RetrogeneDB ID: retro_pabe_3778

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:72996655..72997197(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PCNP
• Ensembl ID: ENSPPYG00000013591
• Aliases: None
• Description: PEST proteolytic signal-containing nuclear protein [Source:UniProtKB/Swiss-Prot;Acc:Q5RCI9]

Sequence

>retro_pabe_3778
GGCTTGGCTGCAGGGTAGGCCACGGCAGAGAAAATGGCAGATGGGAAGGTGGGAGAGGAGAAGGCTGAAAAGTTGCAGTG
AGCTGGAGCCATTGGAGGACCTGAAGAAGAAGTGAAAAAACCTGTGAAAACTAAGGCTGTTTATTCCGGTAATGGAGAGA
AAAGTGTTCGTCGCAGCACTGAGAAGCCATCAGCTGAAAAAGAAGCTGCAGTCCTCCCAACAAAGCCTACAAAGATCAAG
TTTAGATCTGCCACAGGTAGTCACATGACAAAGAAAGCATCAGCCATATCCATCAAACTTGGATTAAGTAAGCCTAAAGA
ACCTGTTCCAACTCTTGCTTCAAAAATTCTTTTGGTAGCAGCAGGTTTTAATGAAGATGAAGGTAGCCAACCTGAGGCAA
TGCCTCCAGAAGCAAAGATGAGGATTAAAAATATTGGAAGAAATACATTAACATCAGCTGGACCAAACTCCTTCAATAAA
AGAAGCATGTGTTTTTTGTTAACCAGAAGCTATGGGAACAAAATATAAAACCTCATCTTGGT

Alignment

ORF - retro_pabe_3778 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.77 %
• Parental protein coverage: 91.46 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GVAAGEAAAGKMADGKAGEEKPEKSQRAGAAGGPEEEAEKPVKTKTVSSSNGGESSSRSAEKRSAEEEAV
          G.AAG.A.A.KMADGK.GEEK.EK.Q.AGA.GGPEEE..KPVKTK.V.S.NG..S..RS.EK.SAE.EA.
Retrocopy GLAAG*ATAEKMADGKVGEEKAEKLQ*AGAIGGPEEEVKKPVKTKAVYSGNGEKSVRRSTEKPSAEKEAA

Parental  DLPTKPTKISKFGFAIGSQTTKKASAISIKLGSSKPKETVPTLAPKTLSVAAAFNEDEDSEPEEMPPEAK
          .LPTKPTKI.KF..A.GS..TKKASAISIKLG.SKPKE.VPTLA.K.L.VAA.FNEDE.S.PE.MPPEAK
Retrocopy VLPTKPTKI-KFRSATGSHMTKKASAISIKLGLSKPKEPVPTLASKILLVAAGFNEDEGSQPEAMPPEAK

Parental  MRMKNIGRDTPTSAGPNSFNK-GKHGFSDNQKLWERNIKSHLG
          MR.KNIGR.T.TSAGPNSFNK..KH.F..NQKLWE.NIK.HLG
Retrocopy MRIKNIGRNTLTSAGPNSFNK<KKHVFFVNQKLWEQNIKPHLG

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	53.69 RPM
SRP007412_cerebellum	0.00 RPM	67.61 RPM
SRP007412_heart	0.00 RPM	34.05 RPM
SRP007412_kidney	0.00 RPM	40.44 RPM
SRP007412_liver	0.00 RPM	25.40 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3778 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3778 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3778 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_2598

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 70 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007972	11 retrocopies	retro_chof_1170, retro_chof_1215, retro_chof_2070, retro_chof_2280, retro_chof_2290, retro_chof_2553, retro_chof_2575, retro_chof_594, retro_chof_651, retro_chof_806, retro_chof_819,
Callithrix jacchus	ENSCJAG00000000508	6 retrocopies	retro_cjac_101, retro_cjac_1569, retro_cjac_1722, retro_cjac_3205, retro_cjac_3332, retro_cjac_401,
Dasypus novemcinctus	ENSDNOG00000008873	5 retrocopies	retro_dnov_1606, retro_dnov_259, retro_dnov_370, retro_dnov_910, retro_dnov_98,
Homo sapiens	ENSG00000081154	3 retrocopies	retro_hsap_1130, retro_hsap_1155, retro_hsap_1264,
Gorilla gorilla	ENSGGOG00000025423	4 retrocopies	retro_ggor_882, retro_ggor_901, retro_ggor_902, retro_ggor_994,
Loxodonta africana	ENSLAFG00000005518	2 retrocopies	retro_lafr_1189, retro_lafr_458,
Microcebus murinus	ENSMICG00000008072	10 retrocopies	retro_mmur_1010, retro_mmur_1138, retro_mmur_1286, retro_mmur_148, retro_mmur_1535, retro_mmur_1547, retro_mmur_1625, retro_mmur_167, retro_mmur_458, retro_mmur_887,
Macaca mulatta	ENSMMUG00000017782	3 retrocopies	retro_mmul_1312, retro_mmul_1377, retro_mmul_2598,
Mustela putorius furo	ENSMPUG00000011696	1 retrocopy	retro_mputfur_850,
Mus musculus	ENSMUSG00000071533	4 retrocopies	retro_mmus_2331, retro_mmus_2339, retro_mmus_2822, retro_mmus_3034,
Nomascus leucogenys	ENSNLEG00000003224	2 retrocopies	retro_nleu_2100, retro_nleu_2971,
Oryctolagus cuniculus	ENSOCUG00000011110	7 retrocopies	retro_ocun_1072, retro_ocun_1144, retro_ocun_1496, retro_ocun_1537, retro_ocun_573, retro_ocun_687, retro_ocun_868,
Procavia capensis	ENSPCAG00000007007	3 retrocopies	retro_pcap_161, retro_pcap_194, retro_pcap_273,
Pongo abelii	ENSPPYG00000013591	5 retrocopies	retro_pabe_1051, retro_pabe_1598, retro_pabe_3778 , retro_pabe_935, retro_pabe_961,
Pan troglodytes	ENSPTRG00000015172	3 retrocopies	retro_ptro_676, retro_ptro_790, retro_ptro_864,
Rattus norvegicus	ENSRNOG00000028411	1 retrocopy	retro_rnor_2138,