RetrogeneDB ID: retro_rnor_1597

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:283318533..283319073(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000050659
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Pgam5
• Ensembl ID: ENSRNOG00000037443
• Aliases: Pgam5, RGD1312028
• Description: serine/threonine-protein phosphatase PGAM5, mitochondrial [Source:RefSeq peptide;Acc:NP_001020443]

Sequence

>retro_rnor_1597
AATGTGGAATCTGGAGAAGATGAACTGGCTTCCAGACTGGACCACTATAAGACAAAGGCTACAAGGCACATATTCCTCAT
CTGGCATTCCTAGTACCATGTGGATGGCTCGCTGGAGAAGGACCACACCCTGACCCCATTAGGTGGGGAACAGGCTGAAC
TCAGGGGGCTCCTACTTGCAAGCCTGGGACTAAAGTTTAATAAAATTGTCCATCCCTCTATGACCCATGCAGTAGAGACC
ACAGACATCATCAGTAAGCACCTGCCAGGTGTCTGCAGAGTCAACACAGACTTGCTATGGGAAGGTGGCCCCACTGAACC
GGATCCACCTGCGTCTCACTGGAAGCCAGAGGCTGTGCAGTATTATGAAGATGGAGCCCGGATTGAGGCTACCTTCAGGA
ACTGCAACCACCGAGCTGATGCCAAGCAGGAGGAACACAGTTATGAGATCTTCCTACGTCACGCCAACGTCATCCGCTAT
ATTGTTTGTAGGGCACTGCAGTTTCCCCCAGAAGGTTGGCTCCTCCTGCCCCTCAACAAC

Alignment

ORF - retro_rnor_1597 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.11 %
• Parental protein coverage: 62.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NVESGEDELASRLDHYKAKATRHIFLIRHSQYNVDGSMEKDRTLTPLGREQAELTGIRLASLGLKFNKIV
          NVESGEDELASRLDHYK.KATRHIFLI.HS.Y.VDGS.EKD.TLTPLG.EQAEL.G..LASLGLKFNKIV
Retrocopy NVESGEDELASRLDHYKTKATRHIFLIWHS*YHVDGSLEKDHTLTPLGGEQAELRGLLLASLGLKFNKIV

Parental  HSSMTRAVETTDIISKHLPGVCRVSTDLLREGAPIEPDPPVSHWKPEAVQYYEDGARIEAAFRNYIHRAD
          H.SMT.AVETTDIISKHLPGVCRV.TDLL.EG.P.EPDPP.SHWKPEAVQYYEDGARIEA.FRN..HRAD
Retrocopy HPSMTHAVETTDIISKHLPGVCRVNTDLLWEGGPTEPDPPASHWKPEAVQYYEDGARIEATFRNCNHRAD

Parental  AKQEEDSYEIFICHANVIRYIVCRALQFPPEGWLRLSLNN
          AKQEE.SYEIF..HANVIRYIVCRALQFPPEGWL.L.LNN
Retrocopy AKQEEHSYEIFLRHANVIRYIVCRALQFPPEGWLLLPLNN

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
SRP017611_brain	0.00 RPM	23.87 RPM
SRP017611_kidney	0.00 RPM	22.89 RPM
SRP017611_liver	0.00 RPM	10.56 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1597 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1597 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1597 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013437	2 retrocopies	retro_amel_1052, retro_amel_173,
Choloepus hoffmanni	ENSCHOG00000011867	2 retrocopies	retro_chof_1762, retro_chof_2590,
Felis catus	ENSFCAG00000002503	2 retrocopies	retro_fcat_800, retro_fcat_960,
Homo sapiens	ENSG00000247077	1 retrocopy	retro_hsap_3363,
Myotis lucifugus	ENSMLUG00000013646	1 retrocopy	retro_mluc_1270,
Macaca mulatta	ENSMMUG00000015466	1 retrocopy	retro_mmul_2101,
Mustela putorius furo	ENSMPUG00000002639	1 retrocopy	retro_mputfur_684,
Pan troglodytes	ENSPTRG00000005657	1 retrocopy	retro_ptro_2286,
Rattus norvegicus	ENSRNOG00000037443	1 retrocopy	retro_rnor_1597 ,
Sus scrofa	ENSSSCG00000026764	1 retrocopy	retro_sscr_821,
Tursiops truncatus	ENSTTRG00000010653	1 retrocopy	retro_ttru_208,