RetrogeneDB ID:

retro_rnor_1006

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:14:62058427..62060135(+)
Located in intron of:ENSRNOG00000026472
Retrocopy
information
Ensembl ID:ENSRNOG00000038897
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Hspd1
Ensembl ID:ENSRNOG00000014525
Aliases:Hspd1, Hsp60, Hspd1-30p
Description:60 kDa heat shock protein, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:P63039]


Retrocopy-Parental alignment summary:






>retro_rnor_1006
ATGCTTTGATTACCCACAGTCCTTTGCCAGATCAGACCAGTGTCTCAGGCACTGGCTCCTCATCTCACTCAGGCCTATGC
CAAAGATGTAAAATTTGGTGCGGATCTCAAGCCTTAATGCTTCAAGGTGTAGACCTTTTAGCTGATGCTGTAGCTGTTCC
AATGGGGCCAAAAGGAAGAACAGTGATTATTGAACAGAGTTGGGGAAGTCCCAAAGTGACAAAAGATGGGGTCACTGTTG
CAAAGTCAATCGATTTAAAGGATAAATACAAAAATATTGGAACTGAACTTGTTCAGGATGTTGCCGATAACACAAACAAA
GAGGCTGGGGATGGCACCACCACTGCCACTGTTTTGGCACGGTCTATTGCCAAGGAGGGCTTGGAGAAGATCAGCCAAGG
GGCTAATCCAGTGGAAATCCAGAGACCTGTGATGTTGGCTGTTGATGCTGTAATTGCTGAACTTAAGAAACAATCTAAAC
CTGTGACAACCCCTGAAGAGACTGCTCAGGTTGCTACAACTTCTGCAAACGGAGACAAAGACACTGGGAACATCATTTCT
GATGCAGTGAAGAAGGTTGGAAGAAAGGGCGTCATCACAGTGAATGATGGAAAACCCTGAATGATGAGCTAGAAATTATT
GAAGGCATGAAGTTCGATAGAGGATATATTTCCCCATATTTTATTAACACATCAAAAGGTCAAAAATGTGACTTCCAAGA
TGCCTATGTTTCATTGAGTGAAAAGAAAATTTCTAGTGTTCAGTCCATTGTACCTGCTCTTGAAATTGCCAATGCTCATC
GGAAGCCCTTGGTCACAATTGCTGAAGATGTTGATGGAGAAGCTCTTAGCACACCGGTTTTGAACAGGCTAAAAGTTGGT
CTTCAGGTTGTAGCAGACAAAGCTCCAGGGTTTGGGGACAACAGGAAGAACCAGCTTAAAGATATGACTATCGCTACTGG
TAGTGCAGTGTTTGGAGAAGAGGAGTTGAATCTAAATCTTGAAGATGTTCAAGCTCATGATTTAGGAAAAGTTGGACAGG
TCATTGTCACCAAAGATGATGCCATGCTTTTGAAAGGAAAAGGTGACAAAGCTCACATTGAAAAAATGTATTCAAGAAAT
CACTGAGCAGCTAGACGTCACAACTAGTGAATATGAAAAGGAAAAGCTGAACGAGCGACTTGCTAAACTTCCAGATGGAG
TAGCTGTGTTGAAGGTTGGAGGGACAAGTGATGTTGAAGTGAATGAGAAGAAAGACAGAGTTACAGATGCTCTCAATGCC
ACAAGAGCAGCTGTTGAAGAAGCCATTGTTCTGGAGGGGACTGTGCTCTGCTTTGGTGCATCCCAGCCTTGGATTCATTA
AACCTGCTAATGAAGATCAGAAGATAGGTATAGAAATTGTCAAAAGAGCACTTAAAATTCCTGCAATGACGATTGCTAAG
AATGCAGGTGTTGAAGGATCTTTGATAGTTGAGAAAATTCTGCAGAGTTCCTCAGAGTTGGTTATGACGCCATGCTTGGA
GATTTTGTGAACATGGTGAAAAGGTTGATCCAACAAAGGTTGTAAGAACTGCTTTACTGGATGCTGCTGGGGTGGTCTCC
TTGCTAACTACAGCCGAAGCTGTAGTGACAGAAATTCCTAAAGAAGAGAAGGACCCTGGAATGGGTTCAATGAGTGGAAT
GCGAGGGGCTGTGGGAGGTGGCCTGTTC

