RetrogeneDB ID: retro_mdom_952

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:11351290..11351650(+)
• Located in intron of: ENSMODG00000019413

Retrocopy information

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

Parental gene information

• Parental gene symbol: COX11
• Ensembl ID: ENSMODG00000014855
• Aliases: None
• Description: cytochrome c oxidase assembly homolog 11 (yeast) [Source:HGNC Symbol;Acc:2261]

Sequence

>retro_mdom_952
TTCGATGCCCACGTGCAGGCAAGTCTCTCCCCTGGAATTTTAGACCTCAACAAACCAATCTATGGCGTGAGAGCCGGCTC
CGGCATTTTCCAAGCTAAGACTCCTACTGACAAACCAGTCTTTGGAATTTCTACATCCAATGTGGTACCATTTGAAGCTG
GGCGGGATTTTAATACAATGGGGAGCTTCGTTTTGAAGAACAAAGGCTTAATGCTCCAGAGGAAGTAGACATGCCAGTAT
TTTTCTTCACTGATCCTGAATTTGCTGAAGATCCTAAAATGGCAAAAGTTGATGTGGTCACTCTCTCTTACACATTTTTT
GAAGCAAAAGGACCATCAATTGCCAGTTCCAGGTTATAAT

Alignment

ORF - retro_mdom_952 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.4 %
• Parental protein coverage: 51.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FNADVHASLHWNFRPQQTEIYVVPGETALAFYKAKNPTDKSVIGISTYNVVPFEAGQYFNKIQCFC-FEE
          F.A.V.ASL..........IY.V..........AK.PTDK.V.GIST.NVVPFEAG..FN....F..FEE
Retrocopy FDAHVQASLSPGILDLNKPIYGVRAGSGI--FQAKTPTDKPVFGISTSNVVPFEAGRDFNTMGSFV<FEE

Parental  QRLNPQEEVDMPVFFFIDPEFAEDPKMAKVDVITLSYT-FFEAKEGHKLPVPGYN
          QRLN..EEVDMPVFFF.DPEFAEDPKMAKVDV.TLSYT.F...K..H.LPVPGYN
Retrocopy QRLNAPEEVDMPVFFFTDPEFAEDPKMAKVDVVTLSYT>FLKQKD-HQLPVPGYN

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
SRP007412_brain	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_952 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_952 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000008482	1 retrocopy	retro_cpor_1340,
Dasypus novemcinctus	ENSDNOG00000014862	1 retrocopy	retro_dnov_1933,
Dipodomys ordii	ENSDORG00000001207	1 retrocopy	retro_dord_180,
Homo sapiens	ENSG00000166260	1 retrocopy	retro_hsap_3442,
Microcebus murinus	ENSMICG00000005225	1 retrocopy	retro_mmur_1119,
Monodelphis domestica	ENSMODG00000014855	1 retrocopy	retro_mdom_952 ,
Mus musculus	ENSMUSG00000020544	4 retrocopies	retro_mmus_1318, retro_mmus_2318, retro_mmus_2714, retro_mmus_986,
Nomascus leucogenys	ENSNLEG00000007990	1 retrocopy	retro_nleu_2297,
Ochotona princeps	ENSOPRG00000004138	1 retrocopy	retro_opri_441,
Pongo abelii	ENSPPYG00000008259	2 retrocopies	retro_pabe_156, retro_pabe_2847,
Pan troglodytes	ENSPTRG00000009422	1 retrocopy	retro_ptro_2335,
Rattus norvegicus	ENSRNOG00000046318	1 retrocopy	retro_rnor_1515,