RetrogeneDB ID: retro_hsap_1634

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 16:47296648..47297411(+)
• Located in intron of: ENSG00000129636

Retrocopy information

• Ensembl ID: ENSG00000260012
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PSMB5
• Ensembl ID: ENSG00000100804
• Aliases: PSMB5, LMPX, MB1, X
• Description: proteasome (prosome, macropain) subunit, beta type, 5 [Source:HGNC Symbol;Acc:9542]

Sequence

>retro_hsap_1634
ATGAACCAGTGCAGGTTTTCTGGACTCACAGTTTATGCAGATCTGCTGGATCTGGGTCCAGGGAGTCCCACTGATGGGCT
GAGGCTGGCCATGCCCAGCTGGGGAGTCTCAGAGGAGCAGGGAATCAAAATGCTTCCTGGAATCACCACCCTGGTCTTCA
AGTTCTGGCATGGAGTCATAGTTGCAGCAGACTATAGGGCTGCAGTGGGTGCTTACATTGCCTCCAGATGGTAAAGAAGG
TGACAGAGATCAACCCCTACCCGAAGCCATCATGGCTAGGGGCACAGGGAACTGTAGCTTCTGAGAATGGCTGTTGGCTC
GGCAAAGTCAAATGTATGAGCTTTGAAATAAGGAATGCATCCCTGTAACAGCTGCCTCCAAGCTGCCTGACAACATATTG
TATCAGTACAAAGGCATGGGGCTGTCCATAGGCAACATGATCTGTGGCTGGGATAGGAGAGGCCCTGGCCTCTGCTACAT
GGACACTGAAGGGAATCAGATCTCAGGGGCCACCTTCTCTGTAGGTTCTTGCTCTGTGTATGCTTATGGGGTTATGAATC
AGGGCTATTCCTATAACCTGGAAATGGAGCAGGCCTATGATCTGGCCCATGAGGTAAGCTACCAAGCCATCTACCAAGCC
ACCTGCATAGATGCCTACTCAGGAGGTGCTGCTAACCTCTACCATGTGCAGGAGGATGGCTGGATCCAAGTCTCCAGTGA
CAATGCAGTTGATCTTCATGACAAGTATGATGGATCTACCCCA

Alignment

ORF - retro_hsap_1634 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.82 %
• Parental protein coverage: 95.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VNQRGFFGLGGRADLLDLGPGSLSDGLSLAAPGWGVPEEPGIEMLHGTTTLAFKFRHGVIVAADSRATAG
          .NQ..F.GL...ADLLDLGPGS..DGL.LA.P.WGV.EE.GI.ML.G.TTL.FKF.HGVIVAAD.RA..G
Retrocopy MNQCRFSGLTVYADLLDLGPGSPTDGLRLAMPSWGVSEEQGIKMLPGITTLVFKFWHGVIVAADYRAAVG

Parental  AYIAS-QTVKKVIEIN-PYLLGTMAGGAADCSFWERLLARQCRIYELRNKERISVAAASKLLANMVYQYK
          AYIAS.Q.VKKV.EIN.P.....MA.G...CSF.E.LLARQ...YEL.NKE.I.V.AASKL..N..YQYK
Retrocopy AYIAS<QMVKKVTEIN<PLPEAIMARGTGNCSF*EWLLARQSQMYEL*NKECIPVTAASKLPDNILYQYK

Parental  GMGLSMGTMICGWDKRGPGLYYVDSEGNRISGATFSVGSGSVYAYGVMDRGYSYDLEVEQAYDLAR----
          GMGLS.G.MICGWD.RGPGL.Y.D.EGN.ISGATFSVGS.SVYAYGVM..GYSY.LE.EQAYDLA.....
Retrocopy GMGLSIGNMICGWDRRGPGLCYMDTEGNQISGATFSVGSCSVYAYGVMNQGYSYNLEMEQAYDLAHEVSY

Parental  RAIYQATYRDAYSGGAVNLYHVREDGWIRVSSDNVADLHEKYSGSTP
          .AIYQAT..DAYSGGA.NLYHV.EDGWI.VSSDN..DLH.KY.GSTP
Retrocopy QAIYQATCIDAYSGGAANLYHVQEDGWIQVSSDNAVDLHDKYDGSTP

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	0.10 RPM	40.33 RPM
bodymap2_adrenal	0.00 RPM	51.87 RPM
bodymap2_brain	0.12 RPM	57.17 RPM
bodymap2_breast	0.00 RPM	54.05 RPM
bodymap2_colon	0.00 RPM	53.00 RPM
bodymap2_heart	0.00 RPM	43.48 RPM
bodymap2_kidney	0.00 RPM	62.48 RPM
bodymap2_liver	0.00 RPM	56.84 RPM
bodymap2_lung	0.00 RPM	38.98 RPM
bodymap2_lymph_node	0.00 RPM	43.25 RPM
bodymap2_ovary	0.02 RPM	45.09 RPM
bodymap2_prostate	0.17 RPM	52.24 RPM
bodymap2_skeletal_muscle	0.15 RPM	74.26 RPM
bodymap2_testis	0.00 RPM	48.66 RPM
bodymap2_thyroid	0.04 RPM	67.10 RPM
bodymap2_white_blood_cells	0.00 RPM	18.13 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_1634 was not detected

EST

No EST(s) were mapped for retro_hsap_1634 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_51701	1215 libraries	320 libraries	281 libraries	13 libraries	0 libraries

The graphical summary, for retro_hsap_1634 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_1634 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1634 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008299	4 retrocopies	retro_cjac_1983, retro_cjac_35, retro_cjac_3888, retro_cjac_4076,
Homo sapiens	ENSG00000100804	2 retrocopies	retro_hsap_1634 , retro_hsap_95,
Latimeria chalumnae	ENSLACG00000015194	1 retrocopy	retro_lcha_3,
Macropus eugenii	ENSMEUG00000003572	1 retrocopy	retro_meug_28,
Myotis lucifugus	ENSMLUG00000014281	1 retrocopy	retro_mluc_1428,
Macaca mulatta	ENSMMUG00000006007	1 retrocopy	retro_mmul_1558,
Mus musculus	ENSMUSG00000022193	1 retrocopy	retro_mmus_2887,
Nomascus leucogenys	ENSNLEG00000014891	2 retrocopies	retro_nleu_1063, retro_nleu_2936,
Oryctolagus cuniculus	ENSOCUG00000013109	1 retrocopy	retro_ocun_176,
Pongo abelii	ENSPPYG00000005654	1 retrocopy	retro_pabe_171,
Sus scrofa	ENSSSCG00000002036	1 retrocopy	retro_sscr_616,