RetrogeneDB ID: retro_mmur_1545

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: scaffold_8064:35074..35632(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB4
• Ensembl ID: ENSMICG00000016746
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 4 [Source:HGNC Symbol;Acc:9541]

Sequence

>retro_mmur_1545
ATCCCATCCACTCCCAGTTACTCCATAGATCTGGTGTCCTCACTCTACGTGGGTCCGATCACGCAGACCCAGAACCCCAT
GGTGACCAGGACCTCAGTCCTCGGCATTAAGTTCGAGGGCAGAGTGGTGATTGCCTCAGACATGCTGGGCTCCTACGTGT
CCTTGGCTTGTTTCTGCAACATCTCTAGCATTATGCTAGTCAACAACAGTACCATTCTGGGTGCTTCTGGAGATTACACT
GATTTCCAGTATTTGAAGCAAGTTCTCAGTCAGATAGTGATTGATGAGGAACTATTGAGAGATGGACACAGTTATAGTCC
TAAAGCTATTCATTCATGACTGACCAGGCCCATGTACAGCTGCTGCTCCAAGATGAACCCTCTGTGGAACACCATGGTCA
TTGGAGGCTATGCTGATGGAGAGAGCTTCCTCGGTTATGTGGACATGCTTGGTGTAGCCTACGAAGCCCCTTCGCTGGCC
ACTAGTTATGGTGCATTCTTGTCTCAGCCTCTGCTGCGAGAAGTTCTGTAGAAGCAGCCAGTGACAAGCCAAACTGAG

Alignment

ORF - retro_mmur_1545 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.41 %
• Parental protein coverage: 70.45 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IPSTPSACIDPVSSLYGGPITRTQNPMVTGTSVLGVKFEGGVVIAADMLGSYGSLARFRNISRIMRVNNS
          IPSTPS..ID.VSSLY.GPIT.TQNPMVT.TSVLG.KFEG.VVIA.DMLGSY.SLA.F.NIS.IM.VNNS
Retrocopy IPSTPSYSIDLVSSLYVGPITQTQNPMVTRTSVLGIKFEGRVVIASDMLGSYVSLACFCNISSIMLVNNS

Parental  TMLGASGDYADFQYLKQVLGQMVIDEELLGDGHSYSPKAIHSWLTRAMYSRRSKMNPLWNTMVIGGYADG
          T.LGASGDY.DFQYLKQVL.Q.VIDEELL.DGHSYSPKAIHS.LTR.MYS..SKMNPLWNTMVIGGYADG
Retrocopy TILGASGDYTDFQYLKQVLSQIVIDEELLRDGHSYSPKAIHS*LTRPMYSCCSKMNPLWNTMVIGGYADG

Parental  ESFLGYVDMLGVAYEAPSLATGYGAYLAQPLLREVLEKQPVLSQSE
          ESFLGYVDMLGVAYEAPSLAT.YGA.L.QPLLREVL.KQPV.SQ.E
Retrocopy ESFLGYVDMLGVAYEAPSLATSYGAFLSQPLLREVL*KQPVTSQTE

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_1545 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_1545 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000016746	1 retrocopy	retro_mmur_1545 ,
Monodelphis domestica	ENSMODG00000018871	1 retrocopy	retro_mdom_1459,