RetrogeneDB ID:

retro_ptro_595

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:11:19062858..19063589(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PCNA
Ensembl ID:ENSPTRG00000013222
Aliases:None
Description:Proliferating cell nuclear antigen [Source:UniProtKB/TrEMBL;Acc:H2QJX3]


Retrocopy-Parental alignment summary:






>retro_ptro_595
ATGTTCGAGGTACACCTGGTCCAGGGCTCCATCCTGAAGAATGTGTTGGAGGCCCTCGAGGACCTCATCAGTGAGGCCTG
CCGGGACATCAGCTCAAGCAGCTGAATGTGCACAGCATAGACTCGTTCTGCATCTCCTCGTGGCAGCTCACCCACTGCTC
CAAGGGCTTCAACACGTGCTGCTGCGACTACAACCTGGCCATAGGCATGAACCTATCCAGTATGTTCAAAATACTAAACT
GTGCTGGCAATGAAGATGTCATGACGTTAGGAGCTGAAGATAATGCAGACAACTTAGCACTAGTATTTGAAGCACTAAAT
CAGGAGAAAGTTTTGGATTATAAAATGAAGCTAATGGATTTGGATATTGAACAACTTGGAATTCCAAAACAAGAGTACAG
CTGTGTAGTAAAGATGCCTGCTGGTGAATTTGCATGCATATGCTGAGATCTCAATCATATTGGAGATGTTGTTGTAATTT
CCTGTGCAAAAGATGGAGTGAAATTTTCTGCAACTGGAGAACTTGCAAATGGAAACATTAAATTGTCACAAATAAGTAAT
GTTGATAAAGAGAAGGAAGCTGTTGCCATAGAGATGAATGAACTAGTTCAGCTAACTTTTGCACTGATGTACCTGAACTT
CTTCACAAAAGCCACTCCACGCTCTTCTACAGTGACACTCGGTATGTCTGCAGACGTACCACTTGTAGAGTATAACATTG
CTAATATGGGA

ORF - retro_ptro_595 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.64 %
Parental protein coverage: 93.87 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMFEARLVQGSILKKVLEALKDLINEACWDISSSG-VNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMG
MFE..LVQGSILK.VLEAL.DLI.EAC.DISSS...N..S.DS...S..QLT..S.GF.T..CD.NLA.G
RetrocopyMFEVHLVQGSILKNVLEALEDLISEACRDISSSS<LNVHSIDSFCISSWQLTHCSKGFNTCCCDYNLAIG
ParentalVNLTSMSKILKCAGNEDIITLRAEDNADTLALVFEAPNQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKM
.NL.SM.KIL.CAGNED..TL.AEDNAD.LALVFEA.NQEKV.DY.MKLMDLD.EQLGIP.QEYSCVVKM
RetrocopyMNLSSMFKILNCAGNEDVMTLGAEDNADNLALVFEALNQEKVLDYKMKLMDLDIEQLGIPKQEYSCVVKM
ParentalPSGEFARICRDLSHIGDAVVISCAKDGVKFSASGELGNGNIKLSQTSNVDKEEEAVTIEMNEPVQLTFAL
P.GEFA.IC.DL.HIGD.VVISCAKDGVKFSA.GEL.NGNIKLSQ.SNVDKE.EAV.IEMNE.VQLTFAL
RetrocopyPAGEFACIC*DLNHIGDVVVISCAKDGVKFSATGELANGNIKLSQISNVDKEKEAVAIEMNELVQLTFAL
ParentalRYLNFFTKATPLSSTVTLSMSADVPLVVEYKIADMG
.YLNFFTKATP.SSTVTL.MSADVPL.VEY.IA.MG
RetrocopyMYLNFFTKATPRSSTVTLGMSADVPL-VEYNIANMG

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
SRP007412_brain_prefrontal_cortex 0 .00 RPM 13 .03 RPM
SRP007412_cerebellum 0 .00 RPM 14 .30 RPM
SRP007412_heart 0 .00 RPM 12 .80 RPM
SRP007412_kidney 0 .00 RPM 26 .54 RPM
SRP007412_liver 0 .00 RPM 15 .06 RPM
SRP007412_testis 0 .00 RPM 55 .54 RPM

ChIP-Seq - click to see more details

Pan troglodytes was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ptro_595 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_595 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_595 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_857
Gorilla gorilla retro_ggor_700
Pongo abelii retro_pabe_690
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 ENSCJAG000000212783 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 ENSPTRG00000013222 3 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,


Copyright © RetrogeneDB 2014-2017