RetrogeneDB ID: retro_mmur_272

Retrocopy location

• Organism: Mouse Lemur (Microcebus murinus)
• Coordinates: GeneScaffold_2120:147847..148153(-)
• Located in intron of: ENSMICG00000014292

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNCA
• Ensembl ID: ENSMICG00000005634
• Aliases: None
• Description: synuclein, alpha (non A4 component of amyloid precursor) [Source:HGNC Symbol;Acc:11138]

Sequence

>retro_mmur_272
ATGGATATATTCAAGAAAGGACTTTCAAAGGCCAAGAAGGGAGTCGTGGCCGCTGCTGAGAAAACCAAACAGGGTGTGGC
AGAAGCAGCGGGAAAGACAAAAGAGGGCGTTCTCTAGGTAGGCTTCACAATCAAGGATGGAGTGGTGCATGGCATGACTA
CAGTGCCTGAGAAGACCAAAGAGCAAGTGACAAATGTCGGAGGGGCGTTGGTGACCTGTGTGACCTCAGTAGCCCAGAAG
ACAGTGGAGGGAGCAGGGAGCACTGCAGCTGCCACTGGCTCTTGCAAAAAGGACCAATTTGGCAAG

Alignment

ORF - retro_mmur_272 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.27 %
• Parental protein coverage: 72.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDIFKKGLSKAKEGVVAAAEKTKQGVAEAAGKTKEGVLYVGSKTKEGVVHGVTTVAEKTKEQVTNVGGAV
          MDIFKKGLSKAK.GVVAAAEKTKQGVAEAAGKTKEGVL.VG...K.GVVHG.TTV.EKTKEQVTNVGGA.
Retrocopy MDIFKKGLSKAKKGVVAAAEKTKQGVAEAAGKTKEGVL*VGFTIKDGVVHGMTTVPEKTKEQVTNVGGAL

Parental  VTGVTAVAQKTVEGAGSIAAATGFGKKDQFGK
          VT.VT.VAQKTVEGAGS.AAATG..KKDQFGK
Retrocopy VTCVTSVAQKTVEGAGSTAAATGSCKKDQFGK

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_272 retrocopy.

TSS

Microcebus murinus was not studied using FANTOM5 data.

Lab

retro_mmur_272 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007186	1 retrocopy	retro_chof_92,
Felis catus	ENSFCAG00000011488	1 retrocopy	retro_fcat_452,
Microcebus murinus	ENSMICG00000005634	1 retrocopy	retro_mmur_272 ,
Oryctolagus cuniculus	ENSOCUG00000023825	1 retrocopy	retro_ocun_422,