RetrogeneDB ID: retro_pabe_706

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 11:68817300..68817630(+)
• Located in intron of: ENSPPYG00000003661

Retrocopy information

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

Parental gene information

• Parental gene symbol: NPM3
• Ensembl ID: ENSPPYG00000002589
• Aliases: None
• Description: Nucleoplasmin-3 [Source:UniProtKB/Swiss-Prot;Acc:Q5RC37]

Sequence

>retro_pabe_706
GAGAAACCTTGCAGCGCAGCTGCCAGCACTGCCACCACCTTGAGTCAGGAGAACCAAGCCCAGGCTGGGGTGTTGGAAGT
CTGGGGATTCCAGCCTCAGTCACTATGGACAGTTTTTCTTCATCTGTAGCTCTCTGGCCACACCCACTCCTTTACATTCA
AGGTAGAGGAAGAAGATAATATGAAGCATGTGCTGGCATTAATTATGCTCTGCTTCACCAAGGGGGCTAACAATGAGTGT
AATGTGGTAGAAGGTGTAACCTGGAACTATGACCACCAGGAGATTACAGTCCCTCTGGCAAATCTCAAGTTGTCCTGTCA
ACCCAAGTTA

Alignment

ORF - retro_pabe_706 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.38 %
• Parental protein coverage: 55.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EGPCSMAAGTAAALAFLSQESRTRAG-GVGGLRVPAPVTMDSF-FFGCE-LSGHTRSFTFKVEEEDDAEH
          E.PCS.AA.TA.....LSQE....AG.GVG.L..PA.VTMDSF.FF.C..LSGHT.SFTFKVEEED...H
Retrocopy EKPCSAAASTATT---LSQENQAQAG<GVGSLGIPASVTMDSF<FFICS<LSGHTHSFTFKVEEEDNMKH

Parental  VLALTMLCLTEGAKDECNVVEVVARNHDHQEIAVPVANLKLSCQPML
          VLAL.MLC.T.GA..ECNVVE.V..N.DHQEI.VP.ANLKLSCQP.L
Retrocopy VLALIMLCFTKGANNECNVVEGVTWNYDHQEITVPLANLKLSCQPKL

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	0.06 RPM	16.53 RPM
SRP007412_cerebellum	0.24 RPM	2.43 RPM
SRP007412_heart	0.03 RPM	12.46 RPM
SRP007412_kidney	0.03 RPM	19.29 RPM
SRP007412_liver	0.03 RPM	18.18 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_706 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_706 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_706 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_792
Pan troglodytes	retro_ptro_551
Macaca mulatta	retro_mmul_1072

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017639	2 retrocopies	retro_amel_1233, retro_amel_90,
Bos taurus	ENSBTAG00000016335	1 retrocopy	retro_btau_1164,
Canis familiaris	ENSCAFG00000009919	2 retrocopies	retro_cfam_1968, retro_cfam_2064,
Callithrix jacchus	ENSCJAG00000017650	2 retrocopies	retro_cjac_2491, retro_cjac_3052,
Cavia porcellus	ENSCPOG00000006301	1 retrocopy	retro_cpor_1315,
Dasypus novemcinctus	ENSDNOG00000018876	1 retrocopy	retro_dnov_1279,
Dipodomys ordii	ENSDORG00000003491	1 retrocopy	retro_dord_577,
Felis catus	ENSFCAG00000007178	1 retrocopy	retro_fcat_1906,
Homo sapiens	ENSG00000107833	1 retrocopy	retro_hsap_792,
Macropus eugenii	ENSMEUG00000003465	2 retrocopies	retro_meug_20, retro_meug_25,
Microcebus murinus	ENSMICG00000011739	1 retrocopy	retro_mmur_126,
Myotis lucifugus	ENSMLUG00000004961	1 retrocopy	retro_mluc_2333,
Macaca mulatta	ENSMMUG00000015774	1 retrocopy	retro_mmul_1072,
Mustela putorius furo	ENSMPUG00000016894	2 retrocopies	retro_mputfur_750, retro_mputfur_759,
Mus musculus	ENSMUSG00000056209	2 retrocopies	retro_mmus_2756, retro_mmus_3479,
Ochotona princeps	ENSOPRG00000009229	2 retrocopies	retro_opri_1019, retro_opri_92,
Pongo abelii	ENSPPYG00000002589	1 retrocopy	retro_pabe_706 ,
Pongo abelii	ENSPPYG00000016037	7 retrocopies	retro_pabe_2405, retro_pabe_3072, retro_pabe_3261, retro_pabe_3627, retro_pabe_3699, retro_pabe_486, retro_pabe_532,
Pan troglodytes	ENSPTRG00000002875	1 retrocopy	retro_ptro_551,