RetrogeneDB ID: retro_rnor_2441

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 7:26570040..26570415(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tmem92
• Ensembl ID: ENSRNOG00000042868
• Aliases: None
• Description: transmembrane protein 92 [Source:MGI Symbol;Acc:MGI:3034723]

Sequence

>retro_rnor_2441
TGCCCCAAAGGATTCAGATGCTGTGACAATGAATGCTGCCTAGAAAGAAAGATCTGGAATACTGACAATGAACCCTTCAG
GATCCTGTTCATCATCTTATTGGTCATGCTGCCCCTCTTGTGCATCTGTGGCCTAGTGAGGCGCTTCTGTCCCAAGTACA
GAGAACTACAGCATGAAGTGAGAACAGCAGATCAGACACTTCCAGATCCACCCTCCATTGCTCCCCTAGAGAGCATTTGG
GTCACCTCCTTAGATCCCCCACCACCCTACAGTCAGGTTGTTCAGAAGTCAACACCCACAGAACCACCTCCTCCCTACAT
CCTCAGACCTGAGGACTCTACTTGCCCAATGAGAGAGACTGGCCATGAAACCCTT

Alignment

ORF - retro_rnor_2441 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.24 %
• Parental protein coverage: 77.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CPKGFRCCDNECCLERKIWNTDNEPFRILFIILLVMLPLLCICGLVRRFCPKCRELQHEVRTADHQSPPD
          CPKGFRCCDNECCLERKIWNTDNEPFRILFIILLVMLPLLCICGLVRRFCPK.RELQHEVRTAD.Q..PD
Retrocopy CPKGFRCCDNECCLERKIWNTDNEPFRILFIILLVMLPLLCICGLVRRFCPKYRELQHEVRTAD-QTLPD

Parental  PPSIAPLESIWVTSLDPPPPYSQVVQKSTPTEPPPPYSLRPEDSTCPMRETSHETL
          PPSIAPLESIWVTSLDPPPPYSQVVQKSTPTEPPPPY.LRPEDSTCPMRET.HETL
Retrocopy PPSIAPLESIWVTSLDPPPPYSQVVQKSTPTEPPPPYILRPEDSTCPMRETGHETL

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	0.00 RPM
SRP017611_kidney	0.00 RPM	0.28 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2441 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2441 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2441 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000167105	1 retrocopy	retro_hsap_1328,
Macaca mulatta	ENSMMUG00000001469	1 retrocopy	retro_mmul_2170,
Nomascus leucogenys	ENSNLEG00000009007	1 retrocopy	retro_nleu_1405,
Rattus norvegicus	ENSRNOG00000042868	3 retrocopies	retro_rnor_2441 , retro_rnor_2442, retro_rnor_2443,