RetrogeneDB ID: retro_mdom_1460

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:158830643..158831640(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPS5
• Ensembl ID: ENSMODG00000007838
• Aliases: None
• Description: COP9 signalosome subunit 5 [Source:HGNC Symbol;Acc:2240]

Sequence

>retro_mdom_1460
TTGGCAGCTTCAGGGAGCGGTATGGCCCAGAAGAGCTGGGAACTGGCCAACAACATGCAGAAAACCCAGAGCATATTTGA
GATCTATAAGTATGACAAGAAGCAGCAGCAGGAGATCCTGGTGGCCAAGCCCTGGTCCAAGGATCACCATTATTTTTTGT
ACTGCAAGACCACAGCCTTAGCCCTTCTGAAAATGGTGATGCATGCATGATCAGGAGGCAACTTGGAAGTGATGAGTTTG
ATGCTCCGCAAAGTGGATGGTGAAACCATGATCATTATGAACAGTTTTGCCTTACCAGTAGAGGGCACTGACACTTGAGT
TAATGCTCAAGCTGCTGCATATGAATATATGGCAGCATATATAGAAAATGCAAAACAGGTGGGTCGACTTGAAAATGCAA
TTGGCTGGTATCACAGTCACCCTGGCTATGGTTTTTGCCTCTCTGGGATTGATGTTAGTATCCAGATGCTCAATCAGCAG
TTTCAAGTACCATTTTTGGCAGTAGTTATTGATCCTACAAGAACAATGTCTGCAGGGAAGGTGAATCTTGGTGCCTTTAG
GACCTATCCAAAGGGCTATACACCACCAGATGAAGGTCCCTCTGAGTACCAGACAATTCCATTTAATAAAATAGAAGACT
TTGGAGTACACTGCAAACAGTATTATGCTTTGAAAGTCTCTTACTTTAAATCATCTTTGGATCGTAAAATTGCTTGAACT
TCTGTGGAACAAATATTGGGTAAATACTCTGAGCTCTTCTAGCTTACTTACAAATGCAACCACTGGACAAGTCTTTGATT
TATTTGAAAAATTAGAACAGCCAGAAGCCCAGTTTGGATGGGGGAGTTTCATGTTGGGTTTAGAAACACATGTATGAAAG
TCAGAAGACAAACTTGCTAAAGCAATAAGAGACAGCTGTAAGACTGCCATAGAAGCTATCCATGGATTGATGTCTCAGGT
TATTAAGGATAAACTTTTCAATCAAATTAATATTTCC

Alignment

ORF - retro_mdom_1460 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.55 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAASGSGMAQKSWELANNMQEAQSIDEIYKYDKKQQQEILAAKPWTKDHHYFKYCKISALALLKMVMHAR
          .AASGSGMAQKSWELANNMQ..QSI.EIYKYDKKQQQEIL.AKPW.KDHHYF.YCK..ALALLKMVMHA.
Retrocopy LAASGSGMAQKSWELANNMQKTQSIFEIYKYDKKQQQEILVAKPWSKDHHYFLYCKTTALALLKMVMHA*

Parental  SGGNLEVMGLMLGKVDGETMIIMDSFALPVEGTETRVNAQAAAYEYMAAYIENAKQVGRLENAIGWYHSH
          SGGNLEVM.LML.KVDGETMIIM.SFALPVEGT.T.VNAQAAAYEYMAAYIENAKQVGRLENAIGWYHSH
Retrocopy SGGNLEVMSLMLRKVDGETMIIMNSFALPVEGTDT*VNAQAAAYEYMAAYIENAKQVGRLENAIGWYHSH

Parental  PGYGCWLSGIDVSTQMLNQQFQEPFVAVVIDPTRTISAGKVNLGAFRTYPKGYKPPDEGPSEYQTIPLNK
          PGYG..LSGIDVS.QMLNQQFQ.PF.AVVIDPTRT.SAGKVNLGAFRTYPKGY.PPDEGPSEYQTIP.NK
Retrocopy PGYGFCLSGIDVSIQMLNQQFQVPFLAVVIDPTRTMSAGKVNLGAFRTYPKGYTPPDEGPSEYQTIPFNK

Parental  IEDFGVHCKQYYALEVSYFKSSLDR-KLLELLWNKYWVNTLSSSSLLTNADYTTGQVFDLSEKLEQSEAQ
          IEDFGVHCKQYYAL.VSYFKSSLDR.KLLELLWNKYWVNTLSSSSLLTNA..TTGQVFDL.EKLEQ.EAQ
Retrocopy IEDFGVHCKQYYALKVSYFKSSLDR>KLLELLWNKYWVNTLSSSSLLTNA--TTGQVFDLFEKLEQPEAQ

Parental  LGRGSFMLGLETHDRKSEDKLAKATRDSCKTTIEAIHGLMSQVIKDKLFNQINIS
          .G.GSFMLGLETH..KSEDKLAKA.RDSCKT.IEAIHGLMSQVIKDKLFNQINIS
Retrocopy FGWGSFMLGLETHV*KSEDKLAKAIRDSCKTAIEAIHGLMSQVIKDKLFNQINIS

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_1460 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1460 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002028	1 retrocopy	retro_chof_556,
Callithrix jacchus	ENSCJAG00000004632	1 retrocopy	retro_cjac_2454,
Homo sapiens	ENSG00000121022	1 retrocopy	retro_hsap_3634,
Gorilla gorilla	ENSGGOG00000016289	1 retrocopy	retro_ggor_2451,
Microcebus murinus	ENSMICG00000011042	1 retrocopy	retro_mmur_834,
Myotis lucifugus	ENSMLUG00000011697	1 retrocopy	retro_mluc_1528,
Monodelphis domestica	ENSMODG00000007838	1 retrocopy	retro_mdom_1460 ,
Mustela putorius furo	ENSMPUG00000010175	1 retrocopy	retro_mputfur_397,
Nomascus leucogenys	ENSNLEG00000010914	1 retrocopy	retro_nleu_815,
Pongo abelii	ENSPPYG00000018648	1 retrocopy	retro_pabe_2980,
Pan troglodytes	ENSPTRG00000020317	2 retrocopies	retro_ptro_2457, retro_ptro_638,
Tupaia belangeri	ENSTBEG00000008440	7 retrocopies	retro_tbel_1083, retro_tbel_1833, retro_tbel_1853, retro_tbel_2528, retro_tbel_3147, retro_tbel_3896, retro_tbel_3914,