RetrogeneDB ID: retro_mdom_503

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:75713689..75714090(-)
• Located in intron of: ENSMODG00000004965

Retrocopy information

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

Parental gene information

• Parental gene symbol: NME1
• Ensembl ID: ENSMODG00000028492
• Aliases: None
• Description: nucleoside diphosphate kinase A [Source:RefSeq peptide;Acc:NP_001191452]

Sequence

>retro_mdom_503
CCATGGATCATGGCCAACACCAAGCATACCTTCATTGCCATCCAGCTGGACAGCATCCAGTGGGGCCAGTGGGGTCTGGT
AGGGACATCATCAAGCATTTTGAGCACAAAGGATTCTGCCTTGTGGCCATGAAGTTCTGTGGGGACTCAGAGAAACATTT
GAATCAACATTTTGTAAACCTGAAGAACAGGCCATTTCCCCCTCTGGCTTGTGAAATGCATAAACTCTGGACCTGTGTGG
CCATAGTCTGGGAGGTCTTGAATGCGGTGAAGACAGGCAGAATGATGCTGGGGCAGACCAACTCAAAGGATTCCAAACCA
GGCACCATTCGTGGGGACATCAGCAGGAATATCATGTGTGGCAGTGATTCTGTAAAAAGTGCTGAGAAGGAAATCAATCT
G

Alignment

ORF - retro_mdom_503 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.57 %
• Parental protein coverage: 70.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PGIMANSERTFIAIKPDGV---QRGLIG-EIVKRFEQKGFHLVALKFMQASEDLLREHYIDLKDRP-FYA
          P.IMAN...TFIAI..D.....Q.GL.G..I.K.FE.KGF.LVA.KF...SE..L..H...LK.RP.F..
Retrocopy PWIMANTKHTFIAIQLDSIQWGQWGLVG<DIIKHFEHKGFCLVAMKFCGDSEKHLNQHFVNLKNRP>FPL

Parental  GLVKYMHSGPV-VAMVWEGLNVVKTGRMMVGETNPADSKPGTVRGDFCIQSGRNIIHGSDSVESAEKEIG
          .LVK...SGPV.VA.VWE.LN.VKTGRMM.G.TN..DSKPGT.RGD......RNI..GSDSV.SAEKEI.
Retrocopy WLVKCINSGPV<VAIVWEVLNAVKTGRMMLGQTNSKDSKPGTIRGDI----SRNIMCGSDSVKSAEKEIN

Parental  L
          L
Retrocopy L

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	0.12 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.20 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_503 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_503 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 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004651	1 retrocopy	retro_btau_1707,
Canis familiaris	ENSCAFG00000023628	7 retrocopies	retro_cfam_117, retro_cfam_1645, retro_cfam_37, retro_cfam_676, retro_cfam_69, retro_cfam_832, retro_cfam_96,
Gorilla gorilla	ENSGGOG00000016526	1 retrocopy	retro_ggor_71,
Monodelphis domestica	ENSMODG00000012580	1 retrocopy	retro_mdom_1811,
Monodelphis domestica	ENSMODG00000028492	1 retrocopy	retro_mdom_503 ,
Mustela putorius furo	ENSMPUG00000015559	5 retrocopies	retro_mputfur_1093, retro_mputfur_1357, retro_mputfur_442, retro_mputfur_667, retro_mputfur_997,
Mus musculus	ENSMUSG00000091228	3 retrocopies	retro_mmus_2712, retro_mmus_3081, retro_mmus_581,
Nomascus leucogenys	ENSNLEG00000007919	2 retrocopies	retro_nleu_1029, retro_nleu_1030,
Oryctolagus cuniculus	ENSOCUG00000022135	1 retrocopy	retro_ocun_1728,
Pan troglodytes	ENSPTRG00000009415	1 retrocopy	retro_ptro_91,
Rattus norvegicus	ENSRNOG00000002693	3 retrocopies	retro_rnor_1198, retro_rnor_1600, retro_rnor_704,