RetrogeneDB ID: retro_rnor_766

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 10:83663812..83664048(-)
• Located in intron of: ENSRNOG00000006500

Retrocopy information

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

Parental gene information

• Parental gene symbol: Psmg4
• Ensembl ID: ENSRNOG00000039265
• Aliases: Psmg4, RGD1305541
• Description: proteasome (prosome, macropain) assembly chaperone 4 [Source:RefSeq peptide;Acc:NP_001123351]

Sequence

>retro_rnor_766
CCGTATCTAAGCAACCTCGCAGTTGCCATGTGCAGCCGCTACGACTCCATCCCTGTGGGCACCCCTCTTTTTGGAGACAC
TTCTGATACGACTTCCATGGGCCTCCCTCTGCACTTAGCCAGAAGACCAGCAAGCAGGTGTTAGTCAGCTACAACCTCTC
CAATACAGACAGTGACTTAACATTACTCATAGAAGCCAGGATTAAAGAAGAAACGGAGACCTTTCGGGAAAGGTTC

Alignment

ORF - retro_rnor_766 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.5 %
• Parental protein coverage: 65.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PHLRNLAVAMCSRFDSIPVCTSLFGDTSDTTSTGLAQRLAR-KTSKQVFVSYNLSNTDSNFTLLVENRIK
          P.L.NLAVAMCSR.DSIPV.T.LFGDTSDTTS.GL...LAR.KTSKQV.VSYNLSNTDS..TLL.E.RIK
Retrocopy PYLSNLAVAMCSRYDSIPVGTPLFGDTSDTTSMGLPLHLAR<KTSKQVLVSYNLSNTDSDLTLLIEARIK

Parental  EEMETFPEKF
          EE.ETF.E.F
Retrocopy EETETFRERF

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	5.82 RPM
SRP017611_kidney	0.07 RPM	6.49 RPM
SRP017611_liver	0.00 RPM	5.85 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_766 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_766 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_766 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014430	1 retrocopy	retro_amel_1196,
Bos taurus	ENSBTAG00000031249	1 retrocopy	retro_btau_1040,
Myotis lucifugus	ENSMLUG00000024906	1 retrocopy	retro_mluc_802,
Rattus norvegicus	ENSRNOG00000039265	2 retrocopies	retro_rnor_1442, retro_rnor_766 ,
Sus scrofa	ENSSSCG00000001005	3 retrocopies	retro_sscr_362, retro_sscr_656, retro_sscr_657,
Tursiops truncatus	ENSTTRG00000006146	2 retrocopies	retro_ttru_1531, retro_ttru_1849,