RetrogeneDB ID: retro_rnor_732

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 10:17086918..17087501(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000004053
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Tmem134
• Ensembl ID: ENSRNOG00000022153
• Aliases: Tmem134, RGD1305824
• Description: transmembrane protein 134 isoform a [Source:RefSeq peptide;Acc:NP_001072115]

Sequence

>retro_rnor_732
ATGAGCGCCATCCGGCCCCAGTTCAGCATCGATGACGCATTCGAGCTGATCCTGGAGAACGTGGGGCCTGGGCCGGAGTC
CAGCGGGGTCCCCCCGCTTCGGGCCGCTGCACTTCGAACGCTGGGCCCAGTTTGAGGTAGCTGATGAAGACAAGCAGTCC
CGACTAGCTACCAGAACCTGGAAAGTGATGAGGATGGAGCCCAGGCCTCTCCGGAGCCTGATGGGGAGTCAGCACCAGGG
GTTCTGGGCACATGTCTATCCGTAGCTCCCAGTGTTCCTCCAGCACTATCAGCAGTAGCACCCAGCGCTCCTGCAATGCT
TGCTGCAGCTGGACCCAACATCCTTTGATCCAGAAAAACGGCCGGGTAGTGCTGGCCTCCTTCCTGCTTCTTCTGTTGGG
ACTAGTGCTTATCCTGGACGGAGTGGGACTGGAGGTGGCCCCCTCTCCAGGTGTTTCCAGCGCCATCTTCTTCAAGCCGG
GTGTCCTACTGCTAGTCCCGGGAGTCTACCACGTGATCTTCATCTACGGTGCTGTCAAGGGCCACCGGGCTTCGGATTCG
TCTACCTGCCCTGCTTTGAGAAG

Alignment

ORF - retro_rnor_732 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.93 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSAARPQFSIDDAFELTLEDAGPGPESSGVA-RFGPLHFDRRARFEVTDEEKQSRLR-YQNLENDEDGAQ
          MSA.RPQFSIDDAFEL.LE..GPGPESSGV..RFGPLHF.R.A.FEV.DE.KQSRL..YQNLE.DEDGAQ
Retrocopy MSAIRPQFSIDDAFELILENVGPGPESSGVP>RFGPLHFERWAQFEVADEDKQSRLA<YQNLESDEDGAQ

Parental  ASPEPDG-GVSTRGSGHMSIRSSQWSFSTISSSTQRSYNACCSWTQHPLIQKNRRVVLASFLLLLLGLVL
          ASPEPDG.GVSTRGSGHMSIRSSQ.S.STISSSTQRS.NACCSWTQHPLIQKN.RVVLASFLLLLLGLVL
Retrocopy ASPEPDG<GVSTRGSGHMSIRSSQCSSSTISSSTQRSCNACCSWTQHPLIQKNGRVVLASFLLLLLGLVL

Parental  ILVGVGLEVAPSPGVSSAIFFVPGILLLVPGVYHVIFIYCAVKGRR-GFQFFYLPYFEK
          IL.GVGLEVAPSPGVSSAIFF.PG.LLLVPGVYHVIFIY.AVKG.R.GF.F.YLP.FEK
Retrocopy ILDGVGLEVAPSPGVSSAIFFKPGVLLLVPGVYHVIFIYGAVKGHR<GFGFVYLPCFEK

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	13.95 RPM
SRP017611_kidney	0.00 RPM	33.01 RPM
SRP017611_liver	0.00 RPM	18.02 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_732 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_732 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_732 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000016857	1 retrocopy	retro_ecab_382,
Myotis lucifugus	ENSMLUG00000005143	1 retrocopy	retro_mluc_1560,
Rattus norvegicus	ENSRNOG00000022153	1 retrocopy	retro_rnor_732 ,