RetrogeneDB ID:

retro_btau_1021

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:23:22221079..22222330(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSBTAG00000019762
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PGK1
Ensembl ID:ENSBTAG00000000894
Aliases:None
Description:Phosphoglycerate kinase 1 [Source:UniProtKB/Swiss-Prot;Acc:Q3T0P6]


Retrocopy-Parental alignment summary:






>retro_btau_1021
ATGTCTCTTTCTAAGAAGTTAACTTTGGACAAAGTGGATGTGAAAGGGAAGCGAGTCGTCATGAGAGTTGACTTCAATGT
CCCCATGAAGAAGAACCAGATTACAAACAACCAAAGAATCAAGGCCTCTCTCCCAAGCATCAAGTACTGTCTGGATAATG
GAGCCAAGTCAGTAGTTCTTATGAGTCATTTAGGTAGACCTGATGGTGTTCCGATGCCTGATAAATACTCCTTAGAGCCT
GTTGCTGCTGAACTCAAATCCTTGTTGGGCAAAGACGTAGTGTTCCTAAAGGACTGTGTGGGTCCGGAAGTGGAGAAGGC
TTGTGCCAGCCCAGCCACCGGTACAGTCATCTTGCTGGAGAACCTGCGCTTTCATGTGGAAGAAGAAGGGAAGGGCCAAG
ATCCTTCTGGAAATAAGCTTAAAGCTGAGCCAGATAAAATAGAAGCCTTCCGAGCATCCCTCTCCAAGCTAGGGGATGTG
TATGTCAACGATGCTTTTGGCACAGCTCACCGGGCCCACAGTTCCATGGTGGGAGTGAATCTTCCCCAGAAGGCATCTGG
ATTCCTGATGAAAAAGGAGCTAGATTACTTCTCCAAAGCCTTGGAAAACCCAGAGAGACCATTTCTGGCTATACTTGGTG
GAGCCAAAGTGGCAGACAAGATCCAACTCATCAAAAATATGCTGGACAAAGTCAATGAGATGATTATTGGTGGAGGAATG
GCTTACACCTTCCTTAAGGTATTGAACAACATGGAGATTGGTGCTTCCTTGTTCGATGAAGAGGGAGCCAAGATTGTCAA
AGAAATTATGACCAAAGCTGGAAAAAATAGTGTGAACATTACCTTTCCTGTTGACTTTGTCACTGCTGACAAGTTTGAGG
AGAATGCTAAGGTTGGCCAAGCCACTGTAGCATCAGGAATACCTGCCGGCTGGATGGGTTTGGACTGTGGTCCTGAGACC
ATTAAGAAGTATGCAGACGTGGTGGGGCGAGCCAAGTTAATTGTGTGGAATGGACCTGTAGGCGTATTTGAATGGGATGC
TTTTGCTAAAGGAACAAAAGCCCTCATGGATGAAGTTGTGAAAGCCACTTCCAAGGGCTGTATCACCATTATAGGAGGTG
GAGACACTGCTACTTGCTGTGCCAAATGGAACACTGAAGATAAAGTCAGTCACGTGAGCACTGGAGGAGGTGCCAGTCTG
GAGCTTCTGGAAGGTAAAGTCCTTCCTGGAGTGAATGCCCTCAGCAATCTG

ORF - retro_btau_1021 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.97 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMSLSNKLTLDKLDVKGKRVVMRVDFNVPMKNNQITNNQRIKAAVPSIKYCLDSGAKSVVLMSHLGRPDGV
MSLS.KLTLDK.DVKGKRVVMRVDFNVPMK.NQITNNQRIKA..PSIKYCLD.GAKSVVLMSHLGRPDGV
RetrocopyMSLSKKLTLDKVDVKGKRVVMRVDFNVPMKKNQITNNQRIKASLPSIKYCLDNGAKSVVLMSHLGRPDGV
ParentalPMPDKYSLQPVAVELKSLLGKDVLFLKDCVGPEVEKACADPAAGSVILLENLRFHVEEEGKGKDASGNKV
PMPDKYSL.PVA.ELKSLLGKDV.FLKDCVGPEVEKACA.PA.G.VILLENLRFHVEEEGKG.D.SGNK.
RetrocopyPMPDKYSLEPVAAELKSLLGKDVVFLKDCVGPEVEKACASPATGTVILLENLRFHVEEEGKGQDPSGNKL
ParentalKAEPTKIEAFRASLSKLGDVYVNDAFGTAHRAHSSMVGVNLPKKAGGFLMKKELNYFAKALESPERPFLA
KAEP.KIEAFRASLSKLGDVYVNDAFGTAHRAHSSMVGVNLP.KA.GFLMKKEL.YF.KALE.PERPFLA
RetrocopyKAEPDKIEAFRASLSKLGDVYVNDAFGTAHRAHSSMVGVNLPQKASGFLMKKELDYFSKALENPERPFLA
ParentalILGGAKVADKIQLISNMLDKVNEMIIGGGMAFTFLKVLNNMEIGTSLFDEEGSKIVKDLMSKADKNGVKI
ILGGAKVADKIQLI.NMLDKVNEMIIGGGMA.TFLKVLNNMEIG.SLFDEEG.KIVK..M.KA.KN.V.I
RetrocopyILGGAKVADKIQLIKNMLDKVNEMIIGGGMAYTFLKVLNNMEIGASLFDEEGAKIVKEIMTKAGKNSVNI
ParentalTLPVDFVTADKFDENAKTGQATVASGIPAGWMGLDCGPESSKKYAEAVARAKQIVWNGPVGVFEWEAFAR
T.PVDFVTADKF.ENAK.GQATVASGIPAGWMGLDCGPE..KKYA..V.RAK.IVWNGPVGVFEW.AFA.
RetrocopyTFPVDFVTADKFEENAKVGQATVASGIPAGWMGLDCGPETIKKYADVVGRAKLIVWNGPVGVFEWDAFAK
ParentalGTKALMDEVVKATSRGCITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGKVLPGVDALSSV
GTKALMDEVVKATS.GCITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGKVLPGV.ALS..
RetrocopyGTKALMDEVVKATSKGCITIIGGGDTATCCAKWNTEDKVSHVSTGGGASLELLEGKVLPGVNALSNL

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 0 .00 RPM 50 .76 RPM
ERP005899_muscle 0 .00 RPM 177 .00 RPM
SRP017611_brain 0 .00 RPM 215 .01 RPM
SRP017611_kidney 0 .00 RPM 304 .06 RPM
SRP017611_liver 0 .00 RPM 53 .61 RPM
SRP030211_testis 393 .43 RPM 29 .96 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_1021 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_1021 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_1021 has 9 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_90
Pan troglodytes retro_ptro_2
Gorilla gorilla retro_ggor_2420
Pongo abelii retro_pabe_134
Macaca mulatta retro_mmul_144
Callithrix jacchus retro_cjac_137
Sus scrofa retro_sscr_933
Canis familiaris retro_cfam_510
Equus caballus retro_ecab_557
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 ENSBTAG00000000894 1 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 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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