RetrogeneDB ID:

retro_btau_988

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:22:13679566..13681231(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSBTAG00000047441
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:BT.89909
Ensembl ID:ENSBTAG00000012586
Aliases:HSPD1, HSP60
Description:60 kDa heat shock protein, mitochondrial [Source:RefSeq peptide;Acc:NP_001160080]


Retrocopy-Parental alignment summary:






>retro_btau_988
ATGCTTCGATTACCCGCAGTCCTTCGTCAAATGAGGCCAGTGTCCAGGGCACTGGCTCTTCATCTCACTCGGGCTTATGC
CAAAGATGTAAAATTCGGTGCAGATGCTCGAGCCTTAATGCTTCAAGGTGTAGACCTTTTAGCCGATGCTGTAGCCGTTA
CTATGGGGCCAAAGGGAAGGACAGTGATTATTGAACAGAGTTGGGGAAGTCCCAGAGTGACAAAAGATGGTGTGACTGTT
GCAAAGTCTATTGATTTAAAAGATAAATATAAAAATATTGGCGCTAAACTTGTTCAAGATGTTGCCAATAACACAAATGA
AGAGGCGGGGGATGGCACCACTACTGCTACTGTACTGGCACGCTCTATTGCCAAGGAAGGCTTCGAGAAGATTAGCAAAG
GTGCTAATCCAGTGGAAATCAGGAGAGGTGTGATGTTAGCTGTTGATGCTGTAATTGTTGAACTTAAGAAGCAGTCTAAA
CCTGTGACAACCCCCGAAGAGATTGCTCAGGTTGCTACAATTTCTGCAAATGGAGACAAAGAAATTGGCAACATCATTTC
TGATGCCATGAAAAAAGTTGGAAGAAAGGGTGTTATCACAGTAAAGGATGGAAAAACACTGAATGATGAATTAGAAATTA
TTGAAGGCATGAAGTTTGACAGAGGATATATTTCTCCATACTTTATTAATACATCAAAAGGTCAGAAATGTGAATTCCAA
GATGCATATGTTCTATTGAGTGAAAAGAAAATTTCTAGTGTCCAATCCATTGTTCCTGCTCTTGAAATTGCCAATGCTCA
CCGGAAGCCCTTGGTCATAATTGCTGAAGATGTGGATGGAGAAGCTCTAAGTACCCTTGTTTTGAATAGGTTGAAAGTTG
GTCTTCAAGTTGTGGCAGTCAAAGCTCCAGGTTTTGGTGACAATAGAAAGAACCAGCTTAAAGACATGGCTATTGCTACT
GGTGGTGCAGTATTTGGAGAAGAAGGACTAAATCTAAATCTTGAAGATGTTCAGCCTCATGACTTAGGAAAAGTTGGAGA
GGTCATTGTGACCAAAGATGATGCCATGCTCTTGAAAGGAAAAGGTGACAAGGCTCAAATTGAGAAGCGTATCCAAGAGA
TCATTGAGCAGTTAGATATCACAACTAGTGAATATGAAAAGGAAAAACTGAATGAACGTCTGGCAAAACTCTCAGATGGT
GTTGCTGTGTTGAAGGTTGGTGGGACAAGTGATGTTGAAGTGAATGAAAAGAAAGACAGAGTTACAGATGCTCTTAATGC
CACACGAGCTGCTGTTGAAGAAGGCATTGTTCTGGGAGGGGACTGTGCCCTGCTTCGGTGCATTCCAGCCTTGGAGTCAA
TAACTCCAGCTAATGAAGATCAAAAAACAGGTATAGAAATAATTAAAAAAACACTCAAAATTCCTGCAATGACCATTGCT
AAGAATGCAGGTGTTGAAGGATCATTGATAGTTGAGAAAATTATGCAGAGTTCTTCAGAAGTCGGTTATGATGCTATGCT
TGGAGATTTTGTGAATATGGTGGAAAAAGGAATCATTGATCCAACTAAGGTTGTAAGAACTGCATTACTGGATGCTGCCG
GAGTGGCCTCTCTCTTAACAACAGCAGAAGTTGTCGTCACAGAAATTCCTAAAGAAGAGAAGGAT

