RetrogeneDB ID: retro_mdom_600

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:472571773..472572187(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COQ10B
• Ensembl ID: ENSMODG00000012281
• Aliases: None
• Description: coenzyme Q10 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:25819]

Sequence

>retro_mdom_600
AGATCTCTGCAAGAACTTTCTTCAAAATTCTTAAAAAAAAGAAATGACTATTCAGAGAGGAGAATTCTAGGATATTCTAT
GCAAGAAATGTATGATGTAGTATCTGGTATGGAAGATTACAAGAATTTTGTTCCTTGTGGCAAAAAATCAGATGTAATAT
CAAAGAAATCTGGATATTGCAAAACAATGGTTAGAAATTGGGTTTCCATCTGTGTTGGAGTGATATACATCCATAGTAAC
CTTGGTGAAACCACATTTGGTCAAGGCATCCTGCACAGATGGAAAACTTTCCAATCACTTAAAATAGTTTGGTGTTTCAG
CTCTGACCTTCCTAGATAACCAATGACTTGTACAGTGAATTTTTCTATTTCTTTTGAGTTTCATTCACTTCTACACTCTC
AGTTCTTTACACTA

Alignment

ORF - retro_mdom_600 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.57 %
• Parental protein coverage: 57.02 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RTFFKIAAPLINKRKEYSERRIIGYSMQEMYDVVSGMEDYKNFVPWCKKSDVISKRSGYCKTR-LEIGFP
          R...............YSERRI.GYSMQEMYDVVSGMEDYKNFVP..KKSDVISK.SGYCKT..LEIGFP
Retrocopy RSLQELSSKFXXXXNDYSERRILGYSMQEMYDVVSGMEDYKNFVPCGKKSDVISKKSGYCKTM>LEIGFP

Parental  PVLERYTSIVTLVKPHLVKASCTDGKLFNH-LETVWRFSPGLPGYPRTCTVDFSISFEFRSLLHSQLATL
          .VLE.YTSIVTLVKPHLVKASCTDGKL.NH.L..VW.FS..LP..P.TCTV.FSISFEF.SLLHSQ..TL
Retrocopy SVLE*YTSIVTLVKPHLVKASCTDGKLSNH<LKIVWCFSSDLPR*PMTCTVNFSISFEFHSLLHSQFFTL

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	0.20 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_600 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_600 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 19 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004659	2 retrocopies	retro_btau_1595, retro_btau_1832,
Choloepus hoffmanni	ENSCHOG00000005807	1 retrocopy	retro_chof_1504,
Callithrix jacchus	ENSCJAG00000003971	1 retrocopy	retro_cjac_1836,
Dasypus novemcinctus	ENSDNOG00000003229	2 retrocopies	retro_dnov_1571, retro_dnov_2203,
Dipodomys ordii	ENSDORG00000004090	1 retrocopy	retro_dord_508,
Erinaceus europaeus	ENSEEUG00000001626	1 retrocopy	retro_eeur_401,
Felis catus	ENSFCAG00000022385	1 retrocopy	retro_fcat_1487,
Homo sapiens	ENSG00000115520	1 retrocopy	retro_hsap_3349,
Gorilla gorilla	ENSGGOG00000023373	2 retrocopies	retro_ggor_2270, retro_ggor_569,
Myotis lucifugus	ENSMLUG00000000865	1 retrocopy	retro_mluc_1236,
Macaca mulatta	ENSMMUG00000010488	1 retrocopy	retro_mmul_2434,
Monodelphis domestica	ENSMODG00000012281	1 retrocopy	retro_mdom_600 ,
Mus musculus	ENSMUSG00000025981	1 retrocopy	retro_mmus_3224,
Nomascus leucogenys	ENSNLEG00000006871	1 retrocopy	retro_nleu_1172,
Ochotona princeps	ENSOPRG00000010091	3 retrocopies	retro_opri_1020, retro_opri_173, retro_opri_664,
Pongo abelii	ENSPPYG00000013045	2 retrocopies	retro_pabe_2758, retro_pabe_576,
Pan troglodytes	ENSPTRG00000012772	1 retrocopy	retro_ptro_2137,
Rattus norvegicus	ENSRNOG00000014456	1 retrocopy	retro_rnor_1620,
Tarsius syrichta	ENSTSYG00000012642	2 retrocopies	retro_tsyr_1213, retro_tsyr_1666,