RetrogeneDB ID: retro_mdom_1711

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:40066107..40066619(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MDH2
• Ensembl ID: ENSMODG00000013680
• Aliases: None
• Description: Malate dehydrogenase [Source:UniProtKB/TrEMBL;Acc:F6QQ58]

Sequence

>retro_mdom_1711
TTTGGTGTAAAAACACTGGATATCATCAGAGCAAATATCTTTGTGGCGGAACTGAAGGGCTTAGATCCAGCTCAGGTCAA
TGTCCCTATTCTTGGTGGCCATGCAGGGAAAACTATTATCCCTCTGATTTCTCAGTGCACACCCAAAGTGCAATTTCCTG
AGGATCAGCTGACAACCCTGACAGGAAGGATTCAGGAGTCTGGACAGAGGTTGTCAAAGCTAAAGCTGGGGCAGGTTCTG
CTACCCTATCAATGGCCTATGCTGGAGCCAGGTTCCTCTTCTCTGTTGTGGTTGCAATGAATGGAAAGGAAGGAATCGTG
GAATACTCCTTTGTCAGATCAGAAGAGACAGAGTGCTCCTATTTTTTCACACCCTTGATGCTTGGGAAAAAGGGCATCAA
GAACAAATTGGGCATTGGCAAGGTCTCCCCTTTTGAAGAGAAGATGATTGCTGTAGCCATTCCTGAGATGAAAGCTTCCA
TCAAGAAAGGAGAAGATTTTGTCAAGAATATG

Alignment

ORF - retro_mdom_1711 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.37 %
• Parental protein coverage: 50.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FGVTTLDIVRANTFVAELKGLDPARVNVPVIGGHAGKTIIPLISQCTPKVEFPEDQLTTLTGRIQEAG-T
          FGV.TLDI.RAN.FVAELKGLDPA.VNVP..GGHAGKTIIPLISQCTPKV.FPEDQLTTLTGRIQE.G.T
Retrocopy FGVKTLDIIRANIFVAELKGLDPAQVNVPILGGHAGKTIIPLISQCTPKVQFPEDQLTTLTGRIQESG<T

Parental  EVVKAKAGAGSATLSMAYAGARFVFSVVDAMNGKEGVVECSFVRSEETECSYFSTPLLLGKKGIEKNLGI
          EVVKAKAGAGSATLSMAYAGARF.FSVV.AMNGKEG.VE.SFVRSEETECSYF.TPL.LGKKGI...LGI
Retrocopy EVVKAKAGAGSATLSMAYAGARFLFSVVVAMNGKEGIVEYSFVRSEETECSYFFTPLMLGKKGIKNKLGI

Parental  GKVSPFEEKMIAEAIPELKASIKKGEDFVKNM
          GKVSPFEEKMIA.AIPE.KASIKKGEDFVKNM
Retrocopy GKVSPFEEKMIAVAIPEMKASIKKGEDFVKNM

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_1711 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1711 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010846	1 retrocopy	retro_amel_361,
Canis familiaris	ENSCAFG00000013515	2 retrocopies	retro_cfam_182, retro_cfam_41,
Myotis lucifugus	ENSMLUG00000017795	1 retrocopy	retro_mluc_1948,
Monodelphis domestica	ENSMODG00000013680	1 retrocopy	retro_mdom_1711 ,
Mustela putorius furo	ENSMPUG00000016000	2 retrocopies	retro_mputfur_1607, retro_mputfur_478,
Mus musculus	ENSMUSG00000019179	1 retrocopy	retro_mmus_2451,
Otolemur garnettii	ENSOGAG00000009705	1 retrocopy	retro_ogar_3068,
Pteropus vampyrus	ENSPVAG00000003397	1 retrocopy	retro_pvam_981,
Tupaia belangeri	ENSTBEG00000003190	1 retrocopy	retro_tbel_440,
Tursiops truncatus	ENSTTRG00000014834	1 retrocopy	retro_ttru_1550,
Drosophila melanogaster	FBgn0262559	2 retrocopies	retro_dmel_54, retro_dmel_76,