RetrogeneDB ID:

retro_pabe_848

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:12:56283517..56285230(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HSPD1
Ensembl ID:ENSPPYG00000013046
Aliases:None
Description:60 kDa heat shock protein, mitochondrial precursor [Source:RefSeq peptide;Acc:NP_001127086]


Retrocopy-Parental alignment summary:






>retro_pabe_848
ATGCTTCCGTTACCCACAGTCTTTTGCCAGATGAGACTTGTGTCCAGGGTACTGGCTCCTCATCTCACTGGGGCTTATGC
CAAAGATGTAAAATTTGGTGCAGATGCCCGAGCCTTAATGCTTCAAGGTATAGACCTTTTAGCTGATGCTGTAGCCCTTA
CAGTGGGGCCAAAGGGAAGAAGAACAGTGATTATTAACAGAGCTGGGGAAGTCCCAAAGTAACAAAAGATGGTGTGACTG
TTGCAAAGTCAATAGACTTAAAGGATAAATATAAAAACATTGGAGCTAAACTTGTTCAAGATGTTGCCAATAACACAAAT
GAAGAGACTGGGGATGGCACTACCACTGCTACTGTACTGGCACGCTCTATAGCCAAGGAAGGCTTCGAGAAGATTAGCAA
AGGTGCTAATCCAGTGGAAATCAGGAGAGGTGTGATGTTAGTTGTTGATGCTGTAATTGCTGAACTTAAAAAGCAGTCTA
AACCTGTGACCACCCCTGAAGAAATTGCACAGGTTGCTACAATTTCTGCAAACGGAGACAAAGAAATTGGCAATATCTCT
GATGCAGTGAAAAAGGTTGGAAGAAAGGATGTCATCACAGTAAAGGATGGAAAAACACTGAATGATGAATTAGAAATTAT
TGAAGGCATAAAGTTTGATCGAGGCTATATTTCTTCATACTTTATTAATATATCAAAAGGACAGAAATGTGAATTCCAGG
ATGCCTATGTTCTGCTGAGTGAAAAGAAAATTTCTAGTGTCCAGTCCATTGTACCTGCTCTTGAAATTGCCAATGCTCAC
CGTAAGCCTTTGGTCATAATCGCTGAAGACGTTGATGGAGAAGCTCTAAGTACACTCGTCTTGAATAGGCTAAAGATTGG
TCTTCAGGTTGTGGCAATCAAGGCTCCAGGGTTTGGTGACAATAGAAAGAACCAGCTTAAAGATATGGCAATTGCTACTG
GTAGTGCAGTGTTTGGAGAAGAGGGGTTGACCCTAAATCTTGAAGATGTTCAGCCTCATGACTTAGGAAACATTGGAGAG
GTCATTGTGACCAAAGACGATGCCATGCTCTTAAAAGGAAAAGGTGACAAGGCTCAAATTGAAAAACGTATTCAAGAAAT
CATTGAGCAGTTAGATGTCACAACTAGTGAATATGAAAAGGAAAAACTGAACGGCTGGCAAAACTTTCAGATGTAGTAGC
TCTGCTGAAGGTTGGTGGGACAAGTGATGCTGAAGTGAATGAAAAGAAAGACAGAGTTCGGATGCCCTTAATGCTACAAG
AGCTGCTGTTGAAGAAGGCATTGTATTTGGAGGGGGTTGTGCCCTGCTTCGATGCATTCTAGCCTTGGACTCACTGACTC
CAGCTAATGAAGATCAAAAAATTGGTATAGAAATTATTAAAAGAACACTCAAAATTCCAGCAATGACCATTGCTAAGAAT
GCAGGTGTTGAAGGATCTTTGATAGTTGAGAAAATTATGCAAATTTCCTCAGAAGTTGGTTATGATGCTATGGTTGGAGA
TTTTGTGAATATGGTGGAAAAATGAATTATCGACCCAACAAAGGTTGCGAGAACTGCTTTATTGGATGCTGCTGGTGTGA
CCTCTCTGTTAACTACAGCAGAAGTTGTAGTCACAGAAATTCCTAAAGAAGAGAAGGACCCTGGAATGGGTGCAATGGGT
GGAATGGGAGGTGGTATGGGAAGTGGCATGTTC

