RetrogeneDB ID: retro_ocun_1685

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018763:543795..543993(-)
• Located in intron of: ENSOCUG00000008602

Retrocopy information

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

Parental gene information

• Parental gene symbol: ISCA1
• Ensembl ID: ENSOCUG00000010945
• Aliases: None
• Description: iron-sulfur cluster assembly 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:28660]

Sequence

>retro_ocun_1685
GTGGTTTAGGCCATCGTGCAAGCTGTGAATGAGAGGAAGCTGCAGCCCAGCCTGGCCACCGGCGCCGTAACACCTTCCGC
AGTAGTGAAGATAAAAGAACTTCCTAGAGATAAGCCTGAGTAGGGCAGGTGTGAAAGTTGGTGTTGGAACCAGGCACCAT
ATGGTGTTTCTTAAACTCTGGAGTATCTGAAGAGAAGG

Alignment

ORF - retro_ocun_1685 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.35 %
• Parental protein coverage: 51.16 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LVRATVRAVSKRKLQPTRAALTLTPSAVNKIKQLLKDKPE-HVGVKVGVRTR-GCNGLSYTLEYTKTK
          .V.A.V.AV..RKLQP..A....TPSAV.KIK.L..DKPE...GVKVGV.TR....G.S.TLEY.K..
Retrocopy VV*AIVQAVNERKLQPSLATGAVTPSAVVKIKELPRDKPE>RAGVKVGVGTR<APYGVS*TLEYLKRR

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	2.15 RPM	41.72 RPM
SRP017611_kidney	0.10 RPM	41.05 RPM
SRP017611_liver	0.08 RPM	10.56 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1685 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1685 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1685 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000046526	2 retrocopies	retro_btau_1787, retro_btau_506,
Callithrix jacchus	ENSCJAG00000001940	6 retrocopies	retro_cjac_1623, retro_cjac_1734, retro_cjac_1870, retro_cjac_2608, retro_cjac_350, retro_cjac_672,
Dasypus novemcinctus	ENSDNOG00000010652	5 retrocopies	retro_dnov_1162, retro_dnov_142, retro_dnov_1956, retro_dnov_431, retro_dnov_95,
Echinops telfairi	ENSETEG00000016537	1 retrocopy	retro_etel_1857,
Gorilla gorilla	ENSGGOG00000007518	2 retrocopies	retro_ggor_1182, retro_ggor_92,
Monodelphis domestica	ENSMODG00000003559	1 retrocopy	retro_mdom_583,
Mus musculus	ENSMUSG00000044792	1 retrocopy	retro_mmus_278,
Oryctolagus cuniculus	ENSOCUG00000010945	1 retrocopy	retro_ocun_1685 ,
Pongo abelii	ENSPPYG00000019339	5 retrocopies	retro_pabe_1287, retro_pabe_2043, retro_pabe_2744, retro_pabe_2745, retro_pabe_367,
Rattus norvegicus	ENSRNOG00000018343	4 retrocopies	retro_rnor_1177, retro_rnor_1805, retro_rnor_2254, retro_rnor_2956,
Tarsius syrichta	ENSTSYG00000012826	2 retrocopies	retro_tsyr_1060, retro_tsyr_1698,