RetrogeneDB ID: retro_chof_293

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_6400:28912..30296(+)
• Located in intron of: ENSCHOG00000013506

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSPA9
• Ensembl ID: ENSCHOG00000013579
• Aliases: None
• Description: heat shock 70kDa protein 9 (mortalin) [Source:HGNC Symbol;Acc:5244]

Sequence

>retro_chof_293
CTATCTGGACTAAATGTTCTTCAAGTGATTAATGAACCCACAGCTGCTGCTCTGGCCTATAGTCTAAAATCAGAAGATAA
AGTCATTGCTGTGTTTGATTTAGATGGTGGAACTTTCAATATTTCCATTCTGGAAATTCAGAAAGGAATGTTTGAGGTAA
AATCCACCAATGGAGATATTTTCTTAGGTGGTGAAGAGGTCTATGAGGCTTTGTTTCAACAACACTGTGAGGGAGTTCAA
GATGAAGACGGGTGGATTTGACCAAAGACAATACGGTGCTTCAAAGGGTGTGAGAAGCTGCTGAGAGGGCCAAATGTAAA
CTCTTCCTCATCTGTGCAGACTGACATCAACTTGCCATATCTTACAATGATGCTTCTGAACCCAAGTATTTGAACATGAA
GCTGACCTGGGCTCAGTTTGAGGGGAATGTCATTGATCTAATCAGGAGGACTGTTGCCCCATGCCAGAAAGCCATGCAAG
ATGCAGAAGTTGGCAAGAGTGACATAGGAAAAGGGATTCTTGTTGGAGGCATGACTAGGCTGCCCAAAGCGCAGCAGACA
GTGCAGGATCTTTTTGGCCAAGCCCCAAGTAAAGTCATAAATCTTGATGAGGCTGTGGCCATTGGAGCTCCATCCAGCGA
GACATGTTGGCTGGTGACATCCCAGATGTGTTGCTCCTGGATCTCGTTCCCCTGTCTCTGGGTATTGAAACTCTGGATGG
GGTCTTTACTAAACTTATTAATGGGAACACTACTATTCCAACCAAGAAGAGCCAGGTGTTCTCTACAGCTGCTGATGGAC
GAACTCAAGAGGAGATTAAAGTATGTCAAGGTGAGAGAGAGATGGATGGAGACAACAGTCTTGGACAAGTTACTTTGATT
GGAATTCCACCAGCCCCTCATGGTGTCCCTCAGGTTGATGTTACATTTGACACTGATGCCAATGGGATTATTCATGTTTC
TGCCAAAGATAAGGGCACAGGATGTGAGCAGCAGATTGTGATCCAATCTTCTGGTGGGTTAAGCAAAGATATTGAAAATA
TGGTTAAAAATGCAGAGAAGTTTGCTGAGGAAGACCGGAAAAAGAAGGAATGAGCTGAAGCAGTTAATATGGCCAAAGGA
ATCATTCGTGACACAGAAAATAAGATGGAAGACTTCAAGAATTGATTGCCTGCAGATGAGCACAACAAGCTAAAAGAAGA
GATTTCCAAGATAAGGGAGCTCCTGGCTCGAAAAGATAGTGAAACAGGAGAAAACATAAGACAGGCAGCATCTTCCCATC
AGCAAGTGTCACTGAAGCTCTTCAAAATGGCATACAAAAAGATGGCATCTGAGCGAGAAGGCTCTGGAAGTTCTGGCTCT
GGGGAACATAAAGAACAAAAGGAA

Alignment

ORF - retro_chof_293 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.24 %
• Parental protein coverage: 68.99 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ISGLNVLRVINEPTAAALAYGLDKSEDKIIAVYDLGGGTFDISILEIQKGVFEVKSTNGDTFLGGEDFDQ
          .SGLNVL.VINEPTAAALAY.L.KSEDK.IAV.DL.GGTF.ISILEIQKG.FEVKSTNGD.FLGGE....
Retrocopy LSGLNVLQVINEPTAAALAYSL-KSEDKVIAVFDLDGGTFNISILEIQKGMFEVKSTNGDIFLGGEEVYE