ORF - retro_rnor_1006 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.69 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 1
Number of frameshifts detected: 7


Retrocopy - Parental Gene Alignment:

ParentalMLRLPTVLRQMRPVSRALAPHLTRAYAKDVKFGAD-ARALMLQGVDLLADAVAVTMGPKGRTVIIEQSWG
ML.LPTVL.Q.RPVS.ALAPHLT.AYAKDVKFGAD...ALMLQGVDLLADAVAV.MGPKGRTVIIEQSWG
RetrocopyML*LPTVLCQIRPVSQALAPHLTQAYAKDVKFGAD<SQALMLQGVDLLADAVAVPMGPKGRTVIIEQSWG
ParentalSPKVTKDGVTVAKSIDLKDKYKNIGAKLVQDVANNTNEEAGDGTTTATVLARSIAKEGFEKISKGANPVE
SPKVTKDGVTVAKSIDLKDKYKNIG..LVQDVA.NTN.EAGDGTTTATVLARSIAKEG.EKIS.GANPVE
RetrocopySPKVTKDGVTVAKSIDLKDKYKNIGTELVQDVADNTNKEAGDGTTTATVLARSIAKEGLEKISQGANPVE
ParentalIRRGVMLAVDAVIAELKKQSKPVTTPEEIAQVATISANGDKDIGNIISDAMKKVGRKGVITVKDGK-TLN
I.R.VMLAVDAVIAELKKQSKPVTTPEE.AQVAT.SANGDKD.GNIISDA.KKVGRKGVITV.DGK.TLN
RetrocopyIQRPVMLAVDAVIAELKKQSKPVTTPEETAQVATTSANGDKDTGNIISDAVKKVGRKGVITVNDGK<TLN
ParentalDELEIIEGMKFDRGYISPYFINTSKGQKCEFQDAYVLLSEKKISSVQSIVPALEIANAHRKPLVIIAEDV
DELEIIEGMKFDRGYISPYFINTSKGQKC.FQDAYV.LSEKKISSVQSIVPALEIANAHRKPLV.IAEDV
RetrocopyDELEIIEGMKFDRGYISPYFINTSKGQKCDFQDAYVSLSEKKISSVQSIVPALEIANAHRKPLVTIAEDV
ParentalDGEALSTLVLNRLKVGLQVVAVKAPGFGDNRKNQLKDMAIATGGAVFGEEGLNLNLEDVQAHDLGKVGEV
DGEALST.VLNRLKVGLQVVA.KAPGFGDNRKNQLKDM.IATG.AVFGEE.LNLNLEDVQAHDLGKVG.V
RetrocopyDGEALSTPVLNRLKVGLQVVADKAPGFGDNRKNQLKDMTIATGSAVFGEEELNLNLEDVQAHDLGKVGQV
ParentalIVTKDDAMLLKGKGDKAHIEKR-IQEITEQLDITTSEYEKEKLNERLAKLSDGVAVLKVGGTSDVEVNEK
IVTKDDAMLLKGKGDKAHIEK..IQEITEQLD.TTSEYEKEKLNERLAKL.DGVAVLKVGGTSDVEVNEK
RetrocopyIVTKDDAMLLKGKGDKAHIEKM>IQEITEQLDVTTSEYEKEKLNERLAKLPDGVAVLKVGGTSDVEVNEK
ParentalKDRVTDALNATRAAVEEGIVL-GGGCALLRCIPALDSL-KPANEDQKIGIEIIKRALKIPAMTIAKNAGV
KDRVTDALNATRAAVEE.IVL.GG.CALL.CIPALDSL.KPANEDQKIGIEI.KRALKIPAMTIAKNAGV
RetrocopyKDRVTDALNATRAAVEEAIVL<GGDCALLWCIPALDSL<KPANEDQKIGIEIVKRALKIPAMTIAKNAGV
ParentalEGSLIVEKILQSSSE-VGYDAMLGDFVNMV-EKGIIDPTKVVRTALLDAAGVASLLTTAEAVVTEIPKEE
EGSLIVEKILQSSSE.VGYDAMLGDFVNMV.EK...DPTKVVRTALLDAAGV.SLLTTAEAVVTEIPKEE
RetrocopyEGSLIVEKILQSSSE<VGYDAMLGDFVNMV<EK--VDPTKVVRTALLDAAGVVSLLTTAEAVVTEIPKEE
ParentalKDPGMGAMGGMGGGMGGGMF
KDPGMG.M.GM.G..GGG.F
RetrocopyKDPGMGSMSGMRGAVGGGLF

