RetrogeneDB ID:

retro_pabe_2542

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:4:103431503..103432208(-)
Located in intron of:ENSPPYG00000014947
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PCNA
Ensembl ID:ENSPPYG00000010795
Aliases:None
Description:proliferating cell nuclear antigen [Source:HGNC Symbol;Acc:8729]


Retrocopy-Parental alignment summary:






>retro_pabe_2542
GCCTGCTGGGACAACAGTTGAAGCAGGTGAACCTACACAGCATGAAAGTATCACACATTTTCTTAGTGCAGCTCACCCTG
TGTGACCAGGGCTTCAACACATACCACTGTGACCACAACCTAGCCATGAGCATGAGCCTCACCAGCATGTCGAAAATGCT
AAAATACAACGATGGCAGTGAAGACATCATTACATGGAGGGCTGAAGGTAACCATGGACCTCTTGGTGCTAGAATTTGAA
GCACTAAATCAAGAGAACTTTTAGACTATGAATTGAAGTTAATGACTCTAGATGTTGAGCAACTTGAAATTCCAGAACAA
GAGTACAGCTGTGTAAATAAAGATGCATTCTAGTGAATTTGTTCATATATGCCAAGATCTCAGTCATATTGGAGAGTCTG
TTATAATTTCCTGTCCAAAAGATGGAGTGAAATTTTCTGCAAATGGAGAACTTGGACATGGAAACATTGTCACAAACAAG
TAATTACAATAAAGAAGAGGAGGCTGTTGCCATAATGATGAATGTGCCAGTTCAGCTAACTTTTGCACTAAGGTACTTAA
ATTTCTTTATAACAGGCACTCCACTCTCTCTTCCCAGTAACACTCAGTATGTCTGCAGATGCACCCCTTGTTGTAGAGTA
TAAGATTGCCAGATATGGAACATTTAAAGTATTATTTGGCTCCCAAAATTGAGGATGAAAAAGGA

ORF - retro_pabe_2542 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.31 %
Parental protein coverage: 90.04 %
Number of stop codons detected: 1
Number of frameshifts detected 7


Retrocopy - Parental Gene Alignment:

ParentalACWDISSSG-VNLQSMDSSHVSLVQLTLRSEGFDTYRCDRNLAMGVNLTSMSKILKCA-GNEDIITLRAE
ACWD.S.S..VNL.SM..SH..LVQLTL...GF.TY.CD.NLAM...LTSMSK.LK...G.EDIIT.RAE
RetrocopyACWDNS*SR<VNLHSMKVSHIFLVQLTLCDQGFNTYHCDHNLAMSMSLTSMSKMLKYNDGSEDIITWRAE
ParentalDN-ADTLALVFEAPNQE-KVSDYEMKLMDLDVEQLGIPEQEYSCV-VKMPSGEFARICRDLSHIGDAVVI
.N..D.L.L.FEA.NQE....DYE.KLM.LDVEQL.IPEQEYSCV..KM.S.EF..IC.DLSHIG..V.I
RetrocopyGN>MDLLVLEFEALNQE<ELLDYELKLMTLDVEQLEIPEQEYSCV>IKMHSSEFVHICQDLSHIGESVII
ParentalSCAKDGVKFSASGELGNGNI-KLSQTSNVDKEEEAVTIEMNEPVQLTFALRYLNFFTKATPLS-STVTLS
SC.KDGVKFSA.GELG.GNI.......N...E..A..I.MN.PVQLTFALRYLNFF...TPLS...VTLS
RetrocopySCPKDGVKFSANGELGHGNI>SQTSNYNKEEEAVA--IMMNVPVQLTFALRYLNFFITGTPLS>FPVTLS
ParentalMSADVPLVVEYKIA-DMGHLKYYLAPKIEDEEG
MSAD.PLVVEYKIA.DM.HLKYYLAPKIEDE.G
RetrocopyMSADAPLVVEYKIA>DMEHLKYYLAPKIEDEKG

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 .06 RPM 5 .14 RPM
SRP007412_cerebellum 0 .00 RPM 10 .94 RPM
SRP007412_heart 0 .00 RPM 5 .51 RPM
SRP007412_kidney 0 .00 RPM 10 .64 RPM
SRP007412_liver 0 .03 RPM 9 .76 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_2542 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_2542 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2542 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3067
Pan troglodytes retro_ptro_2068
Macaca mulatta retro_mmul_1960
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 ENSPPYG00000010795 3 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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