RetrogeneDB ID: retro_rnor_2923

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:59381202..59381691(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RGD1565675
• Ensembl ID: ENSRNOG00000000111
• Aliases: Coprs, Copr5, RGD1565675
• Description: cooperator of PRMT5 [Source:RefSeq peptide;Acc:NP_001162592]

Sequence

>retro_rnor_2923
CCGGGCAAACTGAATGAGCAGGAGGCCCCCAGCGCAGAGGCTGGCTTTGTCACAGTTGACCTCTCTGTTCGGGAGACAGA
GACTGAGCTAGCCGTGGATTGATTAGCCACTGGAGCTCAGAGCATCCCTACTGATGTTCCTACCCATGCCGAGGTCCCAA
GTTCTGAAGAGGAAGGCTTTGCAATGGAGAAGGAAGCAGATGGGGAACTGTATGCCTGGGATTTGTCAGAAGGTCCAGCC
TGCCAACCCGTGGAGCAGGCTGCTGGTCTTTTTAATGAGGACTGGGACTTGGAGCTAAAAGAAGACCAAGGGAATCCTTA
AGATACTGATGACATTCAAGGGAGCATTTCCCAAGAGATTAAACCTTGGGTGTGCTGTGCACCACAAGGAGAAATGATAT
ATGACCCCAGTTGTCACCATCCACCCCCACTGATACCACATTACTCCAAGATGGTCTTTGAAACAGGACATTTTGATGAT
GCAAAAGAC

Alignment

ORF - retro_rnor_2923 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.44 %
• Parental protein coverage: 94.22 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PGEPSAWEAPSAEAGLATADLSGGETETELDVDRLASGAQSIPTDVPTHAEGPSSEEEGFAMEKEADGEL
          PG.....EAPSAEAG..T.DLS..ETETEL.VD.LA.GAQSIPTDVPTHAE.PSSEEEGFAMEKEADGEL
Retrocopy PGKLNEQEAPSAEAGFVTVDLSVRETETELAVD*LATGAQSIPTDVPTHAEVPSSEEEGFAMEKEADGEL

Parental  YAWELSEGPACPPMEQASGLFNEDWDLELKADQGNPYDADDVQGSISQEIKPWVCCAPQGDMMYDPSWHH
          YAW.LSEGPAC.P.EQA.GLFNEDWDLELK.DQGNP.D.DD.QGSISQEIKPWVCCAPQG.M.YDPS.HH
Retrocopy YAWDLSEGPACQPVEQAAGLFNEDWDLELKEDQGNP*DTDDIQGSISQEIKPWVCCAPQGEMIYDPSCHH

Parental  PPPLIPHYSKMVFETGQFDDAED
          PPPLIPHYSKMVFETG.FDDA.D
Retrocopy PPPLIPHYSKMVFETGHFDDAKD

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	21.14 RPM
SRP017611_kidney	0.00 RPM	22.40 RPM
SRP017611_liver	0.00 RPM	2.15 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2923 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2923 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2923 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001885	1 retrocopy	retro_btau_946,
Callithrix jacchus	ENSCJAG00000014110	1 retrocopy	retro_cjac_2739,
Myotis lucifugus	ENSMLUG00000016418	1 retrocopy	retro_mluc_1801,
Pongo abelii	ENSPPYG00000008153	1 retrocopy	retro_pabe_2109,
Rattus norvegicus	ENSRNOG00000000111	1 retrocopy	retro_rnor_2923 ,
Tupaia belangeri	ENSTBEG00000008542	1 retrocopy	retro_tbel_1528,
Tursiops truncatus	ENSTTRG00000009909	1 retrocopy	retro_ttru_225,