RetrogeneDB ID:

retro_cjac_4171

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:X:59791980..59792780(-)
Located in intron of:ENSCJAG00000001702
Retrocopy
information
Ensembl ID:ENSCJAG00000033261
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000021082
Aliases:None
Description:Phosphoglycerate kinase [Source:UniProtKB/TrEMBL;Acc:F7FF54]


Retrocopy-Parental alignment summary:






>retro_cjac_4171
ATGTGGCTTTCTAATAAGCTGACACTGGACAAGCTGCAAGTAAAAGGGAAGCGGGTCATTATGAGAGTCGACTTCAGTGA
AGAAAACCAGATAACAACCAATCACAGGATTAAGGCTACTGTCCCAAACATCAAATTCTGCTTGGAAAATGGAGCCAAGT
CAGTAGTTTTTGTGAGCTACCTAGGCTGGCCTGATGGTGTCCCTATGCCTGACAAGTACTCCTTAAAGCTGGTTGCTGTA
GAACTCAAATCTCTGCTGGGCAAGGATGTTCTGTTCTTGAAGGGCTGTGCAGGCCCAGAAGTGGAGAAAGCCTGTGCCAG
CCCAGCTGCTGGGTCTGTCATCCTGCTGGAGAACCTTCGCTTTCACATGGAGGAAGAAGGGAAGGGAAAAGATGCTTCTG
GGAACAAGGTTAAAGCCGAGCCAGCCAAAATAGAAGGTTTCTGAGCTTCACTTTCCAAGCTGGGCATGTCTATATCAATG
ATGGCACTTTTGGCACTGCTCACAGAACCCACAGCTCCATGGTAGGAGTCAGTCTGCCACTGAAGGCTGGTGGGTTTTTG
ATGAAGAAGAAGCTAAACTACTTTGCCAAGGCCATTGAGAGCCCACAGTGACCTTTCCTGATGATCCTGGGTAGAGCTAA
AGTTACAGACAAGACCCAGCTGATCAATAATATGCTGGACAAAGTCACTGAGATGATTATTGGTGGTGGTGGAATGGCTT
TTACCTTCCTTAAGGCACTCGGCAACATGGAGATTGCCACTTTTCTGTTTGATGAAGAGGGAGCCAAGATTGTCAAAGAC

ORF - retro_cjac_4171 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.55 %
Parental protein coverage: 64.27 %
Number of stop codons detected: 2
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalMSLSNKLTLDKLDVKGKRVVMRVDFNVPMKNNQITNNQRIKAAVPSIKFCLDNGAKSVVLMSHLGRPDGV
M.LSNKLTLDKL.VKGKRV.MRVDF......NQIT.N.RIKA.VP.IKFCL.NGAKSVV..S.LG.PDGV
RetrocopyMWLSNKLTLDKLQVKGKRVIMRVDFS---EENQITTNHRIKATVPNIKFCLENGAKSVVFVSYLGWPDGV
ParentalPMPDKYSLEPVAVELKSLLGKDVLFLKDCVGPEVEKACANPAAGSIILLENLRFYVEEEGKGKDASGNKV
PMPDKYSL..VAVELKSLLGKDVLFLK.C.GPEVEKACA.PAAGS.ILLENLRF..EEEGKGKDASGNKV
RetrocopyPMPDKYSLKLVAVELKSLLGKDVLFLKGCAGPEVEKACASPAAGSVILLENLRFHMEEEGKGKDASGNKV
ParentalKAEPAKIEAFRASLSKL-GDVYVND-AFGTAHRAHSSMVGVNLPQKAGGFLMKKELNYFAKALESPERPF
KAEPAKIE.F.ASLSKL.G.VY.ND..FGTAHR.HSSMVGV.LP.KAGGFLMKK.LNYFAKA.ESP..PF
RetrocopyKAEPAKIEGF*ASLSKL<GHVYINDGTFGTAHRTHSSMVGVSLPLKAGGFLMKKKLNYFAKAIESPQ*PF
ParentalLAILGGAKVADKIQLINNMLDKVNEMII-GGGMAFTFLKVLNNMEIGTSLFDEEGAKIVKD
L.ILG.AKV.DK.QLINNMLDKV.EMII.GGGMAFTFLK.L.NMEI.T.LFDEEGAKIVKD
RetrocopyLMILGRAKVTDKTQLINNMLDKVTEMIIGGGGMAFTFLKALGNMEIATFLFDEEGAKIVKD

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
SRP051959_colon 0 .16 RPM 44 .49 RPM
SRP051959_heart 0 .09 RPM 54 .87 RPM
SRP051959_kidney 0 .13 RPM 79 .78 RPM
SRP051959_liver 0 .04 RPM 108 .24 RPM
SRP051959_lung 0 .05 RPM 30 .78 RPM
SRP051959_lymph_node 0 .07 RPM 34 .98 RPM
SRP051959_skeletal_muscle 0 .02 RPM 86 .22 RPM
SRP051959_spleen 0 .06 RPM 34 .94 RPM

ChIP-Seq - click to see more details

Callithrix jacchus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cjac_4171 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_4171 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_4171 has 0 orthologous retrocopies within eutheria group .

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 ENSCJAG00000021082 3 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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