RetrogeneDB ID: retro_rnor_1442

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 19:10663916..10664184(-)
• Located in intron of: None

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_1442
ACTTTTACGCTCTTCCTGTGGGTGGGGGCGCGCCGCATCTACGCAAACTGGCAGTGGCCATGTGCAGCCGCTTCGACTCC
ATCCCTGTGTGCATCTCCCTTCTTGGAGACATTTCTGAGGCGACTTCCACCGGCCTCGCTCGGCGCTTAGCCAGGAGGAC
CACAAACAGGTGTTTGTCAGCTACGACCTCTCCAATACAGACAGCGACTTCACGTTACTCGTAGAAAACAGGATTATAGA
AGAAATGGAGACCTTCCCAGAACAGTTC

Alignment

ORF - retro_rnor_1442 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.43 %
• Parental protein coverage: 74.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TDSLFLWVGA-TPHLRNLAVAMCSRFDSIPVCTSLFGDTSDTTSTGLAQRLARKTS-KQVFVSYNLSNTD
          T..LFLWVGA..PHLR.LAVAMCSRFDSIPVC.SL.GD.S..TSTGLA.RLAR.T..KQVFVSY.LSNTD
Retrocopy TFTLFLWVGA<APHLRKLAVAMCSRFDSIPVCISLLGDISEATSTGLARRLARRTT<KQVFVSYDLSNTD

Parental  SNFTLLVENRIKEEMETFPEKF
          S.FTLLVENRI.EEMETFPE.F
Retrocopy SDFTLLVENRIIEEMETFPEQF

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	0.22 RPM	5.82 RPM
SRP017611_kidney	0.00 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_1442 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1442 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1442 has 0 orthologous retrocopies within eutheria group .

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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,