
GAGCTTCTGGAAGGCAAAACCCTTCCAGGGGTAGAGGCCCTCAGCAACATGTAA

ORF - retro_rnor_3 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.41 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMSLSNKLTLDKLDVKGKRVVMRVDFNVPMKNNQITNNQRIKAAVPSIKFCLDNGAKSVVLMSHLGRPDGV
M.LS.KLTLDK.DVK.KRV.MRVDFNVPMKNNQITNNQRIKAA.PSIK.CLDNGA.SVVLMSHLGRPDG.
RetrocopyMALSSKLTLDKVDVKEKRVIMRVDFNVPMKNNQITNNQRIKAAIPSIKYCLDNGATSVVLMSHLGRPDGI
ParentalPMPDKYSLEPVAAELKSLLGKDVLFLKDCVGSEVENACANPAAGTVILLENLRFHVEEEGKGKDASGNKV
PMPDKYSL.PVAAELKSLL.KDV.FLKDCVGSE.E.ACANP..G.VILLENLRFHVEEEGKGKDASG.K.
RetrocopyPMPDKYSLQPVAAELKSLLNKDVIFLKDCVGSEIEKACANPGKGSVILLENLRFHVEEEGKGKDASGQKI
ParentalKAEPAKIDAFRASLSKLGDVYVNDAFGTAHRAHSSMVGVNLPQKAGGFLMKKELNYFAKALESPERPFLA
.AEP.K..AFRASLSKLGDVYVNDAFGTAHRAHSSMVG.NLPQKA.GFLMKKEL.YF.K.LE.PERPFLA
RetrocopyTAEPDKVEAFRASLSKLGDVYVNDAFGTAHRAHSSMVGINLPQKASGFLMKKELDYFSKVLEKPERPFLA
ParentalILGGAKVADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNNMEIGTSLYDEEGAKIVKDLMAKAEKNGVKI
ILGGAKV.DKIQLI.NMLDKVN.MIIGG.MAFTFLK.L.NM.IG.SL.DE.GAKIVK..M.KAEKNGVKI
RetrocopyILGGAKVTDKIQLIKNMLDKVNFMIIGGAMAFTFLKELKNMKIGASLFDEDGAKIVKEIMDKAEKNGVKI
ParentalTLPVDFVTADKFDENAKTGQATVASGIPAGWMGLDCGTESSKKYAEAVARAKQIVWNGPVGVFEWEAFAR
T.PVDFVT.DKFDE.AK.GQATV.SGIP.GWMGLDCG.ES.K..A..VA.AK.IVWNGP.GVFEW..FA.
RetrocopyTFPVDFVTGDKFDEHAKVGQATVESGIPSGWMGLDCGPESIKNNAQIVAQAKLIVWNGPLGVFEWDGFAK
ParentalGTKSLMDEVVKATSRGCITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGKVLPGVDALSNV
GTK.LMDEVVKATS.GCITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGK.LPGV.ALSN.
RetrocopyGTKALMDEVVKATSNGCITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGKTLPGVEALSNM

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
SRP017611_brain 0 .00 RPM 322 .24 RPM
SRP017611_kidney 0 .00 RPM 446 .19 RPM
SRP017611_liver 0 .00 RPM 184 .97 RPM

ChIP-Seq - click to see more details

Rattus norvegicus was not studied using ChIP-Seq data.

EST - click to see more details

4 EST(s) were mapped to retro_rnor_3 retrocopy
EST ID Start End Identity Match Mis-match Score
CK468920 22956370 22956987 97.1 597 16 576
CK595428 22956374 22957069 99.9 686 1 678
CK653052 22956349 22957026 99.8 668 1 661
FM090586 22956346 22957031 99.8 683 2 681

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_3 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_3 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Mus musculus retro_mmus_29
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 ENSPTRG000000220522 retrocopies
retro_ptro_2, retro_ptro_3229,
Rattus norvegicus ENSRNOG00000002467 7 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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