RetrogeneDB ID: retro_chof_92

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_1787:37439..37688(-)
• Located in intron of: ENSCHOG00000003460

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNCA
• Ensembl ID: ENSCHOG00000007186
• Aliases: None
• Description: synuclein, alpha (non A4 component of amyloid precursor) [Source:HGNC Symbol;Acc:11138]

Sequence

>retro_chof_92
GAGACCAAAGAGCAAGTGACAAATGCTGGAGAGGCAGTGGTGACAGGTGTGACAGCAGTAGCAAAGAAAACAGTGGAAGG
AGCAGGGAGCATTGCAGCTGCCACGGGCTTTGGCAAAAAGGATCAGTTAGGCAAGAGTAAAGGAGGACGCCCACAGGAAG
GAATTCTGGAAGATAAGCCTGTGGATCCTGACAATGATGCTTATGAAATACATTCTGAAGAAGGATATCAAGGCTACGAA
CCTGAAGCC

Alignment

ORF - retro_chof_92 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.72 %
• Parental protein coverage: 66.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KTKEQVTNVGEAVVTGVTAVAQKTVEGAGSIAAATGFGKKDQLGKNEEGGPQEGILQDMPVDPDNEAYEM
          .TKEQVTN.GEAVVTGVTAVA.KTVEGAGSIAAATGFGKKDQLGK...G.PQEGIL.D.PVDPDN.AYE.
Retrocopy ETKEQVTNAGEAVVTGVTAVAKKTVEGAGSIAAATGFGKKDQLGKSKGGRPQEGILEDKPVDPDNDAYEI

Parental  PSEEGIPDYEPKA
          .SEEG...YEP.A
Retrocopy HSEEGYQGYEPEA

Legend:

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

Expression

RNA-Seq

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST

Choloepus hoffmanni was not studied using EST data.

TSS

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab

retro_chof_92 was not experimentally validated.

Homology

Retrocopy orthology:

Choloepus hoffmanni 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,