ORF - retro_btau_988 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 99.28 %
Parental protein coverage: 96.86 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMLRLPAVLRQMRPVSRALAPHLTRAYAKDVKFGADARALMLQGVDLLADAVAVTMGPKGRTVIIEQSWGS
MLRLPAVLRQMRPVSRALA.HLTRAYAKDVKFGADARALMLQGVDLLADAVAVTMGPKGRTVIIEQSWGS
RetrocopyMLRLPAVLRQMRPVSRALALHLTRAYAKDVKFGADARALMLQGVDLLADAVAVTMGPKGRTVIIEQSWGS
ParentalPKVTKDGVTVAKSIDLKDKYKNIGAKLVQDVANNTNEEAGDGTTTATVLARSIAKEGFEKISKGANPVEI
P.VTKDGVTVAKSIDLKDKYKNIGAKLVQDVANNTNEEAGDGTTTATVLARSIAKEGFEKISKGANPVEI
RetrocopyPRVTKDGVTVAKSIDLKDKYKNIGAKLVQDVANNTNEEAGDGTTTATVLARSIAKEGFEKISKGANPVEI
ParentalRRGVMLAVDAVIAELKKQSKPVTTPEEIAQVATISANGDKEIGNIISDAMKKVGRKGVITVKDGKTLNDE
RRGVMLAVDAVI.ELKKQSKPVTTPEEIAQVATISANGDKEIGNIISDAMKKVGRKGVITVKDGKTLNDE
RetrocopyRRGVMLAVDAVIVELKKQSKPVTTPEEIAQVATISANGDKEIGNIISDAMKKVGRKGVITVKDGKTLNDE
ParentalLEIIEGMKFDRGYISPYFINTSKGQKCEFQDAYVLLSEKKISSVQSIVPALEIANAHRKPLVIIAEDVDG
LEIIEGMKFDRGYISPYFINTSKGQKCEFQDAYVLLSEKKISSVQSIVPALEIANAHRKPLVIIAEDVDG
RetrocopyLEIIEGMKFDRGYISPYFINTSKGQKCEFQDAYVLLSEKKISSVQSIVPALEIANAHRKPLVIIAEDVDG
ParentalEALSTLVLNRLKVGLQVVAVKAPGFGDNRKNQLKDMAIATGGAVFGEEGLNLNLEDVQPHDLGKVGEVIV
EALSTLVLNRLKVGLQVVAVKAPGFGDNRKNQLKDMAIATGGAVFGEEGLNLNLEDVQPHDLGKVGEVIV
RetrocopyEALSTLVLNRLKVGLQVVAVKAPGFGDNRKNQLKDMAIATGGAVFGEEGLNLNLEDVQPHDLGKVGEVIV
ParentalTKDDAMLLKGKGDKAQIEKRIQEIIEQLDITTSEYEKEKLNERLAKLSDGVAVLKVGGTSDVEVNEKKDR
TKDDAMLLKGKGDKAQIEKRIQEIIEQLDITTSEYEKEKLNERLAKLSDGVAVLKVGGTSDVEVNEKKDR
RetrocopyTKDDAMLLKGKGDKAQIEKRIQEIIEQLDITTSEYEKEKLNERLAKLSDGVAVLKVGGTSDVEVNEKKDR
ParentalVTDALNATRAAVEEGIVLGGGCALLRCIPALESITPANEDQKTGIEIIKKTLKIPAMTIAKNAGVEGSLI
VTDALNATRAAVEEGIVLGG.CALLRCIPALESITPANEDQKTGIEIIKKTLKIPAMTIAKNAGVEGSLI
RetrocopyVTDALNATRAAVEEGIVLGGDCALLRCIPALESITPANEDQKTGIEIIKKTLKIPAMTIAKNAGVEGSLI
ParentalVEKIMQSSSEVGYDAMLGDFVNMVEKGIIDPTKVVRTALLDAAGVASLLTTAEVVVTEIPKEEKD
VEKIMQSSSEVGYDAMLGDFVNMVEKGIIDPTKVVRTALLDAAGVASLLTTAEVVVTEIPKEEKD
RetrocopyVEKIMQSSSEVGYDAMLGDFVNMVEKGIIDPTKVVRTALLDAAGVASLLTTAEVVVTEIPKEEKD

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
ERP005899_liver 14 .56 RPM 156 .66 RPM
ERP005899_muscle 18 .21 RPM 184 .29 RPM
SRP017611_brain 6 .30 RPM 63 .86 RPM
SRP017611_kidney 27 .74 RPM 228 .79 RPM
SRP017611_liver 19 .86 RPM 160 .61 RPM
SRP030211_testis 3 .57 RPM 84 .30 RPM

ChIP-Seq - click to see more details

Bos taurus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_btau_988 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_988 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_988 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 16 parental genes, and 51 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000137701 retrocopy
retro_amel_771,
Bos taurus ENSBTAG00000012586 1 retrocopy
retro_btau_988 ,
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,
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,
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,
Otolemur garnettii ENSOGAG000000340535 retrocopies
retro_ogar_2335, retro_ogar_2420, retro_ogar_2740, retro_ogar_3221, retro_ogar_3497,
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,
Tursiops truncatus ENSTTRG000000034173 retrocopies
retro_ttru_1661, retro_ttru_1798, retro_ttru_951,
Xenopus tropicalis ENSXETG000000075091 retrocopy
retro_xtro_63,


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