RetrogeneDB ID: retro_rnor_144

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 10:29152407..29152644(-)
• Located in intron of: ENSRNOG00000003936

Retrocopy information

• Ensembl ID: ENSRNOG00000048034
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Ppp1r14a
• Ensembl ID: ENSRNOG00000020676
• Aliases: Ppp1r14a, Cpi17
• Description: Protein phosphatase 1 regulatory subunit 14A [Source:UniProtKB/Swiss-Prot;Acc:Q99MC0]

Sequence

>retro_rnor_144
GAGTCAGATATGCCAAATGAAGTCAATATTGATGATGAACTGTTGGAATTGGACAGTCAAGAGGAAAGAAGATGCAAAAT
CCAGGGGCTCTTGGAGTACTACACAAATCCAACAGAGGGCATCATCCAGGAGCTGCTGGCCAAGCTGCACGGCATGCATA
AGCAACCACAGCCCAGCCAATCAGATGACTATAGCCCAAGTCCCTGCCAGGACTGGACACACACTGCCCCACCCTGA

Alignment

ORF - retro_rnor_144 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.37 %
• Parental protein coverage: 54.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EADMPDEVNI-DELLELDSEEERCRKIRGLLEACLNPTEDFVQELLAKLRGLHKQPGFPQPSPSDDPSLS
          E.DMP.EVNI.DELLELDS.EER..KI.GLLE...NPTE...QELLAKL.G.HKQP...QPS.SDD.S.S
Retrocopy ESDMPNEVNIDDELLELDSQEERRCKIQGLLEYYTNPTEGIIQELLAKLHGMHKQP---QPSQSDDYSPS

Parental  PRQDPAHTAPP
          P.QD..HTAPP
Retrocopy PCQDWTHTAPP

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	9.56 RPM
SRP017611_kidney	0.00 RPM	2.72 RPM
SRP017611_liver	0.20 RPM	4.98 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_144 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_144 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_144 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000023472	1 retrocopy	retro_btau_282,
Rattus norvegicus	ENSRNOG00000020676	1 retrocopy	retro_rnor_144 ,
Rattus norvegicus	ENSRNOG00000021151	2 retrocopies	retro_rnor_1262, retro_rnor_41,