RetrogeneDB ID: retro_chof_347

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_7982:23821..24246(-)
• Located in intron of: ENSCHOG00000012333

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPX6
• Ensembl ID: ENSCHOG00000007526
• Aliases: None
• Description: glutathione peroxidase 6 (olfactory) [Source:HGNC Symbol;Acc:4558]

Sequence

>retro_chof_347
AAGCACTATGCTGGCAAAGACACCTGTCCGTCAACATGGCCAGCTCCCAAGGCCTGCCGGGCCATCACGCTGAATTGAAC
ACACTACAAGAAGAGCTTGCACCTTTTGGTCTGGTTATTCTGGGCTTCCCCTGCAACCAATTGGGAAAACAGGAACCAGG
AGAGAACGTGGAGATTCTACCCACCCTCAAGTACATGTGCCCAGCCTGGGGCTTTGGCCGTTTCCAGCTCTTTGAGGAAG
GGGATGTGAACAGGGAGAAAGAGAAGTTCTCCACTTCCCTGAAGAACTCCTGTCCTCCCACCTCCGAGCTCCCGTGCACA
CCTGACTGTCTCTTCTGGGAGCCCACGAAGGTCCGTGGCATCCACTGGAACCTTGAGAAGCTCCTGGTGGGACCAGGCAG
TATGCCCATCAGGTGCCGGTACCAC

Alignment

ORF - retro_chof_347 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.38 %
• Parental protein coverage: 75. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KQYAGKHV-LFVNVATYUGLTAQYPELNALQEELKPFGVVVLGFPCNQFGKQEPGKNSEILPGLRYVRPG
          K.YAGK...L.VN.A...GL.....ELN.LQEEL.PFG.V.LGFPCNQ.GKQEPG.N.EILP.L.Y..P.
Retrocopy KHYAGKDT<LSVNMASSQGLPGHHAELNTLQEELAPFGLVILGFPCNQLGKQEPGENVEILPTLKYMCPA

Parental  GGFVPNFQLFEKGDVNGEKEQKIFTFLKNSCPPPSELLGSSSQLFWEPMKVHDIRWNFEKFLVGPDGVPV
          .GF...FQLFE.GDVN.EKE.K..T.LKNSCPP.SEL......LFWEP.KV..I.WN.EK.LVGP...P.
Retrocopy WGF-GRFQLFEEGDVNREKE-KFSTSLKNSCPPTSELPCTPDCLFWEPTKVRGIHWNLEKLLVGPGSMPI

Parental  MRWYH
          ...YH
Retrocopy RCRYH

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_347 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007526	1 retrocopy	retro_chof_347 ,
Tarsius syrichta	ENSTSYG00000000641	1 retrocopy	retro_tsyr_1061,