RetrogeneDB ID: retro_chof_1239

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_23476:8389..9334(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GNL3
• Ensembl ID: ENSCHOG00000002726
• Aliases: None
• Description: guanine nucleotide binding protein-like 3 (nucleolar) [Source:HGNC Symbol;Acc:29931]

Sequence

>retro_chof_1239
GAGAATATGGAGAGCTGGCTAAGTGGTTTTGAGAAAGAAATGTGAATAGCGGTGTTCAGAGCCTCAACAAACCTGAAGGA
CAAAGGGAAGATAATCAAGGTGAAGGAGAAAACTGCTCCGTTCAAAAGAGAAGTCTGCTTTGGGAAAAGAGGGCCTTTGG
AAGCTTCTTCAAGATTTTCAGGAGACTTAATGGCAAAGCCATTCAGGTTGGAGTAATTGGTTTCCCTAATGTGGGAAAAA
AACATCACAATGGCTTAAAACAAGAATGGACATGCAATGCTAGTGTATCCATGGGGTTTACAAACAGCATGCAGGTTGTC
TCCTTGGACAAACAGATCACAATCATAGACAGCCCCAGCTTGATCTTGTCTCCACTTAACTTTGCCACTGCGCTTACTCT
GAGAATCCTGAAAGAATCAAAGTATTAAAACCGATGGGGCCTGCCAGTGCCGTCCTGTCCCAGGCTGACACTCAACAGAT
ATATTGAAATGCACTGTTGCAGACTATAAGAATCCTCTGGATTTTTTTTTTTTTTTTACTTTGCTTGTTTAGAGAAAAAG
ACTGCATCTTCAAGGTAGAACCCATTTGTGGAAGGTACTGCCAAACTGCTATGGTCTAAATGGATAGGAGCCACTTGAGG
CTTCTGTTGCCAGTTCCCTATATCCTGGACTCCTTCCCCACATTTTAATGAGAGTATTGTAGCAAACATGAAATGGGGCT
TTAATGTGGAGGAATGTGAACAATGCACACAGCATATATGCCGTTGGGGGCCCTCCTTTAGCCAGTAGCATCTTTTCTCA
TTCTTCAGGTCTGACAAATGGAATAATAGAAGGAAAGGACATACCTGAGGAATTGCCAAAACAGAAAGAGAGGAAGCAGG
AGGAGCGGAACATTGACAGCGACCAGGAAAGTGTTGATGGTGAAGAAGCTGATGAAAAGAGCACA

Alignment

ORF - retro_chof_1239 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.53 %
• Parental protein coverage: 57.61 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  ENLESWLSYLEKELPTVVFRASTILKDRGKIVKHVKVKKKAAPFKSEICFGK-EGLWKLLRGFQET-YGK
          EN.ESWLS..EKE....VFRAST.LKD.GKI....KVK.K.APFK.E.CFGK.EGLWKLL..FQET..GK
Retrocopy ENMESWLSGFEKEM*IAVFRASTNLKDKGKII---KVKEKTAPFKREVCFGK>EGLWKLLQDFQET>NGK

Parental  AIQVGVIGFPNVGKSSIINSLKQERTCNVGVSMGLTRSMQVVPLDKQITIIDSPSLIVSPLNSATSLALR
          AIQVGVIGFPNVGK....N.LKQE.TCN..VSMG.T.SMQVV.LDKQITIIDSPSLI.SPLN.AT.L.LR
Retrocopy AIQVGVIGFPNVGKKHH-NGLKQEWTCNASVSMGFTNSMQVVSLDKQITIIDSPSLILSPLNFATALTLR

Parental  -SPASIEVIKPVEAASAILSQADTRQV-VLKFTVPDYKNSLEFF---TLLAQRRGLHYKGGS-PNVEGAA
          ..P..I.V.KP...ASA.LSQADT.Q...LK.TV.DYKN.L......TLL..R..LH..G...P.VEG.A
Retrocopy <NPERIKVLKPMGPASAVLSQADTQQI<ILKCTVADYKNPLXXXXXXTLLV*RKRLHLQGRT<PFVEGTA

Parental  KLLWSEWTGATLSFCCQPPTSWTPSPHFNESIVANMKWGFNLEQLEKNNAHCIQAIRGPCLASSILF-QS
          KLLWS.W.GAT..FCCQ.P.SWTPSPHFNESIVANMKWGFN.E..E....H......GP......LF..S
Retrocopy KLLWSKWIGAT*GFCCQFPISWTPSPHFNESIVANMKWGFNVEECEQCTQHICR--WGPSFSQ*HLF>HS

Parental  SGLTNGIIEENDIPEELPKLKERKQEEQEHNSEDIYRDQESVDGEET
          SGLTNGIIE..DIPEELPK.KERKQEE....S.....D.E..D...T
Retrocopy SGLTNGIIEGKDIPEELPKQKERKQEERNIDSDQESVDGEEADEKST

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_1239 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002726	1 retrocopy	retro_chof_1239 ,
Tupaia belangeri	ENSTBEG00000017518	1 retrocopy	retro_tbel_1224,