RetrogeneDB ID: retro_chof_791

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_14839:10664..11953(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TDP1
• Ensembl ID: ENSCHOG00000005456
• Aliases: None
• Description: tyrosyl-DNA phosphodiesterase 1 [Source:HGNC Symbol;Acc:18884]

Sequence

>retro_chof_791
GAAATGCAGCAGAAGCAGGCTGAGAAAGTGGTGGTCAAAGAGGAGAAAGGCATTTCTCCCAAAGACTGCACTGCACAAAG
AACTGGGAATCCCATCAGCCACAAGCTCAAACAGGAGGAGGAAGATGAATTTGGGATGTCAGGGGAAGGACAGGACATGT
GGGACATGCTGGATAAAGGGAAACCCTTCCAATTTTATCTCACTTGGGGCTCAGGGATCAAGCTAAAGTCCAACCCTGGA
GCCCTCCACATCAAGGATATTTTATCTCTGCTATTTGGGACACTTGTTTCTTCAGCTAAGTTTAACTACTGCTTTGATGT
GGACTGGCTCATAAAACGGTATCCACCAGAGTTCAGGAATAGGCCAATTCTGCTTTTACATAGCGATAAGTGCAAAGCTG
AGTCTCACTTACATGCCCAGGCAAAGCCTTGTGGAAACACTTCCCTTTGCCAGGCAAAGTTGGATATTACATTTGGAACA
CACCACATGAAAATGATGTTACTGCTGTACAAAGAAGGCCTCTGGGTTGTCATCCACACCTCCACCTCATCCATGCTAAC
TGGTGCCAGAAAACTCAAGGACTATGGCTGAACCCCTTGTATCCATGAATTTCCCCTGCAACCCACAGCTCTGGAGAATC
AACTACGCATTTTAAAGCTGACCTCATCAGTTACTTGATGGCTTATAATGCTCCTTCTCTCGAGTAGATAGACATCATCC
TTGAATGTGATCTTTCTGAAGCAAATATTTACCTTATTAGATCAACATCAGGACACTTTCAAAGAAATAAAAAAGATAAT
TGGGGATATTTTAAGTTCAGGAACCTTCTGAAGGAATATGCCTCATCCATACGTAAAGCTGAGTCATGGCTTATTGTAGG
TCAGTTTTCAAGCTTTGGTTCTATGGGGCCTGGTGACTCAAAATGATTATGTTCTGAGTTTAAAGAGAGCCTCATGACAC
TGGGAAAGGAAGGCAGAACCCTGGGGGAAAGTGCCATTCATCTTCTGATTTATCATCCTGTGAAAAATGTGCGGACAACT
TTAGAAGGATATCCTTCTGGGGTCTCACTTCCCTATGGCATCCATATAGCTGAAAAATGGAACTGGCTCCTTTCCTACTT
GCACAAACCATCAGCTGAGACATCTGGCCACAGCAATGCCATGCCACATATTAAGACATATATGAGGCCATCTCCAGACT
TCAGCAAAATTGCTTGGTTCCTTGTCACAAGTCCTAATCTCTCCAAGGCTGCCTGGGGGGCTTTAGAGAAAAATGGTGCC
TAGCTGATG

Alignment

ORF - retro_chof_791 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.98 %
• Parental protein coverage: 76.06 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EEQQKQAEKVEVKEEKGILPKDCAVQKTENPISHRLKEEEGDEYETSGEGQDIWDMLDKGNPFQFYLTRV
          E.QQKQAEKV.VKEEKGI.PKDC..Q.T.NPISH.LK.EE.DE...SGEGQD.WDMLDKG.PFQFYLT..
Retrocopy EMQQKQAEKVVVKEEKGISPKDCTAQRTGNPISHKLKQEEEDEFGMSGEGQDMWDMLDKGKPFQFYLTWG

Parental  SGIKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLIKQYPREFRNRPILLVHGDKWEAKAQLQAQ
          SGIK.K.N.GALHIKDILS.LFGTLVSSA.FNYCFDVDWLIK.YP.EFRNRPILL.H.DK..A...L.AQ
Retrocopy SGIKLKSNPGALHIKDILSLLFGTLVSSAKFNYCFDVDWLIKRYPPEFRNRPILLLHSDKCKAESHLHAQ

Parental  AKPYENVSLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTS-NLIHEDWHQKTQGIWLSPLYPRIPPGTH
          AKP..N.SLCQAKLDI.FGTHH.KMMLLLY.EGL.VVIHTS..LIH..W.QKTQG.WL.PLYP.I.P.TH
Retrocopy AKPCGNTSLCQAKLDITFGTHHMKMMLLLYKEGLWVVIHTS<HLIHANWCQKTQGLWLNPLYP*ISPATH

Parental  SSGESTTHFKADLISYLMAYNVPSLKEWIDIIHEHDLSETNVYLIGSTPGRFQGNQKDNWGHFRLRKLLK
          SSGESTTHFKADLISYLMAYN.PSL.E.IDII.E.DLSE.N.YLI.ST.G.FQ.N.KDNWG.F..R.LLK
Retrocopy SSGESTTHFKADLISYLMAYNAPSL-E*IDIILECDLSEANIYLIRSTSGHFQRNKKDNWGYFKFRNLLK

Parental  EYASSIPKADSWPVVGQFSSIGSMGADDSKWLCSEFKESLTTLGKDGKTLGKSAIPLHLIYPSVENVRTS
          EYASSI.KA.SW..VGQFSS.GSMG..DSK.LCSEFKESL.TLGK.G..............P.V.NVRT.
Retrocopy EYASSIRKAESWLIVGQFSSFGSMGPGDSK*LCSEFKESLMTLGKEGXXXXXXXXXXLIYHP-VKNVRTT

Parental  LEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSANLSKA
          LEGYP.G.SLPY.I..AEK.NWL.SY.HK.SAETSG.SNAMPHIKTYMRPSPDFSKIAWFLVTS.NLSKA
Retrocopy LEGYPSGVSLPYGIHIAEKWNWLLSYLHKPSAETSGHSNAMPHIKTYMRPSPDFSKIAWFLVTSPNLSKA

Parental  AWGALEKNGAQLM
          AWGALEKNGA.LM
Retrocopy AWGALEKNGA*LM

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_791 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001905	1 retrocopy	retro_amel_1840,
Choloepus hoffmanni	ENSCHOG00000005456	1 retrocopy	retro_chof_791 ,
Tupaia belangeri	ENSTBEG00000002578	2 retrocopies	retro_tbel_1158, retro_tbel_4636,