RetrogeneDB ID: retro_hsap_3222

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 5:97549105..97549822(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000238000
• 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_3222
ATGGCCAAGCCTTGTGGGGTGCGCCTGAGCGGAGAAGCCCTTAAACAGGTGGAGGTCTTCAGGCAGAATCTTTTCCAGGA
GGCTGAAGAATTCCTCTGCAGATTCTTGCCACAGAAAATCATATATCTGAATCAGCTCTTGCAAGAGGACTCCCTCAATG
TGGCTGACCTGACTTCCCTCCGGTCCCCACTGGACGTCCCCATCCCAGACCCTCCACCCAAGGATGATGAGATGGAAACA
GATAAGCAGGAGAAGAAAGACGTCCCTAAGTGTGGATTTCTCCCTGGGAATGAGAAAGTCCTGTCCCTCTTTGCCCTGGT
TAAGCCAGAAGTCTGGACTCTCAAACAGAAATGCATTCTGGTGATTACGTGGATCCAACACCTGATCCCTAAGATTGACG
ATGGAAATGAGTTTGGGGTAGCAATCCAGGAGAAGGTGCTGGAGAGGGTGAATGCCGTCAAGATCAAAGTGGAAGCTTTC
CAGACAACCATTTCCAAGTACTTCTCAGAACGTGGGGATCCTGTGGCCAAGGCCTCCGAGGAGACTCATGTAATGGATTA
CCGGGCCTTGGTGCTTGAGCCAGATGAGGCAGCCTATGGGGAGCTCAGGGCCATGGTGCTGGACCTGAGGGCCTTCTATG
CTGAGCTTTATCATATCATCAGCAGCAACTTGGAGAAAATTGTCAACCCAAAGGGTGAAGAGAAGCCATCTATGTAC

Alignment

ORF - retro_hsap_3222 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.72 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAKPCGVRLSGEARKQVEVFRQNLFQEAEEFLYRFLPQKIIYLNQLLQEDSLNVADLTSLRAPLDIPIPD
          MAKPCGVRLSGEA.KQVEVFRQNLFQEAEEFL.RFLPQKIIYLNQLLQEDSLNVADLTSLR.PLD.PIPD
Retrocopy MAKPCGVRLSGEALKQVEVFRQNLFQEAEEFLCRFLPQKIIYLNQLLQEDSLNVADLTSLRSPLDVPIPD

Parental  PPPKDDEMETDKQEKKEVHKCGFLPGNEKVLSLLALVKPEVWTLKEKCILVITWIQHLIPKIEDGNDFGV
          PPPKDDEMETDKQEKK.V.KCGFLPGNEKVLSL.ALVKPEVWTLK.KCILVITWIQHLIPKI.DGN.FGV
Retrocopy PPPKDDEMETDKQEKKDVPKCGFLPGNEKVLSLFALVKPEVWTLKQKCILVITWIQHLIPKIDDGNEFGV

Parental  AIQEKVLERVNAVKTKVEAFQTTISKYFSERGDAVAKASKETHVMDYRALVHERDEAAYGELRAMVLDLR
          AIQEKVLERVNAVK.KVEAFQTTISKYFSERGD.VAKAS.ETHVMDYRALV.E.DEAAYGELRAMVLDLR
Retrocopy AIQEKVLERVNAVKIKVEAFQTTISKYFSERGDPVAKASEETHVMDYRALVLEPDEAAYGELRAMVLDLR

Parental  AFYAELYHIISSNLEKIVNPKGEEKPSMY
          AFYAELYHIISSNLEKIVNPKGEEKPSMY
Retrocopy AFYAELYHIISSNLEKIVNPKGEEKPSMY

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	1.49 RPM	41.51 RPM
bodymap2_adrenal	1.23 RPM	115.02 RPM
bodymap2_brain	0.23 RPM	19.60 RPM
bodymap2_breast	1.13 RPM	35.10 RPM
bodymap2_colon	0.12 RPM	36.04 RPM
bodymap2_heart	0.00 RPM	30.94 RPM
bodymap2_kidney	0.25 RPM	92.94 RPM
bodymap2_liver	0.08 RPM	69.10 RPM
bodymap2_lung	0.00 RPM	95.73 RPM
bodymap2_lymph_node	0.13 RPM	77.28 RPM
bodymap2_ovary	2.54 RPM	62.61 RPM
bodymap2_prostate	0.14 RPM	56.55 RPM
bodymap2_skeletal_muscle	0.07 RPM	19.08 RPM
bodymap2_testis	0.85 RPM	46.13 RPM
bodymap2_thyroid	1.58 RPM	45.01 RPM
bodymap2_white_blood_cells	0.33 RPM	122.04 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3222 was not detected

EST

No EST(s) were mapped for retro_hsap_3222 retrocopy.

TSS

No TSS is located nearby retro_hsap_3222 retrocopy 5' end.

Lab

retro_hsap_3222 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3222 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2172
Gorilla gorilla	retro_ggor_2188
Pongo abelii	retro_pabe_2669

---

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	2.65 RPM
CEU_NA11843	1.02 RPM
CEU_NA11930	1.40 RPM
CEU_NA12004	1.52 RPM
CEU_NA12400	1.82 RPM
CEU_NA12751	2.11 RPM
CEU_NA12760	1.80 RPM
CEU_NA12827	2.50 RPM
CEU_NA12872	2.04 RPM
CEU_NA12873	0.73 RPM
FIN_HG00183	1.87 RPM
FIN_HG00277	1.66 RPM
FIN_HG00315	2.43 RPM
FIN_HG00321	1.75 RPM
FIN_HG00328	1.21 RPM
FIN_HG00338	1.96 RPM
FIN_HG00349	1.93 RPM
FIN_HG00375	1.86 RPM
FIN_HG00377	2.77 RPM
FIN_HG00378	1.85 RPM
GBR_HG00099	2.01 RPM
GBR_HG00111	1.96 RPM
GBR_HG00114	3.37 RPM
GBR_HG00119	1.80 RPM
GBR_HG00131	1.44 RPM
GBR_HG00133	1.21 RPM
GBR_HG00134	2.53 RPM
GBR_HG00137	2.67 RPM
GBR_HG00142	1.69 RPM
GBR_HG00143	1.88 RPM
TSI_NA20512	2.40 RPM
TSI_NA20513	1.43 RPM
TSI_NA20518	1.78 RPM
TSI_NA20532	2.72 RPM
TSI_NA20538	2.30 RPM
TSI_NA20756	2.47 RPM
TSI_NA20765	2.01 RPM
TSI_NA20771	2.35 RPM
TSI_NA20786	2.43 RPM
TSI_NA20798	1.84 RPM
YRI_NA18870	2.30 RPM
YRI_NA18907	2.98 RPM
YRI_NA18916	2.53 RPM
YRI_NA19093	2.84 RPM
YRI_NA19099	1.81 RPM
YRI_NA19114	1.97 RPM
YRI_NA19118	3.44 RPM
YRI_NA19213	1.96 RPM
YRI_NA19214	3.71 RPM
YRI_NA19223	1.71 RPM

---

Indel association:

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