RetrogeneDB ID: retro_chof_2335

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_66886:5633..5945(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NPC2
• Ensembl ID: ENSCHOG00000009488
• Aliases: None
• Description: Niemann-Pick disease, type C2 [Source:HGNC Symbol;Acc:14537]

Sequence

>retro_chof_2335
TCTGAGGTGGGAGTTACAAAGGGATTAAATGTGAGCCCGTGTCCCACTCAGCTCTGCCAACTGCAGAAAGGACAGCCTGA
CAGTGTCAACGTGACCTTCAGCAGCAAAATTCAGTCTCAAAATAGCGCAGCCTTGGTGCAGGACATTGTGTTTGGCGTTG
AAGTTCCCTTTATGATTCGTGAACATGATGGTTGTAAGAGTGGAATTAAGTGTCCCATGGTAAAAGACCAGACTTATACC
TACCTGAATAAACTGCCGGTGAAGAGCGAATACCCCTCTGTTAAAGTGGTGGTGAAGTGGGAACTTCAGGAT

Alignment

ORF - retro_chof_2335 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.58 %
• Parental protein coverage: 81.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SEVGVIKELNVSPCPTQPCQLHKGQSYSVNVTFSSKIQSQNSTALVYGIVFGFEVPFMIPEPDGCKSGIK
          SEVGV.K.LNVSPCPTQ.CQL.KGQ..SVNVTFSSKIQSQNS.ALV..IVFG.EVPFMI.E.DGCKSGIK
Retrocopy SEVGVTKGLNVSPCPTQLCQLQKGQPDSVNVTFSSKIQSQNSAALVQDIVFGVEVPFMIREHDGCKSGIK

Parental  CPILKDQTYTYLNKLPVKSEYPSVKVVVKWELKD
          CP..KDQTYTYLNKLPVKSEYPSVKVVVKWEL.D
Retrocopy CPMVKDQTYTYLNKLPVKSEYPSVKVVVKWELQD

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_2335 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016932	1 retrocopy	retro_cfam_2050,
Choloepus hoffmanni	ENSCHOG00000009488	1 retrocopy	retro_chof_2335 ,
Echinops telfairi	ENSETEG00000003719	2 retrocopies	retro_etel_1610, retro_etel_1866,
Loxodonta africana	ENSLAFG00000002876	1 retrocopy	retro_lafr_289,
Tursiops truncatus	ENSTTRG00000013025	1 retrocopy	retro_ttru_85,