RetrogeneDB ID: retro_mdom_438

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:528686853..528687668(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMC6
• Ensembl ID: ENSMODG00000014500
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, ATPase, 6 [Source:HGNC Symbol;Acc:9553]

Sequence

>retro_mdom_438
AGAGATAACTCTCTTAAGAACTACAATACAAAGCTGCTTGAGCACAAGGAGACTTGTGGGTTCCCCAAAGAGTTAAGAGA
ATGATTGAAAGATCTTATGAAGGTTTAGGAAAAGTCTGAAAATGATTTGAAGGTCTTACAAAGTGCTGTACAGATTGTGA
GTTAAATGCCTAAAAAATAATAGAAGAAAAAATTAAGTGTTAAAGCAATGGACCAAGATATATTGTGAGTTGTCAGAGCC
ATCTTGACAAAAGTAATCTGAAACCAGGGACAGGAGTTGCCCTGTATATGACTACAGTTACTATCCTGAGATATTTGCCA
AGAGAAGTTCATCTACTGGTTTATAACATGTCTCAAAGGGACTCTGGGAATGCTTCTTATCCTGAGACTGGAAGGCCATC
TGACGAATCAGAGAACTAAGAGAATTATTCCCTATAAACCCCGAGTTACTCCAGCATGTAGGAATAATTCCTCCAAAAAT
TGTTTTCTAAATAGACTACCATGAATGGGATAAAAACACCCTTGGCAAGAGCTGTTGCTAGCCAGCTGCATTGCAATTTT
TAAAGGTAATATCTAGTTCTGTTATAGATTAGTATGTTCATGAAAGTGCCCATTTGATCAGAGAAATGTTCAGTTATGCC
ACGGATCACTAGTCATGCATCATTTTCATGGATGAAATAGATGCTATTGGTGGCTGTCATTTTTCTAAGGGTATTTCAGC
CAAGAGAGAAATTCAGTGAATTCTAATGGAATCACTGAATCAGATAGATAGATTTGATTCCTTTCACATTAAAAATGATT
AGAGCTGCAAATAGG

Alignment

ORF - retro_mdom_438 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.97 %
• Parental protein coverage: 71.21 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  RDKALQDYRKKLLEHKEIDGRLKELREQLKELTKQYEKSENDLKALQSVGQIVGEVLKQ-LTEEKFIVKA
          RD..L..Y..KLLEHKE..G..KELRE.LK.L.K..EKSENDLK.LQS..QIV....K....EEK.I...
Retrocopy RDNSLKNYNTKLLEHKETCGFPKELRE*LKDLMKV*EKSENDLKVLQSAVQIVS*MPKK<IIEEK-IKC*

Parental  TNGPRYVVGCRRQLDKSKLKPGTRVALDMTTLTIMRYLPREVDPLVYNMSHEDPGNVSYSEIGGLSEQ-I
          .NGPRY.V.C...LDKS.LKPGT.VAL.MTT.TI.RYLPREV..LVYNMS..D.GN.SY.E.G..S...I
Retrocopy SNGPRYIVSCQSHLDKSNLKPGTGVALYMTTVTILRYLPREVHLLVYNMSQRDSGNASYPETGRPSDE<I

Parental  RELREVIELPLTNPELFQRVGIIPP-KGCLLYGPPGTG-KTLLARA-VASQLDCN-FLKVVSSSIVDKYI
          RELRE.......NPEL.Q.VGIIPP.K.C.L...P..G.K..L....VASQL.CN.FLKV.SSS..D.Y.
Retrocopy RELRELFPI---NPELLQHVGIIPP<KNCFLNRLP*MG>KNTLGKS>VASQLHCN<FLKVISSSVID*YV

Parental  GESARLIREMFNYARDHQPCIIFMDEIDAIGGRRFSEGTSADREIQRTLMELLNQMDGFDTLHRVK-MIM
          .ESA.LIREMF.YA.DH..CIIFMDEIDAIGG..FS.G.SA.REIQ..LME.LNQ.D.FD..H..K.MI.
Retrocopy HESAHLIREMFSYATDH*SCIIFMDEIDAIGGCHFSKGISAKREIQ*ILMESLNQIDRFDSFH-IK>MIR

Parental  ATNR
          A.NR
Retrocopy AANR

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	263.78 RPM
SRP007412_cerebellum	0.00 RPM	233.09 RPM
SRP007412_heart	0.00 RPM	264.74 RPM
SRP007412_kidney	0.00 RPM	231.76 RPM
SRP007412_liver	0.50 RPM	256.28 RPM
SRP007412_testis	0.00 RPM	125.32 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_438 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_438 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 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007126	2 retrocopies	retro_cjac_204, retro_cjac_3221,
Cavia porcellus	ENSCPOG00000009477	1 retrocopy	retro_cpor_47,
Homo sapiens	ENSG00000100519	2 retrocopies	retro_hsap_1022, retro_hsap_4059,
Gorilla gorilla	ENSGGOG00000002152	2 retrocopies	retro_ggor_2727, retro_ggor_808,
Macropus eugenii	ENSMEUG00000007084	3 retrocopies	retro_meug_1700, retro_meug_2090, retro_meug_923,
Monodelphis domestica	ENSMODG00000014500	1 retrocopy	retro_mdom_438 ,
Nomascus leucogenys	ENSNLEG00000012518	2 retrocopies	retro_nleu_559, retro_nleu_900,
Otolemur garnettii	ENSOGAG00000010011	1 retrocopy	retro_ogar_3101,
Pongo abelii	ENSPPYG00000005820	2 retrocopies	retro_pabe_3334, retro_pabe_858,
Pan troglodytes	ENSPTRG00000006352	2 retrocopies	retro_ptro_2752, retro_ptro_699,
Rattus norvegicus	ENSRNOG00000007203	1 retrocopy	retro_rnor_1480,
Tursiops truncatus	ENSTTRG00000003880	1 retrocopy	retro_ttru_117,