Parental  ALLQHIVKEFKRETG-VDLTKDNMALQRVREAAEKAKCELF-SSVQTDINLPYLTM-DASGPKHLNMKLT
          AL.Q........E.G.VDLTKDN..LQRV.EAAE.AKC.LF.SSVQTDINLPYLTM.DAS.PK.LNMKLT
Retrocopy ALFQQHCEGVQDEDG<VDLTKDNTVLQRV*EAAERAKCKLF>SSVQTDINLPYLTM<DASEPKYLNMKLT

Parental  RAQFEGIVGDLIRRTVAPCQKAMQDAEVSKSDIGEVILVGGMTRMPKVQQTVQDLFGRAPSKAVNPDEAV
          .AQFEG.V.DLIRRTVAPCQKAMQDAEV.KSDIG..ILVGGMTR.PK.QQTVQDLFG.APSK..N.DEAV
Retrocopy WAQFEGNVIDLIRRTVAPCQKAMQDAEVGKSDIGKGILVGGMTRLPKAQQTVQDLFGQAPSKVINLDEAV

Parental  AIGA-AIQGGVLAGDVTDVLLLDVTPLSLGIETLGGVFTKLINRNTTIPTKKSQVFSTAADGQTQVEIKV
          AIGA..IQ...LAGD..DVLLLD..PLSLGIETL.GVFTKLIN.NTTIPTKKSQVFSTAADG.TQ.EIKV
Retrocopy AIGA<SIQRDMLAGDIPDVLLLDLVPLSLGIETLDGVFTKLINGNTTIPTKKSQVFSTAADGRTQEEIKV

Parental  CQGEREMAGDNKLLGQFTLIGIPPAPRGVPQIEVTFDIDANGIVHVSAKDKGTGREQQIVIQSSGGLSKD
          CQGEREM.GDN.L.GQ.TLIGIPPAP.GVPQ..VTFD.DANGI.HVSAKDKGTG.EQQIVIQSSGGLSKD
Retrocopy CQGEREMDGDNSL-GQVTLIGIPPAPHGVPQVDVTFDTDANGIIHVSAKDKGTGCEQQIVIQSSGGLSKD

Parental  DIENMVKNAEKYAEEDRRKKERVEAVNMAEGIIHDTETKMEEFKNQLPADECNKLKEEISKMRELLARKD
          .IENMVKNAEK.AEEDR.KKE..EAVNMA.GII.DTE.KME.FKN.LPADE.NKLKEEISK.RELLARKD
Retrocopy -IENMVKNAEKFAEEDRKKKE*AEAVNMAKGIIRDTENKMEDFKN*LPADEHNKLKEEISKIRELLARKD

Parental  SETGENIRQAASSLQQASLKLFEMAYKKMASEREGSGSSGSEEQKEEKQ
          SETGENIRQAASS.QQ.SLKLF.MAYKKMASEREGSGSSGS.E.KE.K.
Retrocopy SETGENIRQAASSHQQVSLKLFKMAYKKMASEREGSGSSGSGEHKEQKE

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_293 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013579	2 retrocopies	retro_chof_2539, retro_chof_293 ,
Homo sapiens	ENSG00000113013	1 retrocopy	retro_hsap_2214,
Gorilla gorilla	ENSGGOG00000014154	1 retrocopy	retro_ggor_1747,
Mus musculus	ENSMUSG00000024359	1 retrocopy	retro_mmus_3624,
Pan troglodytes	ENSPTRG00000017290	1 retrocopy	retro_ptro_1680,
Rattus norvegicus	ENSRNOG00000019525	1 retrocopy	retro_rnor_1797,