RetrogeneDB ID: retro_ocun_406

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:153052735..153052936(-)
• Located in intron of: ENSOCUG00000015212

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC169
• Ensembl ID: ENSOCUG00000026427
• Aliases: None
• Description: coiled-coil domain containing 169 [Source:HGNC Symbol;Acc:34361]

Sequence

>retro_ocun_406
GTGGGGGAGGGAAGAGGTGAAAACTTCACAACGTGAGCACCGACTGCCTTACACTGGAGTTGCTGGAAGAAATCCAGTGG
AGAGGATCATGCAACTCTCAATGCTTGGAACGAGATACAAGATAGCAGAACCGGAAGCCAGCTTCAGTGGTGACAAGAAA
GTGGCGAGTGGAAAGCTCCCCAGGAGACACAACTTGAACTG

Alignment

ORF - retro_ocun_406 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.79 %
• Parental protein coverage: 59.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGEGRGENFD-GVSTDRLKLELLEEIHMKD-IVQLSMLEIRHKIAELEAKLKGD-DEGGEWKIRYETQLE
          .GEGRGENF...VSTD.L.LELLEEI.....I.QLSML..R.KIAE.EA...GD..E.GEWK...ETQLE
Retrocopy VGEGRGENFT<NVSTDCLTLELLEEIQWRG<IMQLSMLGTRYKIAEPEASFSGD<QESGEWKAPQETQLE

Parental  L
          L
Retrocopy L

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	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_406 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_406 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_406 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004615	1 retrocopy	retro_amel_120,
Equus caballus	ENSECAG00000011446	1 retrocopy	retro_ecab_111,
Felis catus	ENSFCAG00000008786	1 retrocopy	retro_fcat_39,
Oryctolagus cuniculus	ENSOCUG00000026427	1 retrocopy	retro_ocun_406 ,
Sus scrofa	ENSSSCG00000026564	1 retrocopy	retro_sscr_77,