RetrogeneDB ID: retro_chof_1733

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_371316:3..988(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAR1
• Ensembl ID: ENSCHOG00000003490
• Aliases: None
• Description: fatty acyl CoA reductase 1 [Source:HGNC Symbol;Acc:26222]

Sequence

>retro_chof_1733
AGGTTGAATTCAGTGTATGTTTTGGTGAAGCAGAAAGCTGGACAAACCTCCCAAGAGCCAGTGGAAGAAGTTATTAGTGG
CAAGCTCTTTGACAGATTGAGAGATGAAAATCCAGATTTAGGGAGAAAGTTATAGCAATCAACAGTGAACTCACCCAGCC
TAAACTGGCTCTTAGTGAAGAAGACAAAGAGGTCATTGTAGATTCTACCAATATTATATTCCACTGTGCAGCTACAGTAA
GGTTTAATGAAAATTTAAGAGATGCTGTTCAGTTAAATGCGATTGCTATGTGACAGCTTTTTCTCCTTGCACAACAAATG
AGGAATCTGAAAGTGTTCTTGCTTGTATCAACAGCATATGCATACTGCAATTGAAAGCATATTGATGGAGTAGTCTGCCC
ACCCCCTGTGGATCCCAAGAAGCTGATTGATTCTCTGGAGTGGATGGATGATGGCCTAGTAAATAACATCACTCCAAAAT
TGATAGGAGACAGACCTAATACATACACATACACAAAAGCATTGGAGACTGTGTTGTACAACAAGGAGAAAAGCTGCATG
TGGCAATTCTAAGGCCATCGATTGTTGGTGCCAGTTGGAAAGAACCTTTTCCAGGATGGACTGATAACTTTAATGGGCCA
AGTGCTCTCTTTATTGCAGCAGGGAAAGGAATTCTTTGAACAATGCATGCCTCCAACAATGCCCTTGCAGATCTTGTTCC
TGTAGATGTAGTTGTCAACACGAGTCTTGCAGCAGCCTGGTATTCCGGAGTTAATAGAGCAAGGAACATCAAGGTGTATA
ATTGCTCAACAGGCAGCACTAATCCTTTCCATGGGGGTGAAGTTGAATACCGTGTAATTTCCACTTGCAAGAGGAATCCT
CTCAAACAGGCCTTCAGAAGGCCCAGTGTAAATCTAACCTCCAATCACCTTTTATATCATTACTGGATTGCTGTAAGCTG
TAAGGTCCCAGCATTCCTGTATGAC

Alignment

ORF - retro_chof_1733 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.75 %
• Parental protein coverage: 64.01 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KVNSVYVLVRQKAGQTPQERVEEVISGKLFDRLRDENPD-FREKIIAINSELTQPKLALSEEDKEVIVDS
          ..NSVYVLV.QKAGQT.QE.VEEVISGKLFDRLRDENPD.FREK.IAINSELTQPKLALSEEDKEVIVDS
Retrocopy RLNSVYVLVKQKAGQTSQEPVEEVISGKLFDRLRDENPD<FREKVIAINSELTQPKLALSEEDKEVIVDS

Parental  TNIIFHCAATVRFNENLRDAVQLNVIATRQLILLAQQMRNLEVFMHVSTAYAYCNRKQIDEVVYPPPVDP
          TNIIFHCAATVRFNENLRDAVQLN.IA..QL.LLAQQMRNL.VF..VSTAYAYCN.K.ID.VV.PPPVDP
Retrocopy TNIIFHCAATVRFNENLRDAVQLNAIAM*QLFLLAQQMRNLKVFLLVSTAYAYCN*KHIDGVVCPPPVDP

Parental  KKLIDSLEWMDDGLVNDITPKLIGDR-NTYIYTKAL-AEYVVQQEGAKLNVAIVRPSIVGASWKEPFPGW
          KKLIDSLEWMDDGLVN.ITPKLIGDR.NTY.YTKAL....VVQQ.G.KL.VAI.RPSIVGASWKEPFPGW
Retrocopy KKLIDSLEWMDDGLVNNITPKLIGDRPNTYTYTKAL<GDCVVQQ-GEKLHVAILRPSIVGASWKEPFPGW

Parental  IDNFNGPSGLFIAAGKGILRTMRASNNALADLVPVDVVVNMSLAAAWYSGVNRPRNIMVYNCTTGSTNPF
          .DNFNGPS.LFIAAGKGIL.TM.ASNNALADLVPVDVVVN.SLAAAWYSGVNR.RNI.VYNC.TGSTNPF
Retrocopy TDNFNGPSALFIAAGKGIL*TMHASNNALADLVPVDVVVNTSLAAAWYSGVNRARNIKVYNCSTGSTNPF

Parental  HWGEVEYHVISTFKRNPLEQAFRRPNVNLTSNHLLYHYWIAVSHKAPAFLYD
          H.GEVEY.VIST.KRNPL.QAFRRP.VNLTSNHLLYHYWIAVS.K.PAFLYD
Retrocopy HGGEVEYRVISTCKRNPLKQAFRRPSVNLTSNHLLYHYWIAVSCKVPAFLYD

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_1733 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 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003490	2 retrocopies	retro_chof_1358, retro_chof_1733 ,
Callithrix jacchus	ENSCJAG00000010077	1 retrocopy	retro_cjac_545,
Cavia porcellus	ENSCPOG00000002654	1 retrocopy	retro_cpor_267,
Homo sapiens	ENSG00000197601	1 retrocopy	retro_hsap_1225,
Gorilla gorilla	ENSGGOG00000001180	1 retrocopy	retro_ggor_958,
Macaca mulatta	ENSMMUG00000011990	1 retrocopy	retro_mmul_1301,
Nomascus leucogenys	ENSNLEG00000017695	1 retrocopy	retro_nleu_698,
Oryctolagus cuniculus	ENSOCUG00000004336	2 retrocopies	retro_ocun_1056, retro_ocun_790,
Otolemur garnettii	ENSOGAG00000005064	2 retrocopies	retro_ogar_1353, retro_ogar_341,
Pongo abelii	ENSPPYG00000003470	1 retrocopy	retro_pabe_1019,
Pan troglodytes	ENSPTRG00000024190	1 retrocopy	retro_ptro_840,
Rattus norvegicus	ENSRNOG00000013176	1 retrocopy	retro_rnor_467,