RetrogeneDB ID: retro_ptro_3038

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL392075.1:3985925..3986689(+)
• Located in intron of: ENSPTRG00000005830

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZDHHC4
• Ensembl ID: ENSPTRG00000018915
• Aliases: None
• Description: None

Sequence

>retro_ptro_3038
ATGGACTTCCTGGTTCTCTTCCTGCTCTACTGGCTTTGGTGCTAGTTGGTTATGTTATGACCTGTTTTTGCTAGAAAACT
CATGATTTGAAATGCCTGGTCAGGGCAGGAGCACAGATATTTTCCTGTATAATTCCAGAACGTCTTCAGAAAGCCATGTA
AAGATTGCTTCATTACCTCTTCCATACATGAAACCATACCTTCATTATCCTTCACCTGGTCTTGCAAGGGATGGTAAATA
CTGAATATACCTGGGAAATACTTGGCTACCGTCAGAAGCTAGTTCTCCTGTATTATCTTCTTCTGCTCTATCTGCTTCTG
ATTGTAAACCCGTTTATTTCCACCCTAACTTGTGTAACTGATTCTGGCATTATAAGAAAAGCAAATGAATTATTTCTTCA
AGTTTATGAATTCAGTGATGTTTCTAAAGAGGTGAGGTGCTCTACTTATGATTTACGAACACCAACTCGATCAAAGCACT
GACTGCAGTGTGTGCACCGTTTTGACCATCGTTAGGTTTGGGTGAACAACTGCATCTGGGCTTGGAACACCAGTTATTAA
TACTTTCTCATCTACCTCTTGATGTTGACGGCTTCGGCTGCTGCCATGGCCATTGTGAGCACTGCATTTCTGGTCGATTT
GGTGGTATTGTTGGATTTGTACTAGACTTACACTGATGACCTTGGACACTTCCAGTTTATGGACTTGATATTTCTTATTT
AGTACCTGTTCCTGACCTTTCTAACAATTGTCTTCATGCTGGGG

Alignment

ORF - retro_ptro_3038 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.45 %
• Parental protein coverage: 75.87 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDFLVLFLFY-LASVLMGLVLICVCSKTHSLKGLARGGAQIFSCIIPECLQRAVHGLLHYLFHTRNHTFI
          MDFLVLFL.Y.LA.VL.G.V..C.C.KTH.LK.L.R.GAQIFSCIIPE.LQ.A...LLHYLFHT.NHTFI
Retrocopy MDFLVLFLLY<LALVLVGYVMTCFC*KTHDLKCLVRAGAQIFSCIIPERLQKAM*RLLHYLFHT*NHTFI

Parental  VLHLVLQGMVYTEYTWEVFGYCQELEFSLYYLLLPYLLLVVNLFFFTLTCVTNPGIITKANELLFLHVYE
          .LHLVLQGMV.TEYTWE..GY.Q.L...LYYLLL.YLLL.VN.F..TLTCVT..GII.KANE.LFL.VYE
Retrocopy ILHLVLQGMVNTEYTWEILGYRQKLVL-LYYLLLLYLLLIVNPFISTLTCVTDSGIIRKANE-LFLQVYE

Parental  FDEVMFPKNVRCSTCDLRKPARSKHCSVCNWCVHRFDHHCVWVNNCIGAWNIR--YFLIYLLTLTASAAT
          F..V...K.VRCST.DLR.P.RSKH...C...VHRFDH..VWVNNCI.AWN....YFLIYLL.LTASAA.
Retrocopy FSDV--SKEVRCSTYDLRTPTRSKH*LQC---VHRFDHR*VWVNNCIWAWNTSY*YFLIYLLMLTASAAA

Parental  VAIVSTTFLVHLVVMSDLYQETYIDDLGHLRVMDTVFLIQYLFLTFPRIVFMLG
          .AIVST.FLV.LVV..DLY..TY.DDLGH...MD..FLI.YLFLTF..IVFMLG
Retrocopy MAIVSTAFLVDLVVLLDLY-*TYTDDLGHFQFMDLIFLI*YLFLTFLTIVFMLG

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	0.02 RPM	16.64 RPM
SRP007412_cerebellum	0.00 RPM	14.73 RPM
SRP007412_heart	0.12 RPM	10.43 RPM
SRP007412_kidney	0.05 RPM	35.96 RPM
SRP007412_liver	0.16 RPM	22.68 RPM
SRP007412_testis	0.00 RPM	96.64 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3038 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3038 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3038 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1193
Pongo abelii	retro_pabe_993
Macaca mulatta	retro_mmul_1283

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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,