RetrogeneDB ID: retro_rnor_1546

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:161242350..161242532(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cox16
• Ensembl ID: ENSRNOG00000047115
• Aliases: None
• Description: COX16 cytochrome c oxidase assembly homolog [Source:RefSeq peptide;Acc:NP_001156625]

Sequence

>retro_rnor_1546
ATGGTTGCGCCCGCTGTGTTGCACTCTCTGCGTAAGAACAGACACTTCGCCATGGAGTTCCCTTGTGGTTGATGGTTGTT
GGAGGTTCTTTCAGTCTTCGTGAATTTTCACAAATCCGATATGATGCTGTGACAATTAAGATTGATCCTGAATTGGAGAA
AAAAATGAAAGTGAATAAAATG

Alignment

ORF - retro_rnor_1546 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.26 %
• Parental protein coverage: 57.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MVAPAVLRALRKNK-TLRYGVPMLLLVVGGSFGLREFSQIRYDAVTIKIDPELEKKLKVNKI
          MVAPAVL..LRKN..TLR.GVP..L.VVGGSF.LREFSQIRYDAVTIKIDPELEKK.KVNK.
Retrocopy MVAPAVLHSLRKNR<TLRHGVPLWLMVVGGSFSLREFSQIRYDAVTIKIDPELEKKMKVNKM

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	7.55 RPM
SRP017611_kidney	0.00 RPM	43.40 RPM
SRP017611_liver	0.07 RPM	21.31 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1546 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1546 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1546 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000133983	1 retrocopy	retro_hsap_2038,
Macaca mulatta	ENSMMUG00000011089	2 retrocopies	retro_mmul_1368, retro_mmul_1391,
Nomascus leucogenys	ENSNLEG00000001776	1 retrocopy	retro_nleu_2908,
Otolemur garnettii	ENSOGAG00000028663	1 retrocopy	retro_ogar_3045,
Pongo abelii	ENSPPYG00000005951	2 retrocopies	retro_pabe_1663, retro_pabe_1664,
Pan troglodytes	ENSPTRG00000006494	1 retrocopy	retro_ptro_1355,
Rattus norvegicus	ENSRNOG00000047115	1 retrocopy	retro_rnor_1546 ,
Tarsius syrichta	ENSTSYG00000013313	1 retrocopy	retro_tsyr_1700,
Tursiops truncatus	ENSTTRG00000014791	1 retrocopy	retro_ttru_1513,