RetrogeneDB ID: retro_pabe_1862

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 21:37534645..37535646(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD4
• Ensembl ID: ENSPPYG00000000871
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 4 [Source:HGNC Symbol;Acc:9561]

Sequence

>retro_pabe_1862
AGCAACCCTGAGAACAACATGGCCCTCATCACACTGGCTAATGACTATGAAGTGCTGACCACACTCACTCCAGACACCGG
CCACATCTTGTCCAAGCTACACACCGTCCAACCCAAGGGCAAGATCACCTTCTGCACTGGCATCCACGTGGCTCATCTGG
TTCTGAAGCACCGACGGGGCAAGAATCACAAGACGCATATCATTGCCTTCATGGGAAGCCCGAAGGCAATGAGAAGGATC
TGGTGAAACTGGCTAAATTCCTCAAGAAGGAGAAAGTAAATGTTGACATGATAATTTTTGGGGAAGAGGAGGTGAGCACA
GAAAAGCTGACAGCCTTTGTAAACACATTGAATGGCAAAGATGGAAGCGGTTCTTATCTGGTGCCCGTGCCTCCTGGGCC
CAGCTCGACTGATGCTCTCATCAGTCCTCCGATTTTGGCTGGGGAAGGTGGTGCCATGCCAGGTCTCGGTGCCAGTGACT
TTGAATTTGGAGTAGATCCCAGTGCTGATCCTGAGTTGGCCTTGGCCCTTTGAGTTTCTATGGAGGAGCAGCAGCAGCAG
CAGGAGGAGGAGCCCAGATGAGCAGCTGCAGCTTCTGCTGCTGAGGCCAGGATTGCTACAACTGGGACTGAAGGCTCAGA
CGAGGCCCTGCTGAAGATGACCATTAGCCAAAAAGAGTTTGGCCATACCGGACTTCCTGATGTAAGCAGTGTGACTGAGG
AAGAGGAGATTGCTTATGTCATGCAGATGTCCCTGCAGGGAGCAGAGTTTGGCCAGGCGGAATCAGCAGACATTGATGCC
AGCTCAGCCATGGACACATGCTAGCCAGCCAAGGAGGAGGATGATTACGACATGATGCAGGATCCTGAGTTCCTTCAAAG
TGTCCTAGAGAACCTCCCAGGTGTGGATCCCAACAACGAAGCCATTTGAAATGCTATGGGCTCCCTGGCCTCCCAGGCCA
CCAAGGATGGCAAGAAGGACAGGAAGGAGGAAGACAAGAAG

Alignment

ORF - retro_pabe_1862 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.61 %
• Parental protein coverage: 91.03 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SNPENNVGLITLANDCEVLTTLTPDTGRILSKLHTVQPKGKITFCTGIRVAHLALKHRQGKNHKMRIIAF
          SNPENN..LITLAND.EVLTTLTPDTG.ILSKLHTVQPKGKITFCTGI.VAHL.LKHR.GKNHK..IIAF
Retrocopy SNPENNMALITLANDYEVLTTLTPDTGHILSKLHTVQPKGKITFCTGIHVAHLVLKHRRGKNHKTHIIAF

Parental  V-GSPVEDNEKDLVKLAKRLKKEKVNVDIINFGEEEVNTEKLTAFVNTLNGKDGTGSHLVTVPPGPSLAD
          ..G.P.E.NEKDLVKLAK.LKKEKVNVD.I.FGEEEV.TEKLTAFVNTLNGKDG.GS.LV.VPPGPS..D
Retrocopy M<GKP-EGNEKDLVKLAKFLKKEKVNVDMIIFGEEEVSTEKLTAFVNTLNGKDGSGSYLVPVPPGPSSTD

Parental  ALISSPILAGEGGAMLGLGASDFEFGVDPSADPELALALRVSMEEQRQRQEEEARRAAAASAAEAGIATT
          ALIS.PILAGEGGAM.GLGASDFEFGVDPSADPELALAL.VSMEEQ.Q.QEEE.R.AAAASAAEA.IATT
Retrocopy ALISPPILAGEGGAMPGLGASDFEFGVDPSADPELALAL*VSMEEQQQQQEEEPR*AAAASAAEARIATT

Parental  GTEDSDDALLKMTISQQEFGRTGLPDLSSMTEEEQIAYAMQMSLQGAEFGQAESADIDASSAMDTSEPAK
          GTE.SD.ALLKMTISQ.EFG.TGLPD.SS.TEEE.IAY.MQMSLQGAEFGQAESADIDASSAMDT..PAK
Retrocopy GTEGSDEALLKMTISQKEFGHTGLPDVSSVTEEEEIAYVMQMSLQGAEFGQAESADIDASSAMDTC*PAK

Parental  EEDDYDVMQDPEFLQSVLENLPGVDPNNEAIRNAMGSLASQATKDSKKDKKEEDKK
          EEDDYD.MQDPEFLQSVLENLPGVDPNNEAI.NAMGSLASQATKD.KKD.KEEDKK
Retrocopy EEDDYDMMQDPEFLQSVLENLPGVDPNNEAI*NAMGSLASQATKDGKKDRKEEDKK

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	0.00 RPM	156.69 RPM
SRP007412_cerebellum	0.00 RPM	123.79 RPM
SRP007412_heart	0.00 RPM	61.80 RPM
SRP007412_kidney	0.00 RPM	97.95 RPM
SRP007412_liver	2.08 RPM	91.13 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1862 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1862 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1862 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2531
Pan troglodytes	retro_ptro_1474

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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,