RetrogeneDB ID: retro_mdom_515

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:124706343..124706722(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MNF1
• Ensembl ID: ENSMODG00000013996
• Aliases: None
• Description: mitochondrial nucleoid factor 1 [Source:HGNC Symbol;Acc:21237]

Sequence

>retro_mdom_515
ATGTCAGTCAGTCATTACTGGCATTTCCTCAAGTTCTGTGAAGAATGACCTTTGGATGAGACCAAATGGGGCTGAGACTT
GGGCACTTGCCTGTGACAGTGAATGGCACAGGTCTTTTGAGAGAAAGAGAACACACAAATTGCAGAGCCTGAGACCTGTG
ACCAAATGTATGAAAGTTTAGCATGACTTCTTTCAAACTATTACAAACTCAAATAACCTCTCTGAAAAGACACATGCCTC
AGTGGACTGACAGTGGAAGAATGCAGGATTGTACTGGCTACAGATACCATGGAAGAATTTAAGGAAATGAATAAGGGCTC
ATGTAAAAAATCTTCAGGAGAAGTTAGCCACTAAAAGTCTGGATGATAAAGCTAAGGAG

Alignment

ORF - retro_mdom_515 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.74 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 8
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSASRYRRFLKLCEEWPLDETKRGRDLGAYLRQRVAQVFREGENTQIAEPETCDQMYESLARLHSNYYKL
          MS.S.Y..FLK.CEE.PLDETK.G.DLG..L.Q..AQVF.E.ENTQIAEPETCDQMYESLA.L.SNYYKL
Retrocopy MSVSHYWHFLKFCEE*PLDETKWG*DLGTCL*Q*MAQVF*EKENTQIAEPETCDQMYESLA*LLSNYYKL

Parental  KYPRPKDTCFSGLTVEECRIVLATDTLEEFKEMNKGLWKK-LQEKLASKSLDDKTKE
          K.P..KDTC.SGLTVEECRIVLATDT.EEFKEMNKG..KK.LQEKLA.KSLDDK.KE
Retrocopy K*PL*KDTCLSGLTVEECRIVLATDTMEEFKEMNKGSCKK>LQEKLATKSLDDKAKE

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_515 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_515 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 9 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000031270	1 retrocopy	retro_cfam_1168,
Dasypus novemcinctus	ENSDNOG00000002019	1 retrocopy	retro_dnov_674,
Echinops telfairi	ENSETEG00000006979	2 retrocopies	retro_etel_1912, retro_etel_2009,
Macropus eugenii	ENSMEUG00000005278	3 retrocopies	retro_meug_1335, retro_meug_2027, retro_meug_337,
Monodelphis domestica	ENSMODG00000013996	1 retrocopy	retro_mdom_515 ,
Mustela putorius furo	ENSMPUG00000003032	1 retrocopy	retro_mputfur_511,
Mus musculus	ENSMUSG00000024208	2 retrocopies	retro_mmus_2543, retro_mmus_3376,
Otolemur garnettii	ENSOGAG00000015604	2 retrocopies	retro_ogar_2127, retro_ogar_2204,
Tupaia belangeri	ENSTBEG00000001380	6 retrocopies	retro_tbel_1486, retro_tbel_1573, retro_tbel_1754, retro_tbel_3269, retro_tbel_361, retro_tbel_994,