RetrogeneDB ID: retro_hsap_2531

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 21:37858566..37859269(-)
• Located in intron of: ENSG00000159261

Retrocopy information

• Ensembl ID: ENSG00000223741
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PSMD4
• Ensembl ID: ENSG00000159352
• Aliases: PSMD4, AF, AF-1, ASF, MCB1, Rpn10, S5A, pUB-R5
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 4 [Source:HGNC Symbol;Acc:9561]

Sequence

>retro_hsap_2531
AGCAACCCTGAGAACAACATGGCCCTCATCACACTGGCTAATGACTGTGAAGTGCTGACCACACTCACTCTAGACACCGG
CCGCATCCTGTCCAAGCTACACACCGTCCAACCCAAGGGCAAGATCACCTTCTACACTGGCATCCACATGGCCCATCTGG
CTCTGAAGCGCTGACGGGGCAAGAATCACAAGACGCATATCATTGCCTTCGTGGGAAGCCCAAAGGCAATGAGAAGGATC
TGGTGAAACTGGCTAAATTCCTCAAGAAGGAGAAAGTAAATGTTGACATGATAAATTTGGGGGAAGAGGAGGTGAACAGA
GAAAAGCTGACAGCCTTTGTAAACACGTTGAATGGCAAAGATGGAAGCGGTTCTCATCTGGTGGCAGTGCCTCCTGGGCC
CAGCTTGGCTGATGCTCTCATCAGTTCTCCGATTTTGGCTGGGGAAGGGGGTGCCATGCTGGGTCTCGGTGCCAGTGACT
TTGAATTTGGAGTAGATCCCAGTGCTGATCCTCAGCTGGCCTTGGCCCTCGGGTTTCTATGGAGGAGCAGCAGCAGCGGC
AGGATGAGGAGCCCAGACGAGCAGCTGCAGCCTCTGCTGCTGAGGCCAGGATTGCTACAACTGGGACTGAAGGCTCAGAC
GAGGTCCTGCTGAAGATGACCATTAGCCAACAAGAGTTTGGCCATACCGGACTTCCTGACCTA

Alignment

ORF - retro_hsap_2531 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.55 %
• Parental protein coverage: 62.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SNPENNVGLITLANDCEVLTTLTPDTGRILSKLHTVQPKGKITFCTGIRVAHLALKHRQGKNHKMRIIAF
          SNPENN..LITLANDCEVLTTLT.DTGRILSKLHTVQPKGKITF.TGI..AHLALK...GKNHK..IIAF
Retrocopy SNPENNMALITLANDCEVLTTLTLDTGRILSKLHTVQPKGKITFYTGIHMAHLALKR*RGKNHKTHIIAF

Parental  V-GSPVEDNEKDLVKLAKRLKKEKVNVDIINFGEEEVNTEKLTAFVNTLNGKDGTGSHLVTVPPGPSLAD
          V.G.P...NEKDLVKLAK.LKKEKVNVD.IN.GEEEVN.EKLTAFVNTLNGKDG.GSHLV.VPPGPSLAD
Retrocopy V<GKP-KGNEKDLVKLAKFLKKEKVNVDMINLGEEEVNREKLTAFVNTLNGKDGSGSHLVAVPPGPSLAD

Parental  ALISSPILAGEGGAMLGLGASDFEFGVDPSADPELALAL-RVSMEEQRQRQEEEARRAAAASAAEAGIAT
          ALISSPILAGEGGAMLGLGASDFEFGVDPSADP.LALAL.RVSMEEQ.QRQ.EE.RRAAAASAAEA.IAT
Retrocopy ALISSPILAGEGGAMLGLGASDFEFGVDPSADPQLALAL<RVSMEEQQQRQDEEPRRAAAASAAEARIAT

