RetrogeneDB ID: retro_chof_118

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_2491:17227..18089(+)
• Located in intron of: ENSCHOG00000011952

Retrocopy information

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

Parental gene information

• Parental gene symbol: WDR12
• Ensembl ID: ENSCHOG00000013851
• Aliases: None
• Description: WD repeat domain 12 [Source:HGNC Symbol;Acc:14098]

Sequence

>retro_chof_118
GAAGAGGTTGTAGAACTAGAATACGTGGAGAAGTACAGTGCACCTCAGCCAGAGCAATGCGTGTTCCACAATAACAGGAT
CAGTTCTGTTTAAGGAGCAGAGGAATGGATCTTGACTGGTTCTTACAATAAGACTTCTCAAATCTGGTCCTTGGAAGGAA
AGTCAATAATGACAATTGTGGGACATACAGACATTGTAAAAGATGTGGCCTGGGTGAAAAAAGACAGTTTGTTTTGTTTA
CTACTGAGTGCCTCTGTGAATCAGACTCTTCTCTTATGGGAGTGGAATGTAGAGAGAAACAAAGTGAAAATCCTACATTG
CTGCATAGGTCATGCTGGAAGTGTGGATTCTATAGCTGTTGTTAGCACAGGAACTAAATTTTGCAGTGGCTTCTGGGATA
AGATGCTAAAGATCTGGTCTACAGTCCCTACAAATGAAGAAGATGAAATGGAGGAATCTACTAATCGACCAAGAAAGAAA
CAAAACAAAGCAATTGGGACTAACCAGGACTCCCATGGTGACCCTCTCTGGCCACAAGGAAGCAATTTCCTCAGTCCTCT
GGTCAGATGCTGAAGAAATCTGCACTACATCTTGGGACCACACAAATAGAGTGTGGGGTGTTGAGACTGGCAGTCTTAAG
TCAACTTTGACAGGAAATAAAGTGTTTGACTGTGACTCCTATTCTCCACTTTGTAAATGTTTAGCATCTGAGAGTATAGA
TAAACACATCAGACTGTGGGATCCCTGAACTAAAGACGGTTCTTTGTTGTCACTGTTCCTAACCTCACATACAGGTTGGG
TCACATCAGTAAAGTGGTGTCCTACCCATGAACAGTGGCTGATCTCAGGTTCTTTAGACAAC

Alignment

ORF - retro_chof_118 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.74 %
• Parental protein coverage: 71.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EEVVELEYVEKYSAPQPEQCMFHDDWISSVKGAEEWILTGSYDKTSRIWSLEGKSIMTIVGHTDVVKDVA
          EEVVELEYVEKYSAPQPEQC.FH...ISSV.GAEEWILTGSY.KTS.IWSLEGKSIMTIVGHTD.VKDVA
Retrocopy EEVVELEYVEKYSAPQPEQCVFHNNRISSV*GAEEWILTGSYNKTSQIWSLEGKSIMTIVGHTDIVKDVA

Parental  WVKKDSLSCLLLSASMDQTILFWEWNIERNKVKALHCCRGHAGSVESIAVDNTGTKFCSGSWDKMLKIWS
          WVKKDSL.CLLLSAS..QT.L.WEWN.ERNKVK.LHCC.GHAGSV.SIAV..TGTKFCSG.WDKMLKIWS
Retrocopy WVKKDSLFCLLLSASVNQTLLLWEWNVERNKVKILHCCIGHAGSVDSIAVVSTGTKFCSGFWDKMLKIWS

Parental  TVPTNEEDEMEEPTNRPRKKQKTEQLG-LTRXXXXXXXGHKEAISSVLWSDAEEICTASWDHTIKVWDVE
          TVPTNEEDEMEE.TNRPRKKQ.....G.LTR.......GHKEAISSVLWSDAEEICT.SWDHT..VW.VE
Retrocopy TVPTNEEDEMEESTNRPRKKQ-NKAIG>LTRTPMVTLSGHKEAISSVLWSDAEEICTTSWDHTNRVWGVE

Parental  TGSLKSTLTGNKVFNCISYSPLCKCLASGSTDRHIRLWDPRTKDGSLVSLSLTSHTGWVTSVKWCPTHEQ
          TGSLKSTLTGNKVF.C.SYSPLCKCLAS.S.D.HIRLWDP.TKDGSL.SL.LTSHTGWVTSVKWCPTHEQ
Retrocopy TGSLKSTLTGNKVFDCDSYSPLCKCLASESIDKHIRLWDP*TKDGSLLSLFLTSHTGWVTSVKWCPTHEQ

Parental  QLISGSLDN
          .LISGSLDN
Retrocopy WLISGSLDN

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_118 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 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012519	1 retrocopy	retro_cfam_1759,
Choloepus hoffmanni	ENSCHOG00000013851	1 retrocopy	retro_chof_118 ,
Callithrix jacchus	ENSCJAG00000005171	1 retrocopy	retro_cjac_2690,
Cavia porcellus	ENSCPOG00000008824	1 retrocopy	retro_cpor_1107,
Homo sapiens	ENSG00000138442	1 retrocopy	retro_hsap_1615,
Gorilla gorilla	ENSGGOG00000026073	1 retrocopy	retro_ggor_1222,
Loxodonta africana	ENSLAFG00000011955	1 retrocopy	retro_lafr_1102,
Mus musculus	ENSMUSG00000026019	3 retrocopies	retro_mmus_1394, retro_mmus_2649, retro_mmus_2897,
Nomascus leucogenys	ENSNLEG00000007018	1 retrocopy	retro_nleu_2743,
Pongo abelii	ENSPPYG00000013089	1 retrocopy	retro_pabe_1327,
Pan troglodytes	ENSPTRG00000012823	1 retrocopy	retro_ptro_1083,
Tursiops truncatus	ENSTTRG00000001231	1 retrocopy	retro_ttru_1380,