RetrogeneDB ID: retro_ocun_182

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:66082020..66082470(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000024344
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PDE6D
• Ensembl ID: ENSOCUG00000010403
• Aliases: None
• Description: phosphodiesterase 6D, cGMP-specific, rod, delta [Source:HGNC Symbol;Acc:8788]

Sequence

>retro_ocun_182
CTAGATGCTCCTCCGCGTGGCTGGTTCCTGGTGCTTGGCTTGATCAGAAACTGGATGAACCTGCGGGATGCAGAGACAGG
GAAGATACTCTGGCAAGGAACTGAAGACCTGTCCGTCCCTGGGGTGGAACATGAAGCCCGTGTTCCCAAGAAAATCCTCA
AGTGCAAAGCAGTGTCCCGAGAGCTGAACTTCTCTTCAGCAGAGCAAATGGAGAAATTCCGCCTGGAGCAGAAAGTTTAC
TTCAAAGGGCAGTGCCTAGAAGAATGGTTCTTCGAATTTGGCTTTGTGATTCCCAACTCCACAAATACCTGGCAGTCCCT
GATAGAGGCAGCACCCGAGTCCCAGATGATGCCAGCAAGCGTCCTAACTGGGAACGTTATCATAGAAACAAAGTTTTTTG
ACGACGATCTTCTTGTAAGCACATCCAGAGTGAGACTTTTCTACGTCTGA

Alignment

ORF - retro_ocun_182 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSAEQMEKFRLEQKVYFKGQCL
          NWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSAEQMEKFRLEQKVYFKGQCL
Retrocopy NWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSAEQMEKFRLEQKVYFKGQCL

Parental  EEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV
          EEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV
Retrocopy EEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV

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	6.90 RPM
SRP017611_kidney	0.00 RPM	4.36 RPM
SRP017611_liver	0.00 RPM	1.00 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_182 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_182 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_182 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012101	1 retrocopy	retro_acar_157,
Ailuropoda melanoleuca	ENSAMEG00000016282	1 retrocopy	retro_amel_1563,
Dasypus novemcinctus	ENSDNOG00000000568	1 retrocopy	retro_dnov_2585,
Felis catus	ENSFCAG00000002232	1 retrocopy	retro_fcat_317,
Macropus eugenii	ENSMEUG00000006427	1 retrocopy	retro_meug_1355,
Oryctolagus cuniculus	ENSOCUG00000010403	1 retrocopy	retro_ocun_182 ,
Pteropus vampyrus	ENSPVAG00000004743	1 retrocopy	retro_pvam_544,
Tursiops truncatus	ENSTTRG00000009165	1 retrocopy	retro_ttru_82,