RetrogeneDB ID:

retro_ogar_73

Retrocopy
location
Organism:Bushbaby (Otolemur garnettii)
Coordinates:GL873788.1:1036802..1038056(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOGAG00000016635
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:PGK1
Ensembl ID:ENSOGAG00000011104
Aliases:None
Description:phosphoglycerate kinase 1 [Source:HGNC Symbol;Acc:8896]


Retrocopy-Parental alignment summary:






>retro_ogar_73
ATGTCTTTATCTAAAAAGTTGACTTTGGACAAAGTGGATGTGAAAGGGAAGCGAGTCGTCATGAGAGTAGATTTTAATGT
TCCCATGAAGAACAACCAGATTACAAACAACCAGAGAATCAAGGCTTCCCTCCCCAGCATCAAGTACTGCCTGGACAACG
GGGCCAAGTCAGTGGTTCTCATGAGTCATCTGGGCCGGCCTGATGGCGTCCCCATGCCTGAGAAATACTCCTTAGAGCCC
GTTGCTGCTGAGCTCAAATCCTTGATAGGCAAGGATGTTACGTTCCTGAAGGATTGTGTAGGCCCAGACGTGGAGAAAGC
CTGCGCCAACCCCAATACCGGTTCAGTCATCCTACTGGAGAATCTACGTTTCCATGTGGAGGAAGAAGGGAAGGGCCAAG
ATCCTTCTGGAAAGAAGATTAAGGCTGAGCCAAATCAAATAGAAGCCTTCCGAGCATCACTCTCCAAACTTGGAGATATT
TATGTCAACGATGCCTTTGGAACTGCACACAGAGCTCACAGTTCCATGGTGGGAGTCAATCTGCCCCAGAAGGCATCTGG
ATTCCTCATGAAGAAGGAGCTGGAATACTTTGGCAAAGCCTTAGAAAACCCTGAGAAACCTTTTCTGGCTATACTTGGTG
GAGCCAAAGTGGCAGACAAGATCCAGCTCATCAAAAATATGCTGGATAAGGTCAGTGAAATGATCGTTGGTGGTGGAATG
GCTTTCACCTTCCTCAAGGTCCTCAACAACATGGAGATTGGTGCTTCTCTCTTTGATGCAGAGGGTGCTGCAATTGTCAA
AGATATCATGGCCAAAGCCAGTAGCAAGAATGTAAACATCACTTTTCCTGTTGACTTTGTAACTGGTGACAAGTTTGAAG
AAAATGCTCAAGTTGGACAGGCGTCTTTAGCATCTGGCATACCGGCTGGCTGGATGGGCTTAGACTGTGGTCCTGAGAGC
AACAAGAAGTTTGCTGAAATTGTGGCCCGAGCAAAGCTGATTGTTTGGAACGGACCTTTAGGAGTATTTGAATGGGATGC
CTTTGCTAAGGGAACGAAGACCTTAATGGATGATATTGTGAAAGCCACTTCCAAGGGCTGTGTCACTATTATAGGGGGTG
GAGACACTGCTACTTGCTGTGCCAAATGGAATACAGAAGATAAAGTCAGCCACGTGAGTACTGGAGGCGGTGCCAGTCTA
GAGCTTCTGGAAGGTAAAGTCCTTCCTGGAGTAGATGCCCTCAGCAACTTGTAA

ORF - retro_ogar_73 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.81 %
Parental protein coverage: 76.69 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSLSSKLTLDKLDVKGKRVIMRVDFNVPMKNNQITNNQRIKAAVPSIKFCLDSGAKSVVLMSHLGRPDGV
MSLS.KLTLDK.DVKGKRV.MRVDFNVPMKNNQITNNQRIKA..PSIK.CLD.GAKSVVLMSHLGRPDGV
RetrocopyMSLSKKLTLDKVDVKGKRVVMRVDFNVPMKNNQITNNQRIKASLPSIKYCLDNGAKSVVLMSHLGRPDGV
ParentalPMPDKYSLEPVAVELKSLLSKDVLFLKDCVGPEVEKACANPAAGSVILLENLRFHVEEEGKGKDASGNKV
PMP.KYSLEPVA.ELKSL..KDV.FLKDCVGP.VEKACANP..GSVILLENLRFHVEEEGKG.D.SG.K.
RetrocopyPMPEKYSLEPVAAELKSLIGKDVTFLKDCVGPDVEKACANPNTGSVILLENLRFHVEEEGKGQDPSGKKI
ParentalKAEPAKIEAFRASLSKLGDVYVNDAFGTAHRAHSSMVGVNLPEKAGGFLMKKELNYFAKALESPERPFLA
KAEP..IEAFRASLSKLGD.YVNDAFGTAHRAHSSMVGVNLP.KA.GFLMKKEL.YF.KALE.PE.PFLA
RetrocopyKAEPNQIEAFRASLSKLGDIYVNDAFGTAHRAHSSMVGVNLPQKASGFLMKKELEYFGKALENPEKPFLA
ParentalILGGAKVADKIQLINNMLDKVNEMIIGGGMAFTFLKVLNNMEIGTSLFDEEGAKIVKDLMSKA
ILGGAKVADKIQLI.NMLDKV.EMI.GGGMAFTFLKVLNNMEIG.SLFD.EGA.IVKD.M.KA
RetrocopyILGGAKVADKIQLIKNMLDKVSEMIVGGGMAFTFLKVLNNMEIGASLFDAEGAAIVKDIMAKA

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Otolemur garnettii was not studied using ChIP-Seq data.

EST - click to see more details

Otolemur garnettii was not studied using EST data.

TSS - click to see more details

Otolemur garnettii was not studied using FANTOM5 data.

Lab - click to see more details

retro_ogar_73 was not experimentally validated.

Retrocopy orthology:
Otolemur garnettii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
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 ENSOGAG00000011104 1 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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