RetrogeneDB ID: retro_mdom_1583

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:48073518..48074231(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMC5
• Ensembl ID: ENSMODG00000009873
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, ATPase, 5 [Source:HGNC Symbol;Acc:9552]

Sequence

>retro_mdom_1583
CTATCCAAAATTGGGAAAGTGAAGCTGATTGTAAATGACAAGAATCAAAGTATTTTGGATTTATAAGCACAATGGAATGA
GTTAAATGCAAAAGTATGTCACTATTGGAGGAGCTGTAATTTTTGTTAGAAGAAGGGTCCTATATTTGGGAATTGTGAGA
CATGGATGGAAAGTAAATTTTGATCAAGATATATCCTGAGAGGAAATTTGTGGTATATGTAGATAAATAATCAACATCAA
TTATATTACAACCAATTGCCATGTGATTCTGAGAAATGACACCTATATCTATCACAAAATTCTACCCAACAATATAGATG
CACTAGTGTCTTTGATGAAGGTGGAAAAATGCCTGACTTCATCTATGAGATGATTGGTTGTCTATATAGGCAGATTAATG
CCATTGAAGAAGTGAATAAACTACCTGTTGAGTATCCTTATCTCTTCAAGGAACAGGACATCACCAAAACCAAGGATATG
CTACTATATGGAACTCCAGGGATAGGCAAAAGTCTCTTGGTTTGGGCTGTGGTTCATCAAAATGACTGCAGCTCTATTTT
GTCTTAGGCTCAGAACTTGTAAAGCCATTCCTCATCAGTAAAAGGGAACAACAGCATGAGTTATGTTCATTATGGCATGA
AAACGTTCTCTTATCCATCATCTTCATGGATGATATTGACTTCGTTGATGCCTCACATTTGGAAGGTGGCTCT

Alignment

ORF - retro_mdom_1583 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.51 %
• Parental protein coverage: 58.72 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LSKIEELQLIVNDKSQNLRRLQAQRNELNAKV-RLLREELQLLQEQGSYVGEVVRAMDKKKVLVKVHPEG
          LSKI....LIVNDK.Q....L.AQ.NELNAKV...L.EEL..L.E.GSY..E....MD.K..L.K..PE.
Retrocopy LSKIGKVKLIVNDKNQSILDL*AQWNELNAKV<MSLLEEL*FLLEEGSYIWEL*D-MDGK*ILIKIYPER

Parental  KFVVDVDK-NIDINDVTPNCRVALRNDSYTLHKILPNKVDPLVSLMMVEK-VPDSTYEMIGGLDKQIKEI
          KFVV.VDK..I.IN..T.NC.V.LRND.Y..HKILPN..D.LVSLM.VEK..PD..YEMIG.L..QI..I
Retrocopy KFVVYVDK<IININYITTNCHVILRNDTYIYHKILPNNIDALVSLMKVEK<MPDFIYEMIGCLYRQINAI

Parental  KEVIELPVKHPELFEALGIAQPKGVLLYGPPGTGKTLLARAVAHHTDCTFIR-VSGSELVQKFIGEGARM
          .EV..LPV..P.LF....I...K..LLYG.PG.GK.LL..AV.H..DC..I..V.GSELV..F.......
Retrocopy EEVNKLPVEYPYLFKEQDITKTKDMLLYGTPGIGKSLLVWAVVHQNDCSSIL<VLGSELVKPFLISKREQ

Parental  VRELFVMAREHA-PSIIFMDEIDSIGSSRLEGGS
          ..EL.....E....SIIFMD.ID....S.LEGGS
Retrocopy QHELCSLWHENVLLSIIFMDDIDFVDASHLEGGS

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_1583 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1583 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 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000002393	1 retrocopy	retro_dnov_1508,
Homo sapiens	ENSG00000087191	1 retrocopy	retro_hsap_1949,
Gorilla gorilla	ENSGGOG00000006803	1 retrocopy	retro_ggor_1418,
Macaca mulatta	ENSMMUG00000016769	1 retrocopy	retro_mmul_1354,
Monodelphis domestica	ENSMODG00000009873	2 retrocopies	retro_mdom_1411, retro_mdom_1583 ,
Nomascus leucogenys	ENSNLEG00000004150	1 retrocopy	retro_nleu_1480,
Oryctolagus cuniculus	ENSOCUG00000004329	1 retrocopy	retro_ocun_78,
Otolemur garnettii	ENSOGAG00000008296	1 retrocopy	retro_ogar_911,
Procavia capensis	ENSPCAG00000002653	1 retrocopy	retro_pcap_352,
Pongo abelii	ENSPPYG00000008533	1 retrocopy	retro_pabe_1606,
Pan troglodytes	ENSPTRG00000009525	1 retrocopy	retro_ptro_1303,
Ictidomys tridecemlineatus	ENSSTOG00000008945	1 retrocopy	retro_itri_1046,
Tupaia belangeri	ENSTBEG00000010546	3 retrocopies	retro_tbel_1411, retro_tbel_2422, retro_tbel_3450,
Tursiops truncatus	ENSTTRG00000006984	1 retrocopy	retro_ttru_1532,