RetrogeneDB ID: retro_rnor_50

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 17:53764348..53765104(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000014510
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Psme1
• Ensembl ID: ENSRNOG00000019041
• Aliases: None
• Description: proteasome activator complex subunit 1 [Source:RefSeq peptide;Acc:NP_058960]

Sequence

>retro_rnor_50
CTGGCCATGGCTACACTAAGGGTCCATCCCGAAGCCCAAGCCAAGGTGGATGTGTTTCGTGAAGAGCTGTGTAGTAAGAC
AGAGAACCTGCTTGGGAGCTGTTTTCCCAAGAGGATCTCAGAGTTGGAAGCCTTCTTAAAGGAGCCAGCTCTCAACGAAG
CCAACCTAAGCAATCCAAAGGCTCTATTGGACATCCCAGTCCCTGATCCTATCAAGGAGAAAGAGAAGGAGGAGCGGAAG
AAGCGACAGGAGAAGGAAGAGAAGGACGAAAAGAAGAAAGGGGACGAAGACGACAAAGGTCCTGCCTGTGGCCCAGTGAA
GTGCAATGAGAAGATTGTGGTCCTCCTGCAATGCCTAAAACCCGAGATCAAGGATGTCATTGAGCAACTCAACCTGGTTA
CTACCTGGTTGCAGCTACAGATACCTCGGATAGAGGATGGGAATAATTTTGGCGTGGCTGTCCAGGAAAAGGGGTTTGAG
CTGATGACCAGCCTTCATACCAAGCTGGAAGGCTTCCAAACGCAGATCTCTAAATACTTCTCCGAGAGGGGTGACGCCGT
GGCCAAAGCAGCCAAGCAGCCCCACGTGGGAGATTATCGGCAGCTGGTGCACGAGCTGGACGAGGCAGAATACCAGGAGA
TCCAGCTGATGGTCATGGAGATCCGTAATGTTTATGTTGTGTTATATGACATCATCCTGAAGAACTTTGAGAAGCTCAAG
AAGCCCCGTGAAGAGACAAAGGGGATGATCTATTGA

Alignment

ORF - retro_rnor_50 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.57 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATLRVHPEAQAKVDVFREDLCSKTENLLGSYFPKKISELDAFLKEPALNEANLSNLKAPLDIPVPDPVK
          MATLRVHPEAQAKVDVFRE.LCSKTENLLGS.FPK.ISEL.AFLKEPALNEANLSN.KA.LDIPVPDP.K
Retrocopy MATLRVHPEAQAKVDVFREELCSKTENLLGSCFPKRISELEAFLKEPALNEANLSNPKALLDIPVPDPIK

Parental  EKEKEERKKQQEKEEKDEKKKGDEDDKGPPCGPVNCNEKIVVLLQRLKPEIKDVIEQLNLVTTWLQLQIP
          EKEKEERKK.QEKEEKDEKKKGDEDDKGP.CGPV.CNEKIVVLLQ.LKPEIKDVIEQLNLVTTWLQLQIP
Retrocopy EKEKEERKKRQEKEEKDEKKKGDEDDKGPACGPVKCNEKIVVLLQCLKPEIKDVIEQLNLVTTWLQLQIP

Parental  RIEDGNNFGVAVQEKVFELMTSLHTKLEGFQTQISKYFSERGDAVAKAAKQPHVGDYRQLVHELDEAEYQ
          RIEDGNNFGVAVQEK.FELMTSLHTKLEGFQTQISKYFSERGDAVAKAAKQPHVGDYRQLVHELDEAEYQ
Retrocopy RIEDGNNFGVAVQEKGFELMTSLHTKLEGFQTQISKYFSERGDAVAKAAKQPHVGDYRQLVHELDEAEYQ

Parental  EIRLMVMEIRNAYAVLYDIILKNFEKLKKPRGETKGMIY
          EI.LMVMEIRN.Y.VLYDIILKNFEKLKKPR.ETKGMIY
Retrocopy EIQLMVMEIRNVYVVLYDIILKNFEKLKKPREETKGMIY

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	20.63 RPM
SRP017611_kidney	0.07 RPM	100.49 RPM
SRP017611_liver	0.20 RPM	89.96 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_50 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_50 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_50 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016433	1 retrocopy	retro_amel_637,
Bos taurus	ENSBTAG00000021395	1 retrocopy	retro_btau_1189,
Canis familiaris	ENSCAFG00000011924	1 retrocopy	retro_cfam_246,
Equus caballus	ENSECAG00000016855	1 retrocopy	retro_ecab_1001,
Felis catus	ENSFCAG00000005583	1 retrocopy	retro_fcat_1567,
Macropus eugenii	ENSMEUG00000014712	1 retrocopy	retro_meug_1052,
Mus musculus	ENSMUSG00000022216	1 retrocopy	retro_mmus_466,
Rattus norvegicus	ENSRNOG00000019041	1 retrocopy	retro_rnor_50 ,
Tursiops truncatus	ENSTTRG00000008620	1 retrocopy	retro_ttru_569,