RetrogeneDB ID: retro_hsap_1569

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 15:55734832..55735555(-)
• Located in intron of: ENSG00000261771

Retrocopy information

• Ensembl ID: ENSG00000260036
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: THEM4
• Ensembl ID: ENSG00000159445
• Aliases: None
• Description: thioesterase superfamily member 4 [Source:HGNC Symbol;Acc:17947]

Sequence

>retro_hsap_1569
ATGCTGAGGAGCTGCGCCAGGCGCCTCCGCACGCTGGGGGCCCTTTGCCAGCCGCCACCGGTAGGCAGGCGCCTGCCGGG
TAGTGAGCCGCAACCCGCGCTGAGGTCATTTTCTTCTGAGGAAGTCATTCTTAAGGACTATTCTGTCCCCAACCCCAGCT
GGAACAAGGACCTAAGACTGCTCTTTGACCAGTTTATGAAGAAATGTGAAGACGGCTCCTGGAAACGTTTGCCTTCATAT
AAACGTACACCTACTGAAAGGATTCAAGACTTTAAAACCCATTTTCTTGACCCAAAGCTTATGAAAGAAGAACAAGTGTC
ACAGGCCCAGCTCTTCACCAGAAGCTTTGATGATGGCCTGGGCTTTGAATACGTGATGTTCTACAATGACGTTGAGAAAA
GGATGGTTTGCTTATTTCAAGGAGTCCCTTACCTAGAAGGACCACCTGGATTGATTCATGGAGGTGCCATTGCAACCATG
ATTGATGCTACTGTTGGTATGTGTGCAATGATGGCTGGGGGAATCGTCATGACTGCCAATCTCAACATCAGTTGTAAAAG
ACCTATCCCTCTTTGTTCTGTTGTTAGGATAAATAGCCAACTTGATAAAGTTGAAGGAAAGAAATTTTTTGTTTCCAGTA
ATGTTCAGAGTGTTGATGAGAAGACCCTATATTCAGAGGCGACAAGCTTACTTATAAAGCTGAATCCTGCTAAAAGTCTG
ACA

Alignment

ORF - retro_hsap_1569 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.95 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLRSCAARLRTLGALCLPP-VGRRLPGSEPRPELRSFSSEEVILKDCSVPNPSWNKDLRLLFDQFMKKCE
          MLRSCA.RLRTLGALC.PP.VGRRLPGSEP.P.LRSFSSEEVILKD.SVPNPSWNKDLRLLFDQFMKKCE
Retrocopy MLRSCARRLRTLGALCQPPPVGRRLPGSEPQPALRSFSSEEVILKDYSVPNPSWNKDLRLLFDQFMKKCE

Parental  DGSWKRLPSYKRTPTEWIQDFKTHFLDPKLMKEEQMSQAQLFTRSFDDGLGFEYVMFYNDIEKRMVCLFQ
          DGSWKRLPSYKRTPTE.IQDFKTHFLDPKLMKEEQ.SQAQLFTRSFDDGLGFEYVMFYND.EKRMVCLFQ
Retrocopy DGSWKRLPSYKRTPTERIQDFKTHFLDPKLMKEEQVSQAQLFTRSFDDGLGFEYVMFYNDVEKRMVCLFQ

Parental  GGPYLEGPPGFIHGGAIATMIDATVGMCAMMAGGIVMTANLNINYKRPIPLCSVVMINSQLDKVEGRKFF
          G.PYLEGPPG.IHGGAIATMIDATVGMCAMMAGGIVMTANLNI..KRPIPLCSVV.INSQLDKVEG.KFF
Retrocopy GVPYLEGPPGLIHGGAIATMIDATVGMCAMMAGGIVMTANLNISCKRPIPLCSVVRINSQLDKVEGKKFF

Parental  VSCNVQSVDEKTLYSEATSLFIKLNPAKSLT
          VS.NVQSVDEKTLYSEATSL.IKLNPAKSLT
Retrocopy VSSNVQSVDEKTLYSEATSLLIKLNPAKSLT

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	9.06 RPM
bodymap2_adrenal	0.02 RPM	22.03 RPM
bodymap2_brain	0.00 RPM	8.84 RPM
bodymap2_breast	0.00 RPM	17.32 RPM
bodymap2_colon	0.00 RPM	4.58 RPM
bodymap2_heart	0.00 RPM	13.81 RPM
bodymap2_kidney	0.04 RPM	25.93 RPM
bodymap2_liver	0.00 RPM	9.61 RPM
bodymap2_lung	0.00 RPM	3.69 RPM
bodymap2_lymph_node	0.00 RPM	15.86 RPM
bodymap2_ovary	0.04 RPM	20.14 RPM
bodymap2_prostate	0.00 RPM	15.74 RPM
bodymap2_skeletal_muscle	0.00 RPM	6.17 RPM
bodymap2_testis	0.11 RPM	19.31 RPM
bodymap2_thyroid	0.08 RPM	18.57 RPM
bodymap2_white_blood_cells	0.00 RPM	22.56 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1569 was not detected

EST

No EST(s) were mapped for retro_hsap_1569 retrocopy.

TSS

No TSS is located nearby retro_hsap_1569 retrocopy 5' end.

Lab

retro_hsap_1569 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1569 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1056
Gorilla gorilla	retro_ggor_1195
Pongo abelii	retro_pabe_1295

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000355	1 retrocopy	retro_amel_1301,
Choloepus hoffmanni	ENSCHOG00000000818	1 retrocopy	retro_chof_841,
Dasypus novemcinctus	ENSDNOG00000005970	1 retrocopy	retro_dnov_710,
Felis catus	ENSFCAG00000003443	1 retrocopy	retro_fcat_387,
Homo sapiens	ENSG00000159445	2 retrocopies	retro_hsap_1569 , retro_hsap_978,
Gorilla gorilla	ENSGGOG00000008114	2 retrocopies	retro_ggor_1195, retro_ggor_782,
Microcebus murinus	ENSMICG00000010696	4 retrocopies	retro_mmur_1241, retro_mmur_1436, retro_mmur_1505, retro_mmur_1574,
Nomascus leucogenys	ENSNLEG00000010322	1 retrocopy	retro_nleu_1737,
Oryctolagus cuniculus	ENSOCUG00000005194	1 retrocopy	retro_ocun_1341,
Pongo abelii	ENSPPYG00000000851	1 retrocopy	retro_pabe_1295,
Pan troglodytes	ENSPTRG00000001301	2 retrocopies	retro_ptro_1056, retro_ptro_768,
Tupaia belangeri	ENSTBEG00000003352	2 retrocopies	retro_tbel_2412, retro_tbel_3266,
Tarsius syrichta	ENSTSYG00000005739	1 retrocopy	retro_tsyr_579,

Population studies

Expression level across human populations :

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

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Indel association:

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