RetrogeneDB ID: retro_pabe_3165

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:99844079..99844611(-)
• Located in intron of: ENSPPYG00000017878

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRYZ
• Ensembl ID: ENSPPYG00000001235
• Aliases: None
• Description: quinone oxidoreductase [Source:RefSeq peptide;Acc:NP_001126904]

Sequence

>retro_pabe_3165
GAGAGTGTTCTAGTTCATGGGGCTAGTGGAGGAGCTGGAGTAGCAACATGCCAAATTGCTAGAGTTTATGTCTTAAAGGT
TTTGGGCACAGTTGGTACTGAGAGGGACAAAAGACTTTTGCAAAATGGAGCCCACAAAGTGTTTAATTACAAAGAAGTTA
ACTATGTTGATAAAATTAAGAAATGTGTGGTAAGAAAGGAATTCATGTGATTATTGAAATAATAGCTAATATAAATCTTA
GTAAAGATGTGAATTGTTTGTCATATGGAAGATGAGTAATAGGTGTTGGCAACAGTGGTACCATTGAAATAAACCCATGG
GACACTATGGCAAAAGAGTCTAGTAAAATTGTCGTTACTCTATTTTCCTCAACCAAGGAGGAATCTCAGCAATTTGCAGC
AGCCTGTCAAGCTGGAATGGAAATTGGTTGGCTGAAACCTGTAATGGGTTCTCACTATATGTTGGAGAGGTGGCCCAGGC
TCATGAAAATATCTCTCACGGCAATGGGGCTACTGTAAAAATGATTCTTCTC

Alignment

ORF - retro_pabe_3165 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.93 %
• Parental protein coverage: 54.41 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ESVLVHGASGGVGLAACQIARAYGLKVLGTAGTEEGQKIVLQNGAHEVFNHREVNYIDKIKKYV-GEKGI
          ESVLVHGASGG.G.A.CQIAR.Y.LKVLGT.GTE......LQNGAH.VFN..EVNY.DKIKK.V.G.KGI
Retrocopy ESVLVHGASGGAGVATCQIARVYVLKVLGTVGTERDKRL-LQNGAHKVFNYKEVNYVDKIKKCV<GKKGI

Parental  DVIIEMLANVNLNKDLSLLSHGGQVIVVGSRGTIEINPRDTMAKESSIIGVTVFSSTKEEFQQYAAALQA
          .VIIE..AN.NL.KD...LS.G..VI.VG..GTIEINP.DTMAKESS.I.VT.FSSTKEE.QQ.AAA.QA
Retrocopy HVIIEIIANINLSKDVNCLSYGR*VIGVGNSGTIEINPWDTMAKESSKIVVTLFSSTKEESQQFAAACQA

Parental  GMEIGWLKPVIGSQYPLEK-VAEAHENIIHGSGATGKMILL
          GMEIGWLKPV.GS.Y.LE..VA.AHENI.HG.GAT.KMILL
Retrocopy GMEIGWLKPVMGSHYMLER<VAQAHENISHGNGATVKMILL

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	0.17 RPM	23.00 RPM
SRP007412_cerebellum	0.24 RPM	18.85 RPM
SRP007412_heart	0.06 RPM	31.70 RPM
SRP007412_kidney	0.27 RPM	147.57 RPM
SRP007412_liver	0.18 RPM	153.90 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3165 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3165 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3165 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3884
Macaca mulatta	retro_mmul_1728

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003162	1 retrocopy	retro_btau_1433,
Canis familiaris	ENSCAFG00000020404	1 retrocopy	retro_cfam_870,
Choloepus hoffmanni	ENSCHOG00000005167	1 retrocopy	retro_chof_1772,
Felis catus	ENSFCAG00000030626	1 retrocopy	retro_fcat_1907,
Homo sapiens	ENSG00000116791	1 retrocopy	retro_hsap_3884,
Loxodonta africana	ENSLAFG00000011371	1 retrocopy	retro_lafr_527,
Macaca mulatta	ENSMMUG00000014593	2 retrocopies	retro_mmul_1026, retro_mmul_1728,
Mustela putorius furo	ENSMPUG00000010969	1 retrocopy	retro_mputfur_119,
Mus musculus	ENSMUSG00000028199	1 retrocopy	retro_mmus_1314,
Nomascus leucogenys	ENSNLEG00000009543	2 retrocopies	retro_nleu_1890, retro_nleu_3115,
Otolemur garnettii	ENSOGAG00000011586	1 retrocopy	retro_ogar_179,
Pongo abelii	ENSPPYG00000000475	1 retrocopy	retro_pabe_2539,
Pongo abelii	ENSPPYG00000001235	2 retrocopies	retro_pabe_1909, retro_pabe_3165 ,
Pan troglodytes	ENSPTRG00000000865	1 retrocopy	retro_ptro_1598,
Tupaia belangeri	ENSTBEG00000016750	3 retrocopies	retro_tbel_1665, retro_tbel_2353, retro_tbel_3800,
Tarsius syrichta	ENSTSYG00000004193	2 retrocopies	retro_tsyr_1218, retro_tsyr_1884,
Tursiops truncatus	ENSTTRG00000010471	2 retrocopies	retro_ttru_555, retro_ttru_958,