RetrogeneDB ID: retro_hsap_4720

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: X:79965426..79966204(+)
• Located in intron of: ENSG00000165288

Retrocopy information

• Ensembl ID: ENSG00000225715
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PSMA1
• Ensembl ID: ENSG00000129084
• Aliases: PSMA1, HC2, HEL-S-275, NU, PROS30
• Description: proteasome (prosome, macropain) subunit, alpha type, 1 [Source:HGNC Symbol;Acc:9530]

Sequence

>retro_hsap_4720
TTTAGAAACCAGTATGACAATGATATCATTGTCTGGAGCAGGATTCATCAAACTGAATATGCAATGGAAGCTGTTAAACA
AGGTTCAGCCACAGTTGGTCTGAAATCAAAAACCCATGCAGTATTGGTTGCATTGAAAAGGGCACCATCGGAGCTTGCAG
CTCATCAGAAAAAAATTCTCCATATTGACAAACATATTGGTATCTCAATTGCAGGGCTTACTGATGATGGTAAACTGTTA
CGTAATTTTATGTGCCAGGAGTGTTTCGATTCCAGATTTGTATCTGATAGACCACTTCCTGTGTCTTCTCTTGTATCTCT
AATTGGAAGCAAGACCCAAATATCAACACAACAATATGGCTGGAGACCATATGGTGTTAGGCTACTTACTGCTGGTTATA
ATGATATGGGCCTCACATTTTCCAAACCTGGTCATCTGCTGACTATTTTGACTACAGAGCTACGTCCACTGGGGCCCATT
CTCAGTCAGCTCGTACTTACTTGGAGAGACATATGTCTAAATTTATGGAATACAATTTAAATGAACTGGTTAAACATGGT
CTGCATGCCTGAAGAGAGACAATTCCTGCAGAACAGGACATAACTACAAAAATGTTTCCATTGGAATTGCTGGTAATAAT
TTGGAGTTTACAATCTATCATGATGATGATGATGTGTCTCCAATCCTGGAAGGTCTTGAAGAAAGGCCACAGAGAAAGGC
AAAGCCTGCTCAACCTGCTGATTAACCAGCAGAAAAGGCTGATGAACCAATGGAACAT

Alignment

ORF - retro_hsap_4720 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.02 %
• Parental protein coverage: 99.62 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FRNQYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELAAHQKKILHVDNHIG
          FRNQYDND..VWS...RIHQ.EYAMEAVKQGSATVGLKSKTHAVLVALKRA.SELAAHQKKILH.D.HIG
Retrocopy FRNQYDNDIIVWS---RIHQTEYAMEAVKQGSATVGLKSKTHAVLVALKRAPSELAAHQKKILHIDKHIG

Parental  ISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPTQRYGRRPYGVGLLIAGYDDM-
          ISIAGLT.D..LL.NFM.QEC.DSRFV.DRPLPVS.LVSLIGSKTQI.TQ.YG.RPYGV.LL.AGY.DM.
Retrocopy ISIAGLTDDGKLLRNFMCQECFDSRFVSDRPLPVSSLVSLIGSKTQISTQQYGWRPYGVRLLTAGYNDM<

Parental  GPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFMECNLNELVKHGLRALRETLPAEQDLTT-KN
          GPHIFQT..SA.YFD.RA.S.GA.SQSARTYLERHMS.FME.NLNELVKHGL.A.RET.PAEQD.TT.KN
Retrocopy GPHIFQTWSSADYFDYRATSTGAHSQSARTYLERHMSKFMEYNLNELVKHGLHA*RETIPAEQDITT<KN

Parental  VSIGIVGKDLEFTIY-DDDDVSPFLEGLEERPQRKAQPAQPADEPAEKADEPMEH
          VSIGI.G..LEFTIY.DDDDVSP.LEGLEERPQRKA.PAQPAD.PAEKADEPMEH
Retrocopy VSIGIAGNNLEFTIYHDDDDVSPILEGLEERPQRKAKPAQPAD*PAEKADEPMEH