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 .07 RPM 100 .94 RPM
SRP017611_kidney 0 .00 RPM 459 .10 RPM
SRP017611_liver 0 .00 RPM 225 .04 RPM

ChIP-Seq - click to see more details

Rattus norvegicus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_rnor_1006 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_1006 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_1006 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 25 parental genes, and 94 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000137701 retrocopy
retro_amel_771,
Bos taurus ENSBTAG000000125861 retrocopy
retro_btau_988,
Canis familiaris ENSCAFG000000108654 retrocopies
retro_cfam_1185, retro_cfam_1620, retro_cfam_2165, retro_cfam_614,
Choloepus hoffmanni ENSCHOG000000074015 retrocopies
retro_chof_1105, retro_chof_1300, retro_chof_1822, retro_chof_2000, retro_chof_2397,
Callithrix jacchus ENSCJAG000000039906 retrocopies
retro_cjac_1516, retro_cjac_1534, retro_cjac_1975, retro_cjac_3172, retro_cjac_3400, retro_cjac_4096,
Dasypus novemcinctus ENSDNOG000000132263 retrocopies
retro_dnov_1990, retro_dnov_2113, retro_dnov_2512,
Echinops telfairi ENSETEG000000091844 retrocopies
retro_etel_1440, retro_etel_426, retro_etel_885, retro_etel_925,
Homo sapiens ENSG000001443817 retrocopies
retro_hsap_1006, retro_hsap_2770, retro_hsap_2987, retro_hsap_3151, retro_hsap_3494, retro_hsap_3930, retro_hsap_4018,
Gorilla gorilla ENSGGOG000000082676 retrocopies
retro_ggor_1927, retro_ggor_2069, retro_ggor_2361, retro_ggor_2698, retro_ggor_800, retro_ggor_985,
Loxodonta africana ENSLAFG000000000531 retrocopy
retro_lafr_476,
Macropus eugenii ENSMEUG000000119872 retrocopies
retro_meug_1688, retro_meug_224,
Myotis lucifugus ENSMLUG000000008714 retrocopies
retro_mluc_1458, retro_mluc_2280, retro_mluc_2348, retro_mluc_601,
Macaca mulatta ENSMMUG000000104891 retrocopy
retro_mmul_83,
Monodelphis domestica ENSMODG000000122893 retrocopies
retro_mdom_427, retro_mdom_493, retro_mdom_756,
Mustela putorius furoENSMPUG000000078183 retrocopies
retro_mputfur_1118, retro_mputfur_245, retro_mputfur_434,
Mus musculus ENSMUSG000000259805 retrocopies
retro_mmus_1225, retro_mmus_2494, retro_mmus_3206, retro_mmus_439, retro_mmus_706,
Nomascus leucogenys ENSNLEG000000068747 retrocopies
retro_nleu_1349, retro_nleu_2238, retro_nleu_229, retro_nleu_657, retro_nleu_675, retro_nleu_691, retro_nleu_787,
Otolemur garnettii ENSOGAG000000340535 retrocopies
retro_ogar_2335, retro_ogar_2420, retro_ogar_2740, retro_ogar_3221, retro_ogar_3497,
Pongo abelii ENSPPYG000000130465 retrocopies
retro_pabe_2040, retro_pabe_2244, retro_pabe_2476, retro_pabe_2887, retro_pabe_848,
Pteropus vampyrus ENSPVAG000000083061 retrocopy
retro_pvam_250,
Rattus norvegicus ENSRNOG00000014525 9 retrocopies
retro_rnor_1000, retro_rnor_1006 , retro_rnor_1308, retro_rnor_1578, retro_rnor_1585, retro_rnor_2812, retro_rnor_2835, retro_rnor_596, retro_rnor_905,
Ictidomys tridecemlineatus ENSSTOG000000284701 retrocopy
retro_itri_224,
Tarsius syrichta ENSTSYG000000005136 retrocopies
retro_tsyr_1091, retro_tsyr_1181, retro_tsyr_1445, retro_tsyr_2082, retro_tsyr_395, retro_tsyr_804,
Tursiops truncatus ENSTTRG000000034173 retrocopies
retro_ttru_1661, retro_ttru_1798, retro_ttru_951,
Xenopus tropicalis ENSXETG000000075091 retrocopy
retro_xtro_63,


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