RetrogeneDB ID: retro_chof_1762

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_378274:175..705(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PGAM5
• Ensembl ID: ENSCHOG00000011867
• Aliases: None
• Description: phosphoglycerate mutase family member 5 [Source:HGNC Symbol;Acc:28763]

Sequence

>retro_chof_1762
TGGGACCTCAACTGGGACAGGCGAGAACCACTGTCTCTCATCAACCTGCAGAAAAGGAACCTGGAATCTGGAGAAGAACT
GGTGTCAGACTGGACCACTGCAAAGCCGAGGCCAGGTGACACATCTTCCTCATCCAGCACTCCCAGGACCATGTGGATGG
CTCCCTGGAGAAGGACTGGACTCTGACCCTGCTGGGCCGTGAAGAAGCTGAACTAACTGGTCTCGACTCACAAGCTTGGG
GCTGAAGTTCGTAAAATTGTACATTCCTCCATGACCTGAGCAATAGAAACAGCAGACATAATCAGCAAACACCTGCCAGC
AGTCTGTAGAGTCAGCACAGACCTGCTTAGGGAAGGTGCCCCCATCAAACCAGACCTACTGTGTCCCACTGGAAGACGGA
AGCTGTGTATTTTGAAGATGGAGCCCAAACTGAGGCCGCATTCCAGAACTACATCCACTGGGCAGATGCCAAGCTGGAGG
AGGACAGTTACGAGATGATCTGCTATGCCAACATCATCCATTAAATCATG

Alignment

ORF - retro_chof_1762 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.92 %
• Parental protein coverage: 75.73 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  WDPNWDRREPLSLINLRKRNLESGEEELAS-RLDHCKAKATRHIFLIRHSQYHVDGSREKDRTLTPLGRE
          WD.NWDRREPLSLINL.KRNLESGEE.L.S.RLDHCKA.A..HIFLI.HSQ.HVDGS.EKD.TLT.LGRE
Retrocopy WDLNWDRREPLSLINLQKRNLESGEE-LVS<RLDHCKAEAR*HIFLIQHSQDHVDGSLEKDWTLTLLGRE

Parental  QAELTGL-RLASLGLKF-DKIVHSSMTRAIETADIISKHLPGVYRVSTDLLREGAPIEPD-PPVSHWKPE
          .AELTGL.RL.SLGLKF..KIVHSSMT.AIETADIISKHLP.V.RVSTDLLREGAPI.PD.P.VSHWK.E
Retrocopy EAELTGL<RLTSLGLKF<RKIVHSSMT*AIETADIISKHLPAVCRVSTDLLREGAPIKPD<PTVSHWKTE

Parental  AVQYYEDGARIEAAFRNYIHRADAKQEEDSYEIFICHANVIRYIV
          AV.Y.EDGA..EAAF.NYIH.ADAK.EEDSYE..IC.AN.I..I.
Retrocopy AV-YFEDGAQTEAAFQNYIHWADAKLEEDSYEM-ICYANIIH*IM

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_1762 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013437	2 retrocopies	retro_amel_1052, retro_amel_173,
Choloepus hoffmanni	ENSCHOG00000011867	2 retrocopies	retro_chof_1762 , retro_chof_2590,
Felis catus	ENSFCAG00000002503	2 retrocopies	retro_fcat_800, retro_fcat_960,
Homo sapiens	ENSG00000247077	1 retrocopy	retro_hsap_3363,
Myotis lucifugus	ENSMLUG00000013646	1 retrocopy	retro_mluc_1270,
Macaca mulatta	ENSMMUG00000015466	1 retrocopy	retro_mmul_2101,
Mustela putorius furo	ENSMPUG00000002639	1 retrocopy	retro_mputfur_684,
Pan troglodytes	ENSPTRG00000005657	1 retrocopy	retro_ptro_2286,
Rattus norvegicus	ENSRNOG00000037443	1 retrocopy	retro_rnor_1597,
Sus scrofa	ENSSSCG00000026764	1 retrocopy	retro_sscr_821,
Tursiops truncatus	ENSTTRG00000010653	1 retrocopy	retro_ttru_208,