RetrogeneDB ID: retro_mmul_594

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 10:25104728..25105470(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.403
• Ensembl ID: ENSMMUG00000014232
• Aliases: None
• Description: autophagy-related protein 3 [Source:RefSeq peptide;Acc:NP_001181205]

Sequence

>retro_mmul_594
GAAGGAAAGGCACTAGAAGTAACTGAATACCTGACCTAATTCTCAAGGAATCCGTTTAAGGAAACAGCTGTTATTACCCC
AAAAGAGTTTATGGTGCCTGGAGATCACTTAGCTGTCCACTGCCCAACACAGCAATGAGCTACAGGAGAAGAACTGAAAG
GAGAGGCATAGCCACCAACAGGCAAATAATTTTTGATAACCAAAAATGTGGCCTGCTACGTCCAGTCAAAACAGATGGCA
TGTTCAGGTGAACTGTAAGCATCACCGAAGATGATGGTGGTAGGGCATGGGTACATACACATCACAGCCAGGAATTGCAG
GAATAAACAAATAAGTTGAGGAGATTATACTTACAAGCAAAAATGGTATAAAACTCCAAAATCGCTCAGCCTTATGATAG
GAAGAAGAAAAAGATGAAGGAAAAGCTACATTTATGGAATAATATGAAGAGAGTGGGTTGCTGGAAGCAGATAAAGTTAC
CCTAGACGAAAGGAAAACAGTAGAAGCTTGTAAAGCTAAAAGTGACGTTGGAGGTGAAGATGCTCTTTTGCAAACCAGAA
CTTGTGACCTTTACATCATATATGGTAAATATTACCAGATGGCACAACTATGGTTTTTTGGCTATGATGAAGAACAGCAG
CTTTTCACAGCTGAACACATGTATAAAGACATCATTCAAGACCATGTGAAGAAAACAGTGACCACCAAAAATCCCTCCGC
CAATCTCCCTCCACCTCCTATG

Alignment

ORF - retro_mmul_594 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.85 %
• Parental protein coverage: 79.62 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KGKALEVAEYLTPVLKESKFKETGVITPEEFVAAGDHLVHHCPTWQWATGEELKVKAYLPAGKQFLVTKN
          .GKALEV.EYLT.......FKET.VITP.EF...GDHL..HCPT.Q.ATGEELK..A..P.GK.FL.TKN
Retrocopy EGKALEVTEYLT*-FSRNPFKETAVITPKEFMVPGDHLAVHCPTQQ*ATGEELKGEA*PPTGK*FLITKN

Parental  VPCYKRCKQMEYSDELEA-IIEEDDGDGGWVDTYHN-TGITGITEAVKEITLENKDNIRLQDCSALCEEE
          V.CY...KQM..S.EL.A.I.E.DDG...WV.T.H...GI.GI...V.EI.L..K..I.LQ..SAL..E.
Retrocopy VACYVQSKQMACSGEL*A<ITE-DDGGRAWVHTHHS<PGIAGINK*VEEIILTSKNGIKLQNRSAL**E-

Parental  EEEDEGEAADMEEYEESGLLETDEATLDTSKIVEACKAKTDAGGEDAILQTRTYDLYITYDKYYQTPRLW
          EE.DEG.A..ME.YEESGLLE.D..TLD..K.VEACKAK.D.GGEDA.LQTRT.DLYI.Y.KYYQ...LW
Retrocopy EEKDEGKATFME*YEESGLLEADKVTLDERKTVEACKAKSDVGGEDALLQTRTCDLYIIYGKYYQMAQLW

Parental  LFGYDEQRQPLTVEHMYEDISQDHVKKTVTIEN-HPHLPPPPM
          .FGYDE..Q..T.EHMY.DI.QDHVKKTVT..N....LPPPPM
Retrocopy FFGYDEEQQLFTAEHMYKDIIQDHVKKTVTTKNPSANLPPPPM

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	0.00 RPM	26.11 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	20.15 RPM
SRP007412_cerebellum	0.00 RPM	24.02 RPM
SRP007412_heart	0.00 RPM	19.43 RPM
SRP007412_kidney	0.00 RPM	29.11 RPM
SRP007412_liver	0.00 RPM	28.74 RPM
SRP007412_testis	0.04 RPM	78.36 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_594 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_594 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_594 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2479
Pan troglodytes	retro_ptro_1434
Gorilla gorilla	retro_ggor_1544
Pongo abelii	retro_pabe_1827
Oryctolagus cuniculus	retro_ocun_1219
Equus caballus	retro_ecab_594

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018116	1 retrocopy	retro_amel_645,
Callithrix jacchus	ENSCJAG00000020358	1 retrocopy	retro_cjac_2756,
Equus caballus	ENSECAG00000011954	1 retrocopy	retro_ecab_594,
Homo sapiens	ENSG00000144848	1 retrocopy	retro_hsap_2479,
Gorilla gorilla	ENSGGOG00000006637	1 retrocopy	retro_ggor_1544,
Myotis lucifugus	ENSMLUG00000001573	1 retrocopy	retro_mluc_1025,
Macaca mulatta	ENSMMUG00000014232	1 retrocopy	retro_mmul_594 ,
Mustela putorius furo	ENSMPUG00000000321	2 retrocopies	retro_mputfur_1064, retro_mputfur_1614,
Nomascus leucogenys	ENSNLEG00000004302	2 retrocopies	retro_nleu_268, retro_nleu_331,
Oryctolagus cuniculus	ENSOCUG00000015651	1 retrocopy	retro_ocun_1219,
Pongo abelii	ENSPPYG00000013548	1 retrocopy	retro_pabe_1827,
Pan troglodytes	ENSPTRG00000015220	1 retrocopy	retro_ptro_1434,
Pteropus vampyrus	ENSPVAG00000009568	1 retrocopy	retro_pvam_1399,