RetrogeneDB ID: retro_hsap_2999

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 4:159928271..159928674(+)
• Located in intron of: ENSG00000164123

Retrocopy information

• Ensembl ID: ENSG00000248988
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PSME2
• Ensembl ID: ENSG00000100911
• Aliases: PSME2, PA28B, PA28beta, REGbeta
• Description: proteasome (prosome, macropain) activator subunit 2 (PA28 beta) [Source:HGNC Symbol;Acc:9569]

Sequence

>retro_hsap_2999
ATGGCCAAGCCGTGTGGGGTGCGCCTGAGACGGGAGGCCTGTAAACAGGTGGAGATCTTCAGGCAGAATCTTTTCCAGGA
GGCTGAGGAATTCCTCTACAGATTCTTGCCACAGAAAATCATATACTTGAATCAGCTCTTGCAAGGTACTGCCTCAATGT
GGCTGACCTGACTTCCCTCCGGGCCCCACTGGACATCTCATCCCAGGCCCTCCACCCAAGGATGATGAGATGGAAACAGA
TAAGCAGGAGATGAAAGAAGTCCCTAAGAGTGGATTTCTCCCTAGGAATGAGAAGGTCCTGTTCCTGCTTGCCCTGGTTA
AGCCAGGAGTCTGTAGTCTCAAAGAGAAATGCATTCTAGTGATCACAGGGATCCAGCACCTGATCCTCAAGATTGAAGAT
GGA

Alignment

ORF - retro_hsap_2999 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.67 %
• Parental protein coverage: 56.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAKPCGVRLSGEARKQVEVFRQNLFQEAEEFLYRFLPQKIIYLNQLLQEDS-LNVADLTSLRAPLDIP-I
          MAKPCGVRL..EA.KQVE.FRQNLFQEAEEFLYRFLPQKIIYLNQLLQ....LNVADLTSLRAPLDI..I
Retrocopy MAKPCGVRLRREACKQVEIFRQNLFQEAEEFLYRFLPQKIIYLNQLLQGTA<LNVADLTSLRAPLDIS<I

Parental  PDPPPKDDEMETDKQEKKEVHKCGFLPGNEKVLSLLALVKPEVWTLKEKCILVITWIQHLIPKIEDG
          P.PPPKDDEMETDKQE.KEV.K.GFLP.NEKVL.LLALVKP.V..LKEKCILVIT.IQHLI.KIEDG
Retrocopy PGPPPKDDEMETDKQEMKEVPKSGFLPRNEKVLFLLALVKPGVCSLKEKCILVITGIQHLILKIEDG

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	41.51 RPM
bodymap2_adrenal	0.00 RPM	115.02 RPM
bodymap2_brain	0.02 RPM	19.60 RPM
bodymap2_breast	0.04 RPM	35.10 RPM
bodymap2_colon	0.27 RPM	36.04 RPM
bodymap2_heart	0.00 RPM	30.94 RPM
bodymap2_kidney	0.02 RPM	92.94 RPM
bodymap2_liver	0.00 RPM	69.10 RPM
bodymap2_lung	0.00 RPM	95.73 RPM
bodymap2_lymph_node	0.00 RPM	77.28 RPM
bodymap2_ovary	0.06 RPM	62.61 RPM
bodymap2_prostate	0.09 RPM	56.55 RPM
bodymap2_skeletal_muscle	0.00 RPM	19.08 RPM
bodymap2_testis	0.04 RPM	46.13 RPM
bodymap2_thyroid	0.00 RPM	45.01 RPM
bodymap2_white_blood_cells	0.00 RPM	122.04 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2999 was not detected

EST

No EST(s) were mapped for retro_hsap_2999 retrocopy.

TSS

No TSS is located nearby retro_hsap_2999 retrocopy 5' end.

Lab

retro_hsap_2999 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2999 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2028
Pongo abelii	retro_pabe_2486
Macaca mulatta	retro_mmul_1919

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007167	3 retrocopies	retro_cjac_233, retro_cjac_322, retro_cjac_71,
Homo sapiens	ENSG00000100911	4 retrocopies	retro_hsap_1200, retro_hsap_2999 , retro_hsap_3033, retro_hsap_3222,
Homo sapiens	ENSG00000131467	1 retrocopy	retro_hsap_245,
Gorilla gorilla	ENSGGOG00000016025	4 retrocopies	retro_ggor_2078, retro_ggor_2093, retro_ggor_2188, retro_ggor_935,
Macaca mulatta	ENSMMUG00000012473	4 retrocopies	retro_mmul_1229, retro_mmul_1919, retro_mmul_1940, retro_mmul_2281,
Mus musculus	ENSMUSG00000079197	1 retrocopy	retro_mmus_145,
Nomascus leucogenys	ENSNLEG00000015260	4 retrocopies	retro_nleu_2086, retro_nleu_2726, retro_nleu_3086, retro_nleu_844,
Otolemur garnettii	ENSOGAG00000016584	1 retrocopy	retro_ogar_61,
Pongo abelii	ENSPPYG00000005684	4 retrocopies	retro_pabe_1000, retro_pabe_2486, retro_pabe_2512, retro_pabe_2669,
Pan troglodytes	ENSPTRG00000006196	4 retrocopies	retro_ptro_2028, retro_ptro_2046, retro_ptro_2172, retro_ptro_820,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.21 RPM
CEU_NA11843	0.14 RPM
CEU_NA11930	0.13 RPM
CEU_NA12004	0.30 RPM
CEU_NA12400	0.07 RPM
CEU_NA12751	0.29 RPM
CEU_NA12760	0.09 RPM
CEU_NA12827	0.19 RPM
CEU_NA12872	0.22 RPM
CEU_NA12873	0.32 RPM
FIN_HG00183	0.16 RPM
FIN_HG00277	0.11 RPM
FIN_HG00315	0.30 RPM
FIN_HG00321	0.06 RPM
FIN_HG00328	0.07 RPM
FIN_HG00338	0.09 RPM
FIN_HG00349	0.23 RPM
FIN_HG00375	0.24 RPM
FIN_HG00377	0.35 RPM
FIN_HG00378	0.21 RPM
GBR_HG00099	0.26 RPM
GBR_HG00111	0.17 RPM
GBR_HG00114	0.21 RPM
GBR_HG00119	0.29 RPM
GBR_HG00131	0.17 RPM
GBR_HG00133	0.14 RPM
GBR_HG00134	0.24 RPM
GBR_HG00137	0.27 RPM
GBR_HG00142	0.19 RPM
GBR_HG00143	0.29 RPM
TSI_NA20512	0.20 RPM
TSI_NA20513	0.02 RPM
TSI_NA20518	0.08 RPM
TSI_NA20532	0.34 RPM
TSI_NA20538	0.32 RPM
TSI_NA20756	0.12 RPM
TSI_NA20765	0.21 RPM
TSI_NA20771	0.17 RPM
TSI_NA20786	0.26 RPM
TSI_NA20798	0.12 RPM
YRI_NA18870	0.17 RPM
YRI_NA18907	0.38 RPM
YRI_NA18916	0.25 RPM
YRI_NA19093	0.42 RPM
YRI_NA19099	0.29 RPM
YRI_NA19114	0.08 RPM
YRI_NA19118	0.23 RPM
YRI_NA19213	0.22 RPM
YRI_NA19214	0.34 RPM
YRI_NA19223	0.12 RPM

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Indel association:

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