RetrogeneDB ID: retro_mdom_1540

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:160226059..160226993(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMC3
• Ensembl ID: ENSMODG00000019911
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, ATPase, 3 [Source:HGNC Symbol;Acc:9549]

Sequence

>retro_mdom_1540
AAATGCACCGTTATCAAAACCTATTTCTTGCAAGTGACGATTTTGTTGATGCAGAAAAGTTGAAGTCTGGAGACCTGGTG
AGAGAAAACAAAGCATCCTATCTGATCCTAGAGATTCTACCCACTGAGTATGAATCCCATGTGAAAGTCATGGAGGTGAA
TGAAAGACCCACAAAGCAATACAGCATTATTGGAGGGCTGGATAAACACACCCAGATACTCATAGAGGCTATTGGATTGC
TAATGAATGAACCATAAAGAGATATTGAGAATTTGGTTATTCAGTCTCCAAAGGGAGGATTTATATATGGAGCCTGAGGT
ATTGGAAAAAGTCTGCTAGCCCAGACTTGTGGTGCCCAGACCAAGGCCACCTTTCTGAAAGTGGCTGGCCCTCATTTGGT
AAGATGTTAACTGGGAATGGAGCAAAGTTTGTCTGAGATGCCTCTTACTGGCCAAAGGGAATGTGCCTTCCATTATATTC
ACTGATGAACTAGATGCCATTAGAACCAAGCACTTAGACAGTGAGTAGGCCCAGGATCAGAAGTTCAAAGAACTATACTG
AAAACTCCTAAACTATCAGGATGAATTTCAGCATAACACCCAAGGTAATATAATTACTGATATAAATAGGGTGGACCTTC
CTGGACCTTGCCTTGCTCCCTATATGGATCATAAGGTTGAATTCCCAAACTCTACAGAGGAAACCAGAGCCAGGAGCATG
CAGATTCATTCTTGAAAAATGAATGAGAGCCCTGTGAAGTATCAAGAGCTGGCATACTCCAGGAGCAAATTCAGAGGAGT
TCAGTGCAAGGCCATGTGCATTGAAGAAAGGAATGATCCAGCTCTGCCTGGAAGCCACTGAGCTCATACATAAAGACTAG
ATGGAGGGTATGCTTGGGGCTCCAGTCAAGAATAAAGCCAGTTTGCACTTCTAT

Alignment

ORF - retro_mdom_1540 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.81 %
• Parental protein coverage: 69.93 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  KTSTRQTYFLPVIGL-VDAEKLKPGDLVGVNKDSYLILETLPTEYDSRVKAMEVDERPTEQYSDIGGLDK
          K.....TYFL.V..L.VDAEKLK.GDLV..NK.SYLILE.LPTEY.S.VK.MEV.ERPT.QYS.IGGLDK
Retrocopy KCTVIKTYFLQVTIL<VDAEKLKSGDLVRENKASYLILEILPTEYESHVKVMEVNERPTKQYSIIGGLDK

Parental  QIQELVEAIVLPMNHK-EKFENLGIQPPKGVLMYGPPGTGKTLLARACAAQTKATFLKLAGPQLV-QMFI
          ..Q.L.EAI.L.MN......ENL.IQ.PKG...YG..G.GK.LLA..C.AQTKATFLK.AGP.LV..M..
Retrocopy HTQILIEAIGLLMNEP*RDIENLVIQSPKGGFIYGA*GIGKSLLAQTCGAQTKATFLKVAGPHLV<KMLT

Parental  GDGAKLVRDA-FALAKEKAPSIIFIDELDAIGTKRFDSEKAGDR-EVQRTML-ELLNQLDGFQPNTQVKV
          G.GAK.V.DA...LAK...PSIIF.DELDAI.TK..DSE.A.D..EVQRT.L..LLN..D.FQ.NTQ...
Retrocopy GNGAKFV*DA<LLLAKGNVPSIIFTDELDAIRTKHLDSE*AQDQ<EVQRTIL>KLLNYQDEFQHNTQGNI

Parental  IAATNRVDILDPALLRSGRLDRKIEFPMPNEEARARIMQIHSRKMNVSPDVNYEELARCTDDFNGAQCKA
          I...NRVD...P.L......D.K.EFP...EE.RAR.MQIHS.KMN.SP.V.Y.ELA.....F.G.QCKA
Retrocopy ITDINRVDLPGPCL--APYMDHKVEFPNSTEETRARSMQIHS*KMNESP-VKYQELAYSRSKFRGVQCKA

Parental  VCVE-AGMIALRRGATELTHEDYMEGILEVQAKKKANLQYY
          .C.E..GMI.L...ATEL.H.D.MEG.L....K.KA.L..Y
Retrocopy MCIE>KGMIQLCLEATELIHKD*MEGMLGAPVKNKASLHFY

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_1540 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1540 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008701	1 retrocopy	retro_cfam_52,
Monodelphis domestica	ENSMODG00000019911	2 retrocopies	retro_mdom_1035, retro_mdom_1540 ,
Mustela putorius furo	ENSMPUG00000003992	1 retrocopy	retro_mputfur_1487,