RetrogeneDB ID: retro_ocun_1425

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 8:83997338..83997655(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPP14
• Ensembl ID: ENSOCUG00000027202
• Aliases: None
• Description: ribonuclease P/MRP 14kDa subunit [Source:HGNC Symbol;Acc:30327]

Sequence

>retro_ocun_1425
AATCCCTCCGAGTGCCACTACATGAAAGCCTGCCTAGAATTTCAAGAACCTGGAGTTGGACTGAACGCCGCACAATTCAA
GCAGCCGCTCGCCGCAGCCGTGAAGGAGCTGTGTGGGGAGGTTGATGCTGCCTTGCCCTTGGCCTTCCTAACCTGTGAAG
AGAAGACCTCATCAGCAATCTTGAGAATATGTAGCAGTGGTCTTGTCAAATTGTGGAGCTCTTTAACCATGTTAGGGTCC
TAAAAGGGGAAAATTGTGCTGTCAGAGTGATTCAGGTTTCTCCATTTCCTGTTGTCCCATCTGGTAATAGTAGGGAA

Alignment

ORF - retro_ocun_1425 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.09 %
• Parental protein coverage: 85.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DPSDYHYMKVRLEFEEHGIGLNAAQFKQLLVSALQELFGEVGAALPFDVLTYEEKTLSAILRVCNSGFVK
          .PS..HYMK..LEF.E.G.GLNAAQFKQ.L..A..EL.GEV.AALP...LT.EEKT.SAILR.C.SG.VK
Retrocopy NPSECHYMKACLEFQEPGVGLNAAQFKQPLAAAVKELCGEVDAALPLAFLTCEEKTSSAILRICSSGLVK

Parental  LWSSLTMLGS-YKGNKCAFRVIQVSPFLLALSGNSRE
          LWSSLTMLGS..KG..CA.RVIQVSPF....SGNSRE
Retrocopy LWSSLTMLGS<LKGENCAVRVIQVSPFPVVPSGNSRE

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	10.43 RPM
SRP017611_kidney	0.00 RPM	17.13 RPM
SRP017611_liver	0.00 RPM	9.25 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1425 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1425 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1425 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019987	1 retrocopy	retro_btau_1621,
Cavia porcellus	ENSCPOG00000004281	2 retrocopies	retro_cpor_476, retro_cpor_566,
Dasypus novemcinctus	ENSDNOG00000013439	1 retrocopy	retro_dnov_762,
Macropus eugenii	ENSMEUG00000010883	1 retrocopy	retro_meug_838,
Microcebus murinus	ENSMICG00000014541	1 retrocopy	retro_mmur_142,
Myotis lucifugus	ENSMLUG00000007998	1 retrocopy	retro_mluc_2291,
Ornithorhynchus anatinus	ENSOANG00000022513	1 retrocopy	retro_oana_119,
Oryctolagus cuniculus	ENSOCUG00000027202	3 retrocopies	retro_ocun_1160, retro_ocun_1359, retro_ocun_1425 ,
Rattus norvegicus	ENSRNOG00000039829	1 retrocopy	retro_rnor_1530,
Ictidomys tridecemlineatus	ENSSTOG00000015394	1 retrocopy	retro_itri_1072,
Tarsius syrichta	ENSTSYG00000013343	1 retrocopy	retro_tsyr_218,
Vicugna pacos	ENSVPAG00000000935	1 retrocopy	retro_vpac_202,