RetrogeneDB ID: retro_ocun_1678

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018760:435143..435571(-)
• Located in intron of: ENSOCUG00000024710

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM210B
• Ensembl ID: ENSOCUG00000017897
• Aliases: None
• Description: family with sequence similarity 210, member B [Source:HGNC Symbol;Acc:16102]

Sequence

>retro_ocun_1678
CTGCTGCGCTCGGCCCGCGGGCACTGCCGCGGGCGCAGGACCCCAGGAGAGTGACCGCGGTCCCAGGCAGCGCTGTGGGC
AGCACAGGAGGTAGCAAGCAAAGCAAGGCACAGCAGCTGCGAAAGATCTTCCAGCAGTACGGAGCTGTTGGCGTGTCACT
GCACGTTGGGATCTCGCTCATCTCCCTGGGCTTGTTCTACACGGTGGTTTCAAGCGGTGTGGACATGTCTGCAATCCTGC
TTAAACTCGGATTTAAAGAGTCGCTGGTCCAGTCCAAAATGGCAGCAGGCACGCGCACTTTCGTGGTGGCCTACGCAGTA
CACAAGCTGTTCGCGTCTGTGAGAATCAGCATCACCTTAGTCTCTGTGCCCTTCATTGTCAGATATTTTCGAAAAGTAGG
ATTTTTTAAACCTCCAGCTGCAAAACCT

Alignment

ORF - retro_ocun_1678 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.36 %
• Parental protein coverage: 73.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LLRSARGDCRGR-QDPSRVTEVTGSAVGSTGGSRQSKAQQLRKIFQEYGAVGVSLHIGISLISLGLFYTV
          LLRSARG.CRGR.QDP.RVT.V.GSAVGSTGGS.QSKAQQLRKIFQ.YGAVGVSLH.GISLISLGLFYTV
Retrocopy LLRSARGHCRGR<QDPRRVTAVPGSAVGSTGGSKQSKAQQLRKIFQQYGAVGVSLHVGISLISLGLFYTV

Parental  VSSGVDMSAILLKLGFKESLVQSKMAAGTSTFVVAYAIHKLFAPVRISITLVSVPFIVRYFRKVGFFKPP
          VSSGVDMSAILLKLGFKESLVQSKMAAGT.TFVVAYA.HKLFA.VRISITLVSVPFIVRYFRKVGFFKPP
Retrocopy VSSGVDMSAILLKLGFKESLVQSKMAAGTRTFVVAYAVHKLFASVRISITLVSVPFIVRYFRKVGFFKPP

Parental  AAKP
          AAKP
Retrocopy AAKP

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	19.32 RPM
SRP017611_kidney	0.10 RPM	18.45 RPM
SRP017611_liver	0.00 RPM	22.51 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1678 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1678 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1678 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006630	1 retrocopy	retro_cpor_1046,
Homo sapiens	ENSG00000124098	1 retrocopy	retro_hsap_653,
Nomascus leucogenys	ENSNLEG00000007028	1 retrocopy	retro_nleu_1733,
Oryctolagus cuniculus	ENSOCUG00000017897	1 retrocopy	retro_ocun_1678 ,
Pongo abelii	ENSPPYG00000011147	2 retrocopies	retro_pabe_577, retro_pabe_659,
Pan troglodytes	ENSPTRG00000013645	1 retrocopy	retro_ptro_475,