ORF - retro_pabe_848 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.68 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMLRLPTVFRQMRPVSRVLAPHLTRAYAKDVKFGADARALMLQGVDLLADAVAVTMGPKGR-TVIIE-QSW
ML.LPTVF.QMR.VSRVLAPHLT.AYAKDVKFGADARALMLQG.DLLADAVA.T.GPKGR.TVII..QSW
RetrocopyMLPLPTVFCQMRLVSRVLAPHLTGAYAKDVKFGADARALMLQGIDLLADAVALTVGPKGRRTVIIN<QSW
ParentalGSPKVTKDGVTVAKSIDLKDKYKNIGAKLVQDVANNTNEEAGDGTTTATVLARSIAKEGFEKISKGANPV
GSPKVTKDGVTVAKSIDLKDKYKNIGAKLVQDVANNTNEE.GDGTTTATVLARSIAKEGFEKISKGANPV
RetrocopyGSPKVTKDGVTVAKSIDLKDKYKNIGAKLVQDVANNTNEETGDGTTTATVLARSIAKEGFEKISKGANPV
ParentalEIRRGVMLAVDAVIAELKKQSKPVTTPEEIAQVATISANGDKEIGNIISDAMKKVGRKGVITVKDGKTLN
EIRRGVML.VDAVIAELKKQSKPVTTPEEIAQVATISANGDKEIGNI.SDA.KKVGRK.VITVKDGKTLN
RetrocopyEIRRGVMLVVDAVIAELKKQSKPVTTPEEIAQVATISANGDKEIGNI-SDAVKKVGRKDVITVKDGKTLN
ParentalDELEIIEGMKFDRGYISPYFINTSKGQKCEFQDAYVLLSEKKISSVQSIVPALEIANAHRKPLVIIAEDV
DELEIIEG.KFDRGYIS.YFIN.SKGQKCEFQDAYVLLSEKKISSVQSIVPALEIANAHRKPLVIIAEDV
RetrocopyDELEIIEGIKFDRGYISSYFINISKGQKCEFQDAYVLLSEKKISSVQSIVPALEIANAHRKPLVIIAEDV
ParentalDGEALSTLVLNRLKVGLQVVAVKAPGFGDNRKNQLKDMAIATGGAVFGEEGLTLNLEDVQPHDLGKVGEV
DGEALSTLVLNRLK.GLQVVA.KAPGFGDNRKNQLKDMAIATG.AVFGEEGLTLNLEDVQPHDLG..GEV
RetrocopyDGEALSTLVLNRLKIGLQVVAIKAPGFGDNRKNQLKDMAIATGSAVFGEEGLTLNLEDVQPHDLGNIGEV
ParentalIVTKDDAMLLKGKGDKAQIEKRIQEIIEQLDVTTSEYE-KEKLNERLAKLSDGVAVLKVGGTSDVEVNEK
IVTKDDAMLLKGKGDKAQIEKRIQEIIEQLDVTTSEYE.K.K..ERLAKLSD.VA.LKVGGTSD.EVNEK
RetrocopyIVTKDDAMLLKGKGDKAQIEKRIQEIIEQLDVTTSEYE<KGK-TERLAKLSDVVALLKVGGTSDAEVNEK
ParentalKDRV-TDALNATRAAVEEGIVLGGGCALLRCIPALDSLTPANEDQKIGIEIIKRTLKIPAMTIAKNAGVE
KDRV..DALNATRAAVEEGIV.GGGCALLRCI.ALDSLTPANEDQKIGIEIIKRTLKIPAMTIAKNAGVE
RetrocopyKDRV<SDALNATRAAVEEGIVFGGGCALLRCILALDSLTPANEDQKIGIEIIKRTLKIPAMTIAKNAGVE
ParentalGSLIVEKIMQSSSEVGYDAMVGDFVNMVEKGIIDPTKVVRTALLDAAGVASLLTTAEVVVTEIPKEEKDP
GSLIVEKIMQ.SSEVGYDAMVGDFVNMVEK.IIDPTKV.RTALLDAAGV.SLLTTAEVVVTEIPKEEKDP
RetrocopyGSLIVEKIMQISSEVGYDAMVGDFVNMVEK*IIDPTKVARTALLDAAGVTSLLTTAEVVVTEIPKEEKDP
ParentalGMGAMGGMGGGMGGGMF
.........GGMG.GMF
RetrocopyXXXXXXXXXGGMGSGMF

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 .50 RPM 98 .36 RPM
SRP007412_cerebellum 1 .58 RPM 94 .97 RPM
SRP007412_heart 0 .06 RPM 108 .97 RPM
SRP007412_kidney 0 .17 RPM 263 .12 RPM
SRP007412_liver 1 .62 RPM 241 .60 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_848 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_848 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_848 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1006
Gorilla gorilla retro_ggor_800
Parental genes homology:
Parental genes homology involve 18 parental genes, and 74 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000137701 retrocopy
retro_amel_771,
Canis familiaris ENSCAFG000000108654 retrocopies
retro_cfam_1185, retro_cfam_1620, retro_cfam_2165, retro_cfam_614,
Callithrix jacchus ENSCJAG000000039906 retrocopies
retro_cjac_1516, retro_cjac_1534, retro_cjac_1975, retro_cjac_3172, retro_cjac_3400, retro_cjac_4096,
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 ENSPPYG00000013046 5 retrocopies
retro_pabe_2040, retro_pabe_2244, retro_pabe_2476, retro_pabe_2887, retro_pabe_848 ,
Rattus norvegicus ENSRNOG000000145259 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,
Xenopus tropicalis ENSXETG000000075091 retrocopy
retro_xtro_63,


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