RetrogeneDB ID: retro_hsap_1997

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 19:36912542..36913445(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000267142
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ACOT4
• Ensembl ID: ENSG00000177465
• Aliases: None
• Description: acyl-CoA thioesterase 4 [Source:HGNC Symbol;Acc:19748]

Sequence

>retro_hsap_1997
CGCGCGTCCCTGCGCGACGAGAAGGCTGGGCTCTTCCGCTACTGCGCCGACGCCCGCGGCGAGCTGGACCTGGAGCGCGC
GCCCGTGCTGGGCGGCAGCTTTAGGGGGCTAGAGTCCATGGGGCTGCTCTGGGCCCTGGAATCCAAGAAACCTTTTTGGC
GCTTTCTGAAGCGGGACGTACAGATTCCCTTTATCGTGGAGTTGGAGGTGCTGGACGGCCACGACCCCGAGCCTGGACGG
CTGTTGTGACAGGCGCGGCACGAGCGCGACTTCCTCCCACAAGGGGTGCGGAGCGATTCGGTGCGCGCGGGCCGGGTGCG
CGCCACGCTCTTCCTGCCGCCAGGACCTGGACCCTTCCTAGGGATCATTGGCATCTTTGGTAATGGAGGGAGCCTGTTGG
AATATCGAGCCAGCCTCCTTGCTGGCCATGGCTTTGCCACGTTCGCTCTAGCTTGTTATAACTTTGAAGATCTCCCCAAG
AACGTGGACAACATACCCCTGGAGTACTTCGAAGAAGCCCTATGCTACATGCTTCAACATCCCCAGGTAAAAGGCCCAGG
CACTGGGCTTTGGGGCATTTCTCTAGGAGCTGATATTTGTCTCTCAATGGCCTCATTCTTGAAGAATGACTCAGACACAG
TTTCCATCAATGGATCCGGGATCAGTGGGAACAGAGGCATAAACTGTAAGCAGAATAGCATTCCACCATTGGGCTATGAC
CTGAGGAGAATCAAGGTAGCTTTCTCAGGCCTCGTGGACGTCGTGGATATAAAGAATGATCTTGTAGGAGGGTATAAGAA
CCCCAGCATGATTTCAATGGAGAAGGCCCAGGGCCCCATCATTTTCATTGTTGGTCAGGATGACCATAACTGGAGGAGTG
AGTTGTATGCCCAGTCTCTGAAC

Alignment

ORF - retro_hsap_1997 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.59 %
• Parental protein coverage: 72.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RASLRDEKGALFRAHARYCADARGELDLERAPALGGSFAGLEPMGLLWALEPEKPFWRFLKRDVQIPFVV
          RASLRDEK..LF....RYCADARGELDLERAP.LGGSF.GLE.MGLLWALE..KPFWRFLKRDVQIPF.V
Retrocopy RASLRDEKAGLF----RYCADARGELDLERAPVLGGSFRGLESMGLLWALESKKPFWRFLKRDVQIPFIV

Parental  ELEVLDGHDPEPGRLLCQAQHERHFLPPGVRRQSVRAGRVRATLFLPPGPGPFPGIIDIFGIGGGLLEYR
          ELEVLDGHDPEPGRLL.QA.HER.FLP.GVR..SVRAGRVRATLFLPPGPGPF.GII.IFG.GG.LLEYR
Retrocopy ELEVLDGHDPEPGRLL*QARHERDFLPQGVRSDSVRAGRVRATLFLPPGPGPFLGIIGIFGNGGSLLEYR

Parental  ASLLAGHGFATLALAYYNFEDLPNNMDNISLEYFEEAVCYMLQHPQVKGPGIGLLGISLGADICLSMASF
          ASLLAGHGFAT.ALA.YNFEDLP.N.DNI.LEYFEEA.CYMLQHPQVKGPG.GL.GISLGADICLSMASF
Retrocopy ASLLAGHGFATFALACYNFEDLPKNVDNIPLEYFEEALCYMLQHPQVKGPGTGLWGISLGADICLSMASF

Parental  LKNVSATVSINGSGISGNTAINYKHSSIPPLGYDLRRIKVAFSGLVDIVDIRNALVGGYKNPSMIPIEKA
          LKN.S.TVSINGSGISGN..IN.K..SIPPLGYDLRRIKVAFSGLVD.VDI.N.LVGGYKNPSMI..EKA
Retrocopy LKNDSDTVSINGSGISGNRGINCKQNSIPPLGYDLRRIKVAFSGLVDVVDIKNDLVGGYKNPSMISMEKA

Parental  QGPILLIVGQDDHNWRSELYAQTVS
          QGPI..IVGQDDHNWRSELYAQ...
Retrocopy QGPIIFIVGQDDHNWRSELYAQSLN

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	0.04 RPM	1.55 RPM
bodymap2_adrenal	0.16 RPM	1.99 RPM
bodymap2_brain	0.16 RPM	3.54 RPM
bodymap2_breast	0.06 RPM	8.31 RPM
bodymap2_colon	0.00 RPM	0.70 RPM
bodymap2_heart	0.02 RPM	0.72 RPM
bodymap2_kidney	0.02 RPM	7.44 RPM
bodymap2_liver	0.00 RPM	15.53 RPM
bodymap2_lung	0.00 RPM	1.35 RPM
bodymap2_lymph_node	0.00 RPM	0.69 RPM
bodymap2_ovary	0.02 RPM	0.83 RPM
bodymap2_prostate	0.00 RPM	1.54 RPM
bodymap2_skeletal_muscle	0.00 RPM	0.02 RPM
bodymap2_testis	0.04 RPM	2.96 RPM
bodymap2_thyroid	0.09 RPM	1.22 RPM
bodymap2_white_blood_cells	0.00 RPM	2.34 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1997 was not detected

EST

No EST(s) were mapped for retro_hsap_1997 retrocopy.

TSS

No TSS is located nearby retro_hsap_1997 retrocopy 5' end.

Lab

retro_hsap_1997 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1997 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000177465	1 retrocopy	retro_hsap_1997 ,
Macaca mulatta	ENSMMUG00000006856	1 retrocopy	retro_mmul_1376,
Nomascus leucogenys	ENSNLEG00000016052	1 retrocopy	retro_nleu_897,
Pongo abelii	ENSPPYG00000029617	1 retrocopy	retro_pabe_1638,
Pan troglodytes	ENSPTRG00000006518	1 retrocopy	retro_ptro_1369,

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	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.06 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 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	0.00 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	0.02 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).