RetrogeneDB ID: retro_ptro_1474

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 21:22589477..22590476(-)
• Located in intron of: ENSPTRG00000013892

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PSMD4
• Ensembl ID: ENSPTRG00000013893
• Aliases: None
• Description: Pan troglodytes proteasome (prosome, macropain) 26S subunit, non-ATPase, 4 (PSMD4), mRNA. [Source:RefSeq mRNA;Acc:NM_001137557]

Sequence

>retro_ptro_1474
AGCAACCCTGAGAACAACACGGCCCTCATCACACTGGCTAATGACTATGAAGTGCTGACCACACTCACTCCAGACACCAG
CCGTATCCTGTCCAAGCTACACACCGTCCAACCCAAGGGCAAGATCACCTTCTGCACTGGCATCCACATGGCCCATCTGG
CTCTGAAGCGGCGACGGGGCAAGAATCACAAGACGCATATCATTGCCTTCGTGGCAAGCCCAAAGGCAATGAGAAGGATC
TGGTGAAACTGGCTAAATTCCTCAAGAAGGAGAAAGTAAATGTTGACATGATAAATTTGGGGGAAGAGGAGGTGAACACA
GAAAAGCTGACAGCCTTTGTAAACACGTTGAATGGCAAAGATGGAAGCGGTTCTCATCTGGTGGCAGTGCCTCCTGGGCC
CAGCTTGGCTGATGCTCTCATCAGTTCTCCAATTTTGGCTGGGGAAGGGGGTGCCATGCTGGGTCTCGGTGCCAGTGACT
TTGAATTTGGAGTAGATCCCAGTGCTGATCCTGAGCTGGCCTTGGCCCTCAGGTTTCTATGGAGGAGCAGCAGCAGCGGC
AGGAGGAGGAGCCCAGACGAGCAGCTGCAGCCTCTGCTGCTGAGGCCAGGATTGCTACAACTGGGACTGAAGGCTCAGAC
GAGGCCCTGCTGAAGATGACCATTAGCCAACAAGAGTTTGGCCATACCGGACTTCCTGACCTAAGCAGTGTGACTGAGGA
AGAGGGGATTGCTTATGTCATGCAGATGTCCCTGCAGGAGCAGAGTTTGGCCAGGCGGAATCAGCAGACATTGATGCCAG
CTCAGCCATGGACACTTGCCAGCCAGCCAAGGAGGAGGATGATTACGACGTGATGCAGGATCCCGAGTTCCTTCAGAGTG
TCCTGGAGAACCTCCCAGGTGTGGATCCCAACAATGAAGACATTTGAAACGCTGTGGGCTCCCTGGCCTGCCAGGCCACC
AAGGATGGCAAGAAGGACAAGAAGGAGGAAGACAAGAAG

Alignment

ORF - retro_ptro_1474 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.05 %
• Parental protein coverage: 88.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SNPENNVGLITLANDCEVLTTLTPDTGRILSKLHTVQPKGKITFCTGIRVAHLALKHRQGKNHKMRIIAF
          SNPENN..LITLAND.EVLTTLTPDT.RILSKLHTVQPKGKITFCTGI..AHLALK.R.GKNHK..IIAF
Retrocopy SNPENNTALITLANDYEVLTTLTPDTSRILSKLHTVQPKGKITFCTGIHMAHLALKRRRGKNHKTHIIAF

Parental  V-GSPVEDNEKDLVKLAKRLKKEKVNVDIINFGEEEVNTEKLTAFVNTLNGKDGTGSHLVTVPPGPSLAD
          V.G.P...NEKDLVKLAK.LKKEKVNVD.IN.GEEEVNTEKLTAFVNTLNGKDG.GSHLV.VPPGPSLAD
Retrocopy V<GKP-KGNEKDLVKLAKFLKKEKVNVDMINLGEEEVNTEKLTAFVNTLNGKDGSGSHLVAVPPGPSLAD

Parental  ALISSPILAGEGGAMLGLGASDFEFGVDPSADPELALALR-VSMEEQRQRQEEEARRAAAASAAEAGIAT
          ALISSPILAGEGGAMLGLGASDFEFGVDPSADPELALALR.VSMEEQ.QRQEEE.RRAAAASAAEA.IAT
Retrocopy ALISSPILAGEGGAMLGLGASDFEFGVDPSADPELALALR<VSMEEQQQRQEEEPRRAAAASAAEARIAT

Parental  TGTEDSDDALLKMTISQQEFGRTGLPDLSSMTEEEQIAYAMQMSLQ-GAEFGQAESADIDASSAMDTSEP
          TGTE.SD.ALLKMTISQQEFG.TGLPDLSS.TEEE.IAY.MQMSLQ.GAEFGQAESADIDASSAMDT..P
Retrocopy TGTEGSDEALLKMTISQQEFGHTGLPDLSSVTEEEGIAYVMQMSLQ<GAEFGQAESADIDASSAMDTCQP

Parental  AKEEDDYDVMQDPEFLQSVLENLPGVDPNNEAIRNAMGSLASQATKDGKKDKKEEDKK
          AKEEDDYDVMQDPEFLQSVLENLPGVDPNNE.I.NA.GSLA.QATKDGKKDKKEEDKK
Retrocopy AKEEDDYDVMQDPEFLQSVLENLPGVDPNNEDI*NAVGSLACQATKDGKKDKKEEDKK

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
SRP007412_brain_prefrontal_cortex	0.09 RPM	147.98 RPM
SRP007412_cerebellum	0.07 RPM	106.51 RPM
SRP007412_heart	0.03 RPM	96.88 RPM
SRP007412_kidney	0.08 RPM	93.41 RPM
SRP007412_liver	0.03 RPM	106.78 RPM
SRP007412_testis	0.42 RPM	405.41 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1474 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1474 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1474 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2531
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,