RetrogeneDB ID: retro_chof_1305

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_25587:11553..11913(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000000466
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LEPROTL1
• Ensembl ID: ENSCHOG00000012299
• Aliases: None
• Description: leptin receptor overlapping transcript-like 1 [Source:HGNC Symbol;Acc:6555]

Sequence

>retro_chof_1305
TCCTTTGGAGGAGCGATTGGGCTGATGTTTTTGATGCTTGGATGTGCCCTTCCAATTTACAACCAATACCGGCCCCTCTT
TGTGCTATTGTTGCACATCCTTTCACCTATTCCCCACTGCATGGCAAAAAGACTGGTGGATGATACAGGTGCTATGGGTA
ATGCTTGTAAGGAATTCATCGTATTTCTTACAACAGGCATTGTTGCCTTGGCTTTTGGACTCCCTGTTGGATTTGCCAGA
GCACATCTGATTGAATGGGGAGCTTGTGCACTGGCTCTCACAGGCAGCACTCATCTTTGCTTTTTCTTAGTCTTTTTCTT
GGTCTTTGGATGCAAGGATGGCTTCAGCTGGCAGCAGTGG

Alignment

ORF - retro_chof_1305 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.86 %
• Parental protein coverage: 92.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SFGGAIGLMFLMLGCALPIYNQYWPLFVLFFYILSPIPYCIARRLVDDTDAMSNACKELAIFLTTGIVVS
          SFGGAIGLMFLMLGCALPIYNQY.PLFVL...ILSPIP.C.A.RLVDDT.AM.NACKE...FLTTGIV..
Retrocopy SFGGAIGLMFLMLGCALPIYNQYRPLFVLLLHILSPIPHCMAKRLVDDTGAMGNACKEFIVFLTTGIVAL

Parental  AFGLPIVFARAHLIEWGACALVLTGNTVIFATILGFFLVFGSNDDFSWQQW
          AFGLP..FARAHLIEWGACAL.LTG.T......L.FFLVFG..D.FSWQQW
Retrocopy AFGLPVGFARAHLIEWGACALALTGSTHL-CFFLVFFLVFGCKDGFSWQQW

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_1305 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006530	1 retrocopy	retro_cfam_2171,
Choloepus hoffmanni	ENSCHOG00000012299	1 retrocopy	retro_chof_1305 ,
Dasypus novemcinctus	ENSDNOG00000014538	3 retrocopies	retro_dnov_1528, retro_dnov_2606, retro_dnov_876,
Erinaceus europaeus	ENSEEUG00000001360	1 retrocopy	retro_eeur_139,
Oryctolagus cuniculus	ENSOCUG00000013931	1 retrocopy	retro_ocun_832,