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	35.96 RPM
bodymap2_adrenal	0.00 RPM	53.16 RPM
bodymap2_brain	0.00 RPM	38.56 RPM
bodymap2_breast	0.00 RPM	52.14 RPM
bodymap2_colon	0.00 RPM	46.79 RPM
bodymap2_heart	0.00 RPM	34.52 RPM
bodymap2_kidney	0.12 RPM	42.95 RPM
bodymap2_liver	0.00 RPM	39.97 RPM
bodymap2_lung	0.11 RPM	44.59 RPM
bodymap2_lymph_node	0.05 RPM	39.67 RPM
bodymap2_ovary	0.00 RPM	44.86 RPM
bodymap2_prostate	0.00 RPM	39.84 RPM
bodymap2_skeletal_muscle	0.00 RPM	32.52 RPM
bodymap2_testis	0.00 RPM	50.09 RPM
bodymap2_thyroid	0.09 RPM	53.03 RPM
bodymap2_white_blood_cells	0.00 RPM	38.90 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_4720 was not detected

EST

No EST(s) were mapped for retro_hsap_4720 retrocopy.

TSS

No TSS is located nearby retro_hsap_4720 retrocopy 5' end.

Lab

retro_hsap_4720 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4720 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_3137
Pongo abelii	retro_pabe_3664
Macaca mulatta	retro_mmul_2509

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002440	2 retrocopies	retro_amel_1733, retro_amel_1903,
Bos taurus	ENSBTAG00000006564	1 retrocopy	retro_btau_1833,
Choloepus hoffmanni	ENSCHOG00000005395	11 retrocopies	retro_chof_155, retro_chof_1844, retro_chof_1991, retro_chof_2376, retro_chof_2626, retro_chof_267, retro_chof_2712, retro_chof_459, retro_chof_519, retro_chof_719, retro_chof_77,
Equus caballus	ENSECAG00000024086	1 retrocopy	retro_ecab_1078,
Felis catus	ENSFCAG00000011381	1 retrocopy	retro_fcat_972,
Homo sapiens	ENSG00000129084	1 retrocopy	retro_hsap_4720 ,
Gorilla gorilla	ENSGGOG00000001416	1 retrocopy	retro_ggor_2933,
Macropus eugenii	ENSMEUG00000011112	1 retrocopy	retro_meug_71,
Myotis lucifugus	ENSMLUG00000009251	4 retrocopies	retro_mluc_2444, retro_mluc_2445, retro_mluc_2463, retro_mluc_2515,
Macaca mulatta	ENSMMUG00000016446	1 retrocopy	retro_mmul_2509,
Mustela putorius furo	ENSMPUG00000013199	4 retrocopies	retro_mputfur_1243, retro_mputfur_224, retro_mputfur_338, retro_mputfur_825,
Mus musculus	ENSMUSG00000030751	1 retrocopy	retro_mmus_831,
Nomascus leucogenys	ENSNLEG00000017705	1 retrocopy	retro_nleu_1990,
Oryctolagus cuniculus	ENSOCUG00000000439	2 retrocopies	retro_ocun_1461, retro_ocun_1490,
Otolemur garnettii	ENSOGAG00000011622	3 retrocopies	retro_ogar_2267, retro_ogar_2644, retro_ogar_992,
Ochotona princeps	ENSOPRG00000013677	1 retrocopy	retro_opri_370,
Pongo abelii	ENSPPYG00000003466	2 retrocopies	retro_pabe_1883, retro_pabe_3664,
Pan troglodytes	ENSPTRG00000003385	1 retrocopy	retro_ptro_3137,
Sarcophilus harrisii	ENSSHAG00000015626	1 retrocopy	retro_shar_217,
Ictidomys tridecemlineatus	ENSSTOG00000006270	2 retrocopies	retro_itri_1470, retro_itri_987,
Tupaia belangeri	ENSTBEG00000012037	3 retrocopies	retro_tbel_2629, retro_tbel_323, retro_tbel_982,
Tarsius syrichta	ENSTSYG00000003869	2 retrocopies	retro_tsyr_1723, retro_tsyr_374,
Vicugna pacos	ENSVPAG00000008820	3 retrocopies	retro_vpac_344, retro_vpac_648, retro_vpac_82,