RetrogeneDB ID: retro_chof_1533

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_316669:334..1340(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPID
• Ensembl ID: ENSCHOG00000012069
• Aliases: None
• Description: peptidylprolyl isomerase D [Source:HGNC Symbol;Acc:9257]

Sequence

>retro_chof_1533
ATTGTCTTAGAATTGTTTTGAGATATTGTTCCCAAAACAGCAGGAAATTTTTGTGCATTGTGAACAGGAGGAAAAGGCAT
TGGATCTATCACTGGGAAACCTCTCCATTTCAAAGGATGCCCTTCCAATTGAAATTAATGATTCAGGGTGGAGACTTCTC
AAAATCAGAATGAAACAAGTGGAGAAAGTATTTATGATGAAAAATTTGAAGATGAAAATTTCTATTATAAGCATGATCAT
GAGGGTTTGCAGAGCATGGCAAATGCAGGCTGCAGTACAAATGGTCCTCAGTTCTTTATCACAACAGTTACACTCCTCAT
TTGGATGGGAAACGTGGTGTTTGGCCAAGTAATTAAAGGAATGGGCATGACAAGGATACTGTACAATGTAGAAGTGAAAG
GTGAAAAACCTGCCCAATTGTATGTTATTGCAGAATGTGGAGAATAGAAGGAAGGGGATGATTGGAGAATATTCCCAAAT
GTTGGCTCCAATGACAGTGATCCAGATTTCCCTGAGGAAGCAGATAAAGATTTAAAAGATGTAAATGAAATTTTATTAAT
AGCAGAAGAGTTAAAAAAAATTGGACATACCTTTTTCAAATCCCAGAACTGGGAGATGGCTATTGAAAAATATGCAAAAG
TTTTAATGTATGTGGAAAGTTCAAAGGCTGTTAATGAGAAATCAGATAGCTCCAAACTGCAATCTGTAGCTTTAAGCTTT
GTGTTGAATACTGGTGCTTGTAAACTGAAGATGTCAAATTGGCAGAGTACAGTTGATAGCTGTTTGGAGGCTCTTGAAAT
AGACCCATCAAATATGAAAGCACTGTAGTGCCAAGCCCAAGGATGGCAAGGATTAAAAGAATATGATCAAGCATTGGCTG
ATCTTAAGAAAGCTCAGGAGATTGCACCAGAATATAGAACTATCCAGGAAGAATTGCTAAAATTCAAGCAATAGACAAAA
GGCACAGAAAGATAAAGAGAAAGCAGCTTATACAAAAATATTTGCT

Alignment

ORF - retro_chof_1533 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.61 %
• Parental protein coverage: 99.41 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IVLELFADIVPKTAENFRALCTGEKGIGSTTGKPLH-FKGCPFHRIIKKFMIQGGDFS-NQNGTGGESIY
          IVLELF.DIVPKTA.NF.AL.TG.KGIGS.TGKPLH.F...PF.....K.MIQGGDFS.NQN.T.GESIY
Retrocopy IVLELF*DIVPKTAGNFCAL*TGGKGIGSITGKPLH<FQRMPFQL---KLMIQGGDFS>NQNETSGESIY

Parental  GEKFEDENFHYKHDHEGLLSMANAGRNTNGSQFFITTVPTPHLDGKHVVFGQVIKGMGVARILENVEVKG
          .EKFEDENF.YKHDHEGL.SMANAG..TNG.QFFITTV......G..VVFGQVIKGMG..RIL.NVEVKG
Retrocopy DEKFEDENFYYKHDHEGLQSMANAGCSTNGPQFFITTVTLLIWMG-NVVFGQVIKGMGMTRILYNVEVKG

Parental  ENPAQLCIIAECGELKEGDDWGIFPKDGSGDSHPDFPEDADINLKDVNKILLIAEDLKNIGNTFFKSQNW
          E.PAQL..IAECGE.KEGDDW.IFP..GS.DS.PDFPE.AD..LKDVN.ILLIAE.....G.TFFKSQNW
Retrocopy EKPAQLYVIAECGE*KEGDDWRIFPNVGSNDSDPDFPEEADKDLKDVNEILLIAEEXXXXGHTFFKSQNW

Parental  EMAIKKYAKVLRYLEGSKAVTEKSDSSKLQPVALSCVLNIGACKLKMSDWQGAVDSCLEALEIDPSNTKA
          EMAI.KYAKVL.Y.E.SKAV.EKSDSSKLQ.VALS.VLN.GACKLKMS.WQ..VDSCLEALEIDPSN.KA
Retrocopy EMAIEKYAKVLMYVESSKAVNEKSDSSKLQSVALSFVLNTGACKLKMSNWQSTVDSCLEALEIDPSNMKA

Parental  LYRQAQGWQGLKEYDKALADLKKAQEIAPEDKAIQAELLKVKQ-KIKAQKDKEKAAYAKMFA
          L..QAQGWQGLKEYD.ALADLKKAQEIAPE...IQ.ELLK.KQ...KAQKDKEKAAY.K.FA
Retrocopy L*CQAQGWQGLKEYDQALADLKKAQEIAPEYRTIQEELLKFKQ>RQKAQKDKEKAAYTKIFA

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_1533 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 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016680	1 retrocopy	retro_btau_1672,
Choloepus hoffmanni	ENSCHOG00000012069	1 retrocopy	retro_chof_1533 ,
Callithrix jacchus	ENSCJAG00000001437	2 retrocopies	retro_cjac_2321, retro_cjac_4162,
Echinops telfairi	ENSETEG00000012655	2 retrocopies	retro_etel_10, retro_etel_633,
Felis catus	ENSFCAG00000028926	2 retrocopies	retro_fcat_494, retro_fcat_559,
Myotis lucifugus	ENSMLUG00000009317	1 retrocopy	retro_mluc_1667,
Macaca mulatta	ENSMMUG00000017768	2 retrocopies	retro_mmul_281, retro_mmul_348,
Mustela putorius furo	ENSMPUG00000018108	1 retrocopy	retro_mputfur_1415,
Oryctolagus cuniculus	ENSOCUG00000006602	1 retrocopy	retro_ocun_1625,
Otolemur garnettii	ENSOGAG00000003317	2 retrocopies	retro_ogar_2355, retro_ogar_2680,
Pongo abelii	ENSPPYG00000015159	1 retrocopy	retro_pabe_3594,
Rattus norvegicus	ENSRNOG00000027408	1 retrocopy	retro_rnor_188,
Ictidomys tridecemlineatus	ENSSTOG00000001552	1 retrocopy	retro_itri_1422,
Tursiops truncatus	ENSTTRG00000016269	1 retrocopy	retro_ttru_1027,