RetrogeneDB ID: retro_rnor_429

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:32932775..32933095(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000039785
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Bcl2l13
• Ensembl ID: ENSRNOG00000012394
• Aliases: None
• Description: bcl-2-like protein 13 [Source:RefSeq peptide;Acc:NP_001101355]

Sequence

>retro_rnor_429
ATATCTCTAGGATTCACCATGAAACAAAGTATGCTGTTCTCAGCTACTTGGGACCTCTCTCGCAGAAGAAACAAAAAGGT
CCCTCACCCCAAGGAGTTCATCTAGATTGCGCACTACGGTCTCTGAATCCAGAAGTTTTATTAAAAGTTAAATCTGAGAT
TGAGGAGGAACTGAAATCTTTGGACAAAGAAGTCTCTGAAGCCTTCACCAGCACAGGCTTTGACTGTCACACCTCATTGG
TGTTTAGCCTTGCTACCCCTGAAAGCTCCTTAGAAGACTGCTTGGCCCATCTTGAAGAAAGGGTATCACAAGATCTAAAC

Alignment

ORF - retro_rnor_429 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.63 %
• Parental protein coverage: 53.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VPLGF-HYETKYVVLSYLGLLSQEKQQGPSPQGSQLDVAPQSLNPEVLLKIKSEIEEELKSLDKEVSEAF
          ..LGF.H.ETKY.VLSYLG.LSQ.KQ.GPSPQG..LD.A..SLNPEVLLK.KSEIEEELKSLDKEVSEAF
Retrocopy ISLGF<HHETKYAVLSYLGPLSQKKQKGPSPQGVHLDCALRSLNPEVLLKVKSEIEEELKSLDKEVSEAF

Parental  TSTGFDCHTSPVFSPANPESSVEDCLAQLGERVSRDLS
          TSTGFDCHTS.VFS.A.PESS.EDCLA.L.ERVS.DL.
Retrocopy TSTGFDCHTSLVFSLATPESSLEDCLAHLEERVSQDLN

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	9.78 RPM
SRP017611_kidney	0.00 RPM	9.63 RPM
SRP017611_liver	0.00 RPM	6.45 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_429 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_429 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_429 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	ENSECAG00000010335	1 retrocopy	retro_ecab_1010,
Otolemur garnettii	ENSOGAG00000002830	1 retrocopy	retro_ogar_430,
Rattus norvegicus	ENSRNOG00000012394	1 retrocopy	retro_rnor_429 ,