Parental  TGTEDSDDALLKMTISQQEFGRTGLPDL
          TGTE.SD..LLKMTISQQEFG.TGLPDL
Retrocopy TGTEGSDEVLLKMTISQQEFGHTGLPDL

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	96.07 RPM
bodymap2_adrenal	0.02 RPM	87.63 RPM
bodymap2_brain	0.00 RPM	84.27 RPM
bodymap2_breast	0.00 RPM	84.83 RPM
bodymap2_colon	0.00 RPM	113.27 RPM
bodymap2_heart	0.00 RPM	53.57 RPM
bodymap2_kidney	0.00 RPM	63.84 RPM
bodymap2_liver	0.00 RPM	64.30 RPM
bodymap2_lung	0.00 RPM	56.80 RPM
bodymap2_lymph_node	0.00 RPM	64.71 RPM
bodymap2_ovary	0.00 RPM	66.45 RPM
bodymap2_prostate	0.00 RPM	115.56 RPM
bodymap2_skeletal_muscle	0.62 RPM	247.34 RPM
bodymap2_testis	0.00 RPM	123.79 RPM
bodymap2_thyroid	0.15 RPM	88.70 RPM
bodymap2_white_blood_cells	0.00 RPM	95.29 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2531 was not detected

EST

No EST(s) were mapped for retro_hsap_2531 retrocopy.

TSS

No TSS is located nearby retro_hsap_2531 retrocopy 5' end.

Lab

retro_hsap_2531 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2531 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1474
Pongo abelii	retro_pabe_1862

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012565	1 retrocopy	retro_cfam_591,
Callithrix jacchus	ENSCJAG00000007357	1 retrocopy	retro_cjac_2808,
Dasypus novemcinctus	ENSDNOG00000007446	1 retrocopy	retro_dnov_1556,
Homo sapiens	ENSG00000159352	1 retrocopy	retro_hsap_2531 ,
Nomascus leucogenys	ENSNLEG00000010139	1 retrocopy	retro_nleu_1450,
Pongo abelii	ENSPPYG00000000871	1 retrocopy	retro_pabe_1862,
Pan troglodytes	ENSPTRG00000013893	1 retrocopy	retro_ptro_1474,
Sus scrofa	ENSSSCG00000006628	1 retrocopy	retro_sscr_981,
Tupaia belangeri	ENSTBEG00000016911	1 retrocopy	retro_tbel_238,
Tursiops truncatus	ENSTTRG00000007019	1 retrocopy	retro_ttru_903,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.13 RPM
CEU_NA11843	0.17 RPM
CEU_NA11930	0.07 RPM
CEU_NA12004	0.04 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.02 RPM
CEU_NA12760	0.22 RPM
CEU_NA12827	0.14 RPM
CEU_NA12872	0.11 RPM
CEU_NA12873	0.13 RPM
FIN_HG00183	0.08 RPM
FIN_HG00277	0.11 RPM
FIN_HG00315	0.08 RPM
FIN_HG00321	0.45 RPM
FIN_HG00328	0.05 RPM
FIN_HG00338	0.11 RPM
FIN_HG00349	0.03 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.05 RPM
FIN_HG00378	0.04 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.02 RPM
GBR_HG00114	0.08 RPM
GBR_HG00119	0.24 RPM
GBR_HG00131	0.06 RPM
GBR_HG00133	0.07 RPM
GBR_HG00134	0.07 RPM
GBR_HG00137	0.14 RPM
GBR_HG00142	0.11 RPM
GBR_HG00143	0.06 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.31 RPM
TSI_NA20532	0.03 RPM
TSI_NA20538	0.14 RPM
TSI_NA20756	0.23 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.09 RPM
TSI_NA20786	0.05 RPM
TSI_NA20798	0.16 RPM
YRI_NA18870	0.14 RPM
YRI_NA18907	0.14 RPM
YRI_NA18916	0.08 RPM
YRI_NA19093	0.05 RPM
YRI_NA19099	0.24 RPM
YRI_NA19114	0.03 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.24 RPM
YRI_NA19214	0.22 RPM
YRI_NA19223	0.02 RPM

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Indel association:

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