RetrogeneDB ID: retro_mmur_173

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: GeneScaffold_1567:479024..479450(+)
• Located in intron of: ENSMICG00000008410

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB1
• Ensembl ID: ENSMICG00000007469
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 1 [Source:HGNC Symbol;Acc:9537]

Sequence

>retro_mmur_173
CTGCATAGCACGGGTCAGGCTAACGGAGACCAGTGGGTGCTGTGGGTGGAGCCGCAGAGCGCTGCGGGCCCTTTGCAGCT
GCGCTTTTCACCCTAGGCTTTCAACAGAGGTACTGTATTGGCAGTTGCTGGAGAAGATGTTTCAATTGTTGCTTTTGACA
CTTGATTGAGTAAAGAGTTTTCACTTCATACCTGAGACAGCCCCAAATGTTACAAGTTAATAGACAAAACAGTCATTGGA
TGCAGTGGTGTTCATGGAGACTGTCTTACCCTGACAAAGATTATTGAAGCAAGACTAAAGATGTATAAACATTCCAATAA
TAAGGCCATGACTACAGGGGCAATTGCTACAATGCTGTCTATGATCCTGTATTCAAGGCGCTTCTTTCCATACTGTGTTT
ACAACATTACCAGTGGACTTGATGAA

Alignment

ORF - retro_mmur_173 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.17 %
• Parental protein coverage: 98.61 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSSAAAYSGPGRDLGMEPHSAAGSLQLRFSPYAFNGGTVLAIAGEDFSIVASDTRLSEGFSIHTRDSPKC
          L.S.....G....L..EP.SAAG.LQLRFSP.AFN.GTVLA.AGED.SIVA.DT.LS..FS.HT.DSPKC
Retrocopy LHSTGQANGDQWVLWVEPQSAAGPLQLRFSP*AFNRGTVLAVAGEDVSIVAFDT*LSKEFSLHT*DSPKC

Parental  YKLTDKTVIGCSGFHGDCLTLTKIIEARLKMYKHSNNKAMTTGAIAAMLSTILYSRRFFPYYVYNIIGGL
          YKL.DKTVIGCSG.HGDCLTLTKIIEARLKMYKHSNNKAMTTGAIA.MLS.ILYSRRFFPY.VYNI..GL
Retrocopy YKLIDKTVIGCSGVHGDCLTLTKIIEARLKMYKHSNNKAMTTGAIATMLSMILYSRRFFPYCVYNITSGL

Parental  DE
          DE
Retrocopy DE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Microcebus murinus was not studied using RNA-Seq expression data.

ChIP-Seq

Microcebus murinus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmur_173 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_173 was not experimentally validated.

Homology

Retrocopy orthology:

Microcebus murinus 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017047	1 retrocopy	retro_amel_1066,
Canis familiaris	ENSCAFG00000004116	1 retrocopy	retro_cfam_2108,
Callithrix jacchus	ENSCJAG00000020644	1 retrocopy	retro_cjac_632,
Dasypus novemcinctus	ENSDNOG00000019502	1 retrocopy	retro_dnov_2087,
Felis catus	ENSFCAG00000031269	1 retrocopy	retro_fcat_911,
Gorilla gorilla	ENSGGOG00000022128	1 retrocopy	retro_ggor_1661,
Microcebus murinus	ENSMICG00000007469	1 retrocopy	retro_mmur_173 ,
Macaca mulatta	ENSMMUG00000019919	1 retrocopy	retro_mmul_1135,
Mustela putorius furo	ENSMPUG00000007150	1 retrocopy	retro_mputfur_1196,
Mus musculus	ENSMUSG00000014769	2 retrocopies	retro_mmus_1784, retro_mmus_3664,
Oryctolagus cuniculus	ENSOCUG00000007973	2 retrocopies	retro_ocun_1029, retro_ocun_620,
Procavia capensis	ENSPCAG00000000344	1 retrocopy	retro_pcap_329,
Pongo abelii	ENSPPYG00000017191	1 retrocopy	retro_pabe_130,
Vicugna pacos	ENSVPAG00000006517	1 retrocopy	retro_vpac_521,