RetrogeneDB ID: retro_chof_94

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_1808:12941..13265(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FXN
• Ensembl ID: ENSCHOG00000005107
• Aliases: None
• Description: frataxin [Source:HGNC Symbol;Acc:3951]

Sequence

>retro_chof_94
ATCCAGGACAAAACTCTGGATTCCTTAGTAGGGTTTTTTGAAGAACTTGTAGTTAAGTCTTACACGTTTGAAGATTATGA
TGTCTCATTTGGGAGTGGTGTTTTAACTGTTAAACTGGGTAGAGAGCTGGAGACCTATGTGATCAACAAGGAAACCCCAA
AGAAGCAAATCAGCTTATCTTCTCCATCCAGTGGGCCTAAGTGTTATGATTGAACTGGAAAAAACTGGGTGTGCTCCCAT
GGTAGCCGGTTCCTCCATGAGTTGCTGAATTCAGCTTTGAAGACCAAATTGAATTTATCTTCCTTGTCCTATTCCAAAAA
AGAT

Alignment

ORF - retro_chof_94 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 52.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LAEETLDSLT-FFEDLADKSYTFEDYDVSFGSGVLTIKLGGDLGTYVINKQTPNKQIWLSSPSSGPKRYD
          ....TLDSL..FFE.L..KSYTFEDYDVSFGSGVLT.KLG..L.TYVINK.TP.KQI.LSSPSSGPK.YD
Retrocopy IQDKTLDSLVGFFEELVVKSYTFEDYDVSFGSGVLTVKLGRELETYVINKETPKKQISLSSPSSGPKCYD

Parental  WTGKNWVYSHDGVSLHELLTAELTAALKTKLDLSSLAYSGKD
          .TGKNWV.SH....LHELL......ALKTKL.LSSL.YS.KD
Retrocopy *TGKNWVCSHGSRFLHELL----NSALKTKLNLSSLSYSKKD

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_94 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 13 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006915	1 retrocopy	retro_amel_1496,
Choloepus hoffmanni	ENSCHOG00000005107	2 retrocopies	retro_chof_349, retro_chof_94 ,
Callithrix jacchus	ENSCJAG00000001695	4 retrocopies	retro_cjac_1562, retro_cjac_1927, retro_cjac_3939, retro_cjac_813,
Dasypus novemcinctus	ENSDNOG00000024066	3 retrocopies	retro_dnov_2204, retro_dnov_2317, retro_dnov_307,
Equus caballus	ENSECAG00000019174	1 retrocopy	retro_ecab_311,
Homo sapiens	ENSG00000165060	2 retrocopies	retro_hsap_1447, retro_hsap_4311,
Gorilla gorilla	ENSGGOG00000007636	3 retrocopies	retro_ggor_1112, retro_ggor_2203, retro_ggor_2881,
Macaca mulatta	ENSMMUG00000000357	2 retrocopies	retro_mmul_2038, retro_mmul_826,
Mustela putorius furo	ENSMPUG00000009619	2 retrocopies	retro_mputfur_501, retro_mputfur_803,
Mus musculus	ENSMUSG00000059363	2 retrocopies	retro_mmus_1571, retro_mmus_3058,
Otolemur garnettii	ENSOGAG00000031105	2 retrocopies	retro_ogar_1865, retro_ogar_476,
Rattus norvegicus	ENSRNOG00000015213	1 retrocopy	retro_rnor_2276,
Tursiops truncatus	ENSTTRG00000010336	4 retrocopies	retro_ttru_1281, retro_ttru_175, retro_ttru_546, retro_ttru_831,