RetrogeneDB ID: retro_hsap_1193

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 13:43507993..43508757(+)
• Located in intron of: ENSG00000133106

Retrocopy information

• Ensembl ID: ENSG00000238025
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ZDHHC4
• Ensembl ID: ENSG00000136247
• Aliases: ZDHHC4, ZNF374
• Description: zinc finger, DHHC-type containing 4 [Source:HGNC Symbol;Acc:18471]

Sequence

>retro_hsap_1193
ATGGACTTCCTGGTTCTCTTCCTGCTCTACTGGCTTTGGTGCTAGTTGGTTATGTTATGACCTGTTTTTGCTAGAAAACT
CATGATTTGAAATGCCTGGTCAGGGCAGGGGCACAGATATTTTCCTGTATAATTCCAGAATGTCTTCAGAAAGCCATGTA
AAGATTGCTTCACTACCTCTTCCATACATGAAACCATACCTTCATTATCCTTCACCTGGTCTTGCAAGGAATGGTAAATA
CTGAATATACCTGGGAAATACTGGGCTACCGTCAAAAGCTAGTTCTCCTGTATTACCTTCTTCTGCCCTGTCTGCTTCTG
ATTGTAAACCCGTTTATTTCCACCCTAACTTGTGTAACTGATTCTGGCATTATAAGAAAAGCAAATGAATTATTTCTTCA
AGTTTATGAATTCAGTGATGTTTCTAAAGAGGTGAGGTGCTCTACTTATGAGTTACGAACACCAGCTCGATCAAAGCACT
GACTGCAGTGTGTGCACCGTTTTGACCATCGTTAGGTTTGGGTGAACAACTGCATCTGGGCTTGGAACGCCAGTTATTAA
TACTTTCTCATCTACCTCTTGATGTTGACGGCTTTGGCTGCTGCCATGGCCATTGTGAGCACTGCGTTTCTGGTCGATTT
GGTGGTATTGTTGGATTTGTACTAGACTTACACTGATGACCTTGGACACTTCCAGTTTATAGACTTGATTTTTCTTATTT
AGTACCTGTTCCTGACCTTTCTAACAATTGTCTTCATGCTGGGG

Alignment

ORF - retro_hsap_1193 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.32 %
• 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.GAQIFSCIIPECLQ.A...LLHYLFHT.NHTFI
Retrocopy MDFLVLFLLY<LALVLVGYVMTCFC*KTHDLKCLVRAGAQIFSCIIPECLQKAM*RLLHYLFHT*NHTFI

Parental  VLHLVLQGMVYTEYTWEVFGYCQELELSLHYLLLPYLLLGVNLFFFTLTCGTNPGIITKANELLFLHVYE
          .LHLVLQGMV.TEYTWE..GY.Q.L.L.L.YLLLP.LLL.VN.F..TLTC.T..GII.KANE.LFL.VYE
Retrocopy ILHLVLQGMVNTEYTWEILGYRQKLVL-LYYLLLPCLLLIVNPFISTLTCVTDSGIIRKANE-LFLQVYE

Parental  FDEVMFPKNVRCSTCDLRKPARSKHCSVCNWCVHRFDHHCVWVNNCIGAWNIR--YFLIYVLTLTASAAT
          F..V...K.VRCST..LR.PARSKH...C...VHRFDH..VWVNNCI.AWN....YFLIY.L.LTA.AA.
Retrocopy FSDV--SKEVRCSTYELRTPARSKH*LQC---VHRFDHR*VWVNNCIWAWNASY*YFLIYLLMLTALAAA

Parental  VAIVSTTFLVHLVVMSDLYQETYIDDLGHLHVMDTVFLIQYLFLTFPRIVFMLG
          .AIVST.FLV.LVV..DLY..TY.DDLGH....D..FLI.YLFLTF..IVFMLG
Retrocopy MAIVSTAFLVDLVVLLDLY-*TYTDDLGHFQFIDLIFLI*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
bodymap2_adipose	0.00 RPM	22.80 RPM
bodymap2_adrenal	0.08 RPM	23.27 RPM
bodymap2_brain	0.02 RPM	22.57 RPM
bodymap2_breast	0.00 RPM	27.08 RPM
bodymap2_colon	0.00 RPM	26.78 RPM
bodymap2_heart	0.00 RPM	15.06 RPM
bodymap2_kidney	0.10 RPM	23.87 RPM
bodymap2_liver	0.00 RPM	17.01 RPM
bodymap2_lung	0.00 RPM	14.61 RPM
bodymap2_lymph_node	0.00 RPM	16.65 RPM
bodymap2_ovary	0.00 RPM	31.59 RPM
bodymap2_prostate	0.00 RPM	30.09 RPM
bodymap2_skeletal_muscle	0.00 RPM	25.50 RPM
bodymap2_testis	0.11 RPM	51.71 RPM
bodymap2_thyroid	0.06 RPM	44.37 RPM
bodymap2_white_blood_cells	0.16 RPM	18.21 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1193 was not detected

EST

1 EST(s) were mapped to retro_hsap_1193 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AW809127	43508171	43508327	100	154	0	152

TSS

No TSS is located nearby retro_hsap_1193 retrocopy 5' end.

Lab

retro_hsap_1193 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1193 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_3038
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,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.04 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.16 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.12 RPM
CEU_NA12760	0.04 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.03 RPM
CEU_NA12873	0.03 RPM
FIN_HG00183	0.08 RPM
FIN_HG00277	0.11 RPM
FIN_HG00315	0.11 RPM
FIN_HG00321	0.06 RPM
FIN_HG00328	0.02 RPM
FIN_HG00338	0.02 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.05 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.02 RPM
GBR_HG00099	0.06 RPM
GBR_HG00111	0.02 RPM
GBR_HG00114	0.03 RPM
GBR_HG00119	0.22 RPM
GBR_HG00131	0.11 RPM
GBR_HG00133	0.12 RPM
GBR_HG00134	0.04 RPM
GBR_HG00137	0.05 RPM
GBR_HG00142	0.11 RPM
GBR_HG00143	0.06 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.15 RPM
TSI_NA20518	0.11 RPM
TSI_NA20532	0.10 RPM
TSI_NA20538	0.18 RPM
TSI_NA20756	0.03 RPM
TSI_NA20765	0.06 RPM
TSI_NA20771	0.06 RPM
TSI_NA20786	0.05 RPM
TSI_NA20798	0.03 RPM
YRI_NA18870	0.17 RPM
YRI_NA18907	0.10 RPM
YRI_NA18916	0.02 RPM
YRI_NA19093	0.03 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.03 RPM
YRI_NA19118	0.02 RPM
YRI_NA19213	0.17 RPM
YRI_NA19214	0.07 RPM
YRI_NA19223	0.18 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).