RetrogeneDB ID:

retro_cjac_930

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:11:82609554..82610337(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000031318
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PCNA
Ensembl ID:ENSCJAG00000021278
Aliases:None
Description:proliferating cell nuclear antigen [Source:HGNC Symbol;Acc:8729]


Retrocopy-Parental alignment summary:






>retro_cjac_930
ATGTTCCAGGTAAGCCTGGTCCAAGGCTCCACCCTGAAGAATGTGTTGGAGGCCCTCAAGGACCTCATCAGTGAGGCCTG
CCAGGACATTAGCTCAATCAGCTGAATGTGTACAGCATGGACTCATCCTGCCTCTCCTTGGGGCAGCTCACCCAGCACTC
AAAGGGCTTCAATATATGCTGCTGCAACTGCAACCTGGCCATAGCCATGAACCTCACCAGTATGTTCAAAATACTACACT
GTGCTGGATATAAAGATGTCATGACATTTGGGGCTGAAGATAATGCAGACACCTTAGCACTAGCACTTGAAGCACTAAAT
CAGGAGAAAGTTTCAGACTATAGAATGAAGCTAATGGATTTGGATGTTGAACAGCTTGGAATTCCAGAACATGAGTACAG
CTGCGTAGTAAAGATGGCTGCTGGGGAATCTGCATGCATATGTCAAGATCTCAGTCATACTGGAGATGCTGTTGTAATTT
CCTGTGCAAAAGATGGAATGAAATTTTCTGCAACTGTAGGACTTGCAAATGGAAACATTAAATTGTCACAAATAAGTAAT
GTTGATAAAGAAGAGGAAGCTGTTACCATAGAGATGAATGAATCAGTTCAGCTAACTTTTGCACTGATGTACCTGAACTT
CTTCACAAAAGCCACTCCACGCTCTTCTACAGTGACACTTGGTCTGTCTGCAGATGTACTCTGTGTAGAGCATAACACTG
CTAATATGAAACATTTAAAGCAAATACTACTTGCCTCCCAATATTGAGGATGAAGAAGGATCT

ORF - retro_cjac_930 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.11 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalMFEARLVQGSILKKVLEALKDLINEACWDISS-SGVNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMG
MF...LVQGS.LK.VLEALKDLI.EAC.DISS....N..SMDSS..SL.QLT..S.GF....C..NLA..
RetrocopyMFQVSLVQGSTLKNVLEALKDLISEACQDISS<NQLNVYSMDSSCLSLGQLTQHSKGFNICCCNCNLAIA
ParentalVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKM
.NLTSM.KIL.CAG..D..T..AEDNADTLAL..EA.NQEKVSDY.MKLMDLDVEQLGIPE.EYSCVVKM
RetrocopyMNLTSMFKILHCAGYKDVMTFGAEDNADTLALALEALNQEKVSDYRMKLMDLDVEQLGIPEHEYSCVVKM
ParentalPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSNVDKEEEAVTIEMNEPVQLTFAL
..GE.A.IC.DLSH.GDAVVISCAKDG.KFSA...L.NGNIKLSQ.SNVDKEEEAVTIEMNE.VQLTFAL
RetrocopyAAGESACICQDLSHTGDAVVISCAKDGMKFSATVGLANGNIKLSQISNVDKEEEAVTIEMNESVQLTFAL
ParentalRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKY-YLAP-KIEDEEGS
.YLNFFTKATP.SSTVTL..SADV.L.VE...A.M.HLK..Y..P..IEDEEGS
RetrocopyMYLNFFTKATPRSSTVTLGLSADV-LCVEHNTANMKHLKQ>YYLPPNIEDEEGS

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 .00 RPM 24 .43 RPM
SRP051959_heart 0 .00 RPM 9 .70 RPM
SRP051959_kidney 0 .00 RPM 18 .64 RPM
SRP051959_liver 0 .00 RPM 12 .52 RPM
SRP051959_lung 0 .02 RPM 13 .73 RPM
SRP051959_lymph_node 0 .00 RPM 18 .83 RPM
SRP051959_skeletal_muscle 0 .00 RPM 13 .02 RPM
SRP051959_spleen 0 .00 RPM 22 .18 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_930 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_930 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_930 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 24 parental genes, and 43 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000090891 retrocopy
retro_amel_1719,
Canis familiaris ENSCAFG000000060302 retrocopies
retro_cfam_1626, retro_cfam_946,
Callithrix jacchus ENSCJAG00000021278 3 retrocopies
retro_cjac_2159, retro_cjac_2175, retro_cjac_930 ,
Cavia porcellus ENSCPOG000000092421 retrocopy
retro_cpor_315,
Erinaceus europaeus ENSEEUG000000030691 retrocopy
retro_eeur_358,
Echinops telfairi ENSETEG000000065773 retrocopies
retro_etel_1152, retro_etel_1539, retro_etel_2217,
Felis catus ENSFCAG000000090682 retrocopies
retro_fcat_1363, retro_fcat_1729,
Homo sapiens ENSG000001326463 retrocopies
retro_hsap_3067, retro_hsap_4817, retro_hsap_857,
Gorilla gorilla ENSGGOG000000016952 retrocopies
retro_ggor_2107, retro_ggor_700,
Myotis lucifugus ENSMLUG000000016931 retrocopy
retro_mluc_1658,
Macaca mulatta ENSMMUG000000132593 retrocopies
retro_mmul_1059, retro_mmul_1960, retro_mmul_2570,
Monodelphis domestica ENSMODG000000116491 retrocopy
retro_mdom_933,
Mustela putorius furoENSMPUG000000061952 retrocopies
retro_mputfur_330, retro_mputfur_629,
Mus musculus ENSMUSG000000273421 retrocopy
retro_mmus_114,
Nomascus leucogenys ENSNLEG000000077262 retrocopies
retro_nleu_2192, retro_nleu_424,
Otolemur garnettii ENSOGAG000000331612 retrocopies
retro_ogar_1258, retro_ogar_2960,
Procavia capensis ENSPCAG000000105001 retrocopy
retro_pcap_130,
Pongo abelii ENSPPYG000000107953 retrocopies
retro_pabe_2542, retro_pabe_3745, retro_pabe_690,
Pan troglodytes ENSPTRG000000132223 retrocopies
retro_ptro_2068, retro_ptro_3206, retro_ptro_595,
Pteropus vampyrus ENSPVAG000000028651 retrocopy
retro_pvam_193,
Rattus norvegicus ENSRNOG000000212641 retrocopy
retro_rnor_1035,
Sorex araneus ENSSARG000000040701 retrocopy
retro_sara_640,
Sus scrofa ENSSSCG000000306421 retrocopy
retro_sscr_113,
Tursiops truncatus ENSTTRG000000153682 retrocopies
retro_ttru_1868, retro_ttru_440,


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