RetrogeneDB ID: retro_mmul_1283

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 17:21842417..21843187(+)
• Located in intron of: ENSMMUG00000014926

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZDHHC4
• Ensembl ID: ENSMMUG00000015545
• Aliases: None
• Description: probable palmitoyltransferase ZDHHC4 [Source:RefSeq peptide;Acc:NP_001248568]

Sequence

>retro_mmul_1283
ATGGACTTCCTGGTTTTCTTCCTGCTCTACTGGCTTTGGTGCCAGTTGGTTATGTTGTGACCTGTTTTTTGCTAGAAAAC
CCATGATTTGAAATGCCTGGTCAGGGCAGGAGCACAGATATTTTCCTGTATAATTCCAGAATGTCTTCAGAAAGCCATGT
AAAGATTGCTTCATTACATTTCCCATACATGAAACCATACCTTCATTATCCTTCACCTGGTCTTGCAAGGGATGGTGAAT
GCTGAATATACCTGGGAAATACCTGGCTACCATCAAAAGCTAGTTCTCCTGTATTACCTTCTTCTGCCCTATCTGCTTCT
GATTGTAGACCCGTTTATTTCCACCCTAACTTGTGTAACTGATTCTGGCATTATAACAAAAGCAAGTGAATTATTTCTTC
AAGTTTATAAATTCAATGAAGTGATGTTTCTAAAGAGGTGAGGTGCTCTACTTATGATTTACGAACACCAGCTCGATCTA
AGCACTGACTGCAGTGTGTGCACCGTTTTGATCATCATTGGGTTTGGGTGAACAACTGCATCTGGGCTTGGAACACCAGT
TATTAATACGTTCTCATCTACCTCTTGATGTTGATGACCTCGGCTGCTGCCATGGCCATTGTGAGCAATGCGTTTCTGGT
CAACTTGGTGGTATTGTTGGATTTGCACTAGACTTACACTGATGACCTCAGACACTTCCAGTTTATAGACTTGATTTTTC
TTATTCAGTACCTGTTCCGGACCTTTCCAACAATTGTCTTCATGCTGGGG

Alignment

ORF - retro_mmul_1283 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.54 %
• Parental protein coverage: 75.87 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MDFLILFLFY-LALVVMGLVLICV-CSKTHSLKGLARGGAQIFSCVIPECLQRAMHRSLHYLFHTRNHTF
          MDFL..FL.Y.LALV..G.V..C..C.KTH.LK.L.R.GAQIFSC.IPECLQ.AM.R.LHY..HT.NHTF
Retrocopy MDFLVFFLLY<LALVPVGYVVTCF>C*KTHDLKCLVRAGAQIFSCIIPECLQKAM*RLLHYISHT*NHTF

Parental  IVLHLVLQAMVYTEYTWEVFGYCQELEFSLYYLLLPYLLLVVNLFSFTLTCVTNPGIITKANELLFLHVY
          I.LHLVLQ.MV..EYTWE..GY.Q.L...LYYLLLPYLLL.V..F..TLTCVT..GIITKA.E.LFL.VY
Retrocopy IILHLVLQGMVNAEYTWEIPGYHQKLVL-LYYLLLPYLLLIVDPFISTLTCVTDSGIITKASE-LFLQVY

Parental  EFDEVMF-PKNVRCSTCALRKPARSKHCSVCNWCVHRFDHHCVWVNNCIGAWNIR--YFLIYLLTLTASA
          .F.EVMF..K.VRCST..LR.PARSKH...C...VHRFDHH.VWVNNCI.AWN....Y.LIYLL.L..SA
Retrocopy KFNEVMF<SKEVRCSTYDLRTPARSKH*LQC---VHRFDHHWVWVNNCIWAWNTSY*YVLIYLLMLMTSA

Parental  ATVAIVSTTFLIHLVVMSDLYQETYVDDLGHLHVMDTVFLIQYLFLTFPRIVFMLG
          A..AIVS..FL..LVV..DL...TY.DDL.H....D..FLIQYLF.TFP.IVFMLG
Retrocopy AAMAIVSNAFLVNLVVLLDLH-*TYTDDLRHFQFIDLIFLIQYLFRTFPTIVFMLG

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	6.16 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	6.11 RPM
SRP007412_cerebellum	0.00 RPM	4.58 RPM
SRP007412_heart	0.18 RPM	8.60 RPM
SRP007412_kidney	0.00 RPM	20.89 RPM
SRP007412_liver	0.04 RPM	36.14 RPM
SRP007412_testis	0.08 RPM	72.33 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1283 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1283 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1283 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1193
Pan troglodytes	retro_ptro_3038
Pongo abelii	retro_pabe_993

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009547	1 retrocopy	retro_btau_643,
Dasypus novemcinctus	ENSDNOG00000009165	1 retrocopy	retro_dnov_2610,
Homo sapiens	ENSG00000136247	1 retrocopy	retro_hsap_1193,
Macaca mulatta	ENSMMUG00000015545	1 retrocopy	retro_mmul_1283 ,
Nomascus leucogenys	ENSNLEG00000015607	1 retrocopy	retro_nleu_2081,
Pongo abelii	ENSPPYG00000017352	1 retrocopy	retro_pabe_993,
Pan troglodytes	ENSPTRG00000018915	1 retrocopy	retro_ptro_3038,
Pteropus vampyrus	ENSPVAG00000016104	2 retrocopies	retro_pvam_1175, retro_pvam_758,
Ictidomys tridecemlineatus	ENSSTOG00000011605	1 retrocopy	retro_itri_1054,
Tursiops truncatus	ENSTTRG00000005001	1 retrocopy	retro_ttru_179,
Vicugna pacos	ENSVPAG00000011480	1 retrocopy	retro_vpac_177,