RetrogeneDB ID: retro_chof_2128

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_51844:4078..5086(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDHX
• Ensembl ID: ENSCHOG00000003998
• Aliases: None
• Description: pyruvate dehydrogenase complex, component X [Source:HGNC Symbol;Acc:21350]

Sequence

>retro_chof_2128
AGGCTAGGGTGTTACCCCTGGTGCTCCACTACATCTTGGGCTTCTGCAGTCAGTGAAACCTAGGGCTGGTTAAGGGGGCT
GCTGCATGGTTTATGGGCCATGGAGCTAGTTGGAGATGGTTTCACAGTACCCAGTGGATGCGGATTGATCCTATTAAGAT
ACTAATGCTATCACTGTCTCCTACAATGGAAGAAAGGAACATTGTGAAATGCCTGAAAAACGAAGGTGAAGCTGTGAGTG
CTGGAGATGCATTATGCGAAACTGAGACTGACAAAGCTCTGGCTACCTTAGTTGCAAGTGATGATGGCATCTTGGCCAAA
ATAGTGGTTGAAGAAAGATCTAAAAATAAAAAGCCAGGTTCACTAATTGATTTGATGGTTGAAGAAAGAGGAGACTGGAA
ACATGGTGAAATTCCCAAAGATATAGGTCCTCCCTCACCAGCTTCAAAACTATCAGTGCCTCTCCCGCCACCAGAACCAC
AGATTTCTAGCCCTGTCAAAAAGGAACACACACAGGAAAACTACAGTTCCATTTAAGTCCAGCTGCTTGTAATATTCAGG
ACAAACATGCACTTGATGCTAGCCAGGGCGCAACCACTGGCCCTCGAGGATATTCACTAAAGAGGATGCTCTCAAACTGG
TAGAACTGAAACAGATGGGCAAGATCACAGAATCCAGGCCGCTCCAAGCCCTTCCAACCACTCCTGCAGCAGCACCTTTG
CCCACACAGGCTACAGCTGAGCCCTCTGTATCCTGGCCACTGATCTCACCAGTATCAACTCCTGGACAACCTAATGCATT
GGGCACAATCACTGAAATCCCTGCTAGCAATATTAGCACAGTTATTGCCAAGAAGTTAACTGAATCTAAAAGCACTGTAC
CTCATGCACATGCTACTGCTGACTGTGACCTTGGAGCTGTTTTAAAAGTAAGAGAAGATCTGGTCAAAGATGACATTAAA
GTATCAGTAAACGATTTTATCATCAAGGCAGCAGCTGTTACTCTTAAA

Alignment

ORF - retro_chof_2128 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.18 %
• Parental protein coverage: 67.2 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RLGCDP-RVLRYILGFCGRRSPGLVKGDAGWFVGRGASWRWFHSTQWMWVDPIKILMPSLSPTMEEGNIV
          RLGC.P..VL.YILGFC.....GLVKG.A.WF.G.GASWRWFHSTQWM..DPIKILM.SLSPTMEE.NIV
Retrocopy RLGCYP<LVLHYILGFCSQ*NLGLVKGAAAWFMGHGASWRWFHSTQWMRIDPIKILMLSLSPTMEERNIV

Parental  KWLKKEGEAVSAGDALCEIETDKAVVTLDASDDGILAKIVVEEGSKNIKLGSLIGLMVEEGGDWKHVEIP
          K.LK.EGEAVSAGDALCE.ETDKA..TL.ASDDGILAKIVVEE.SKN.K.GSLI.LMVEE.GDWKH.EIP
Retrocopy KCLKNEGEAVSAGDALCETETDKALATLVASDDGILAKIVVEERSKNKKPGSLIDLMVEERGDWKHGEIP

Parental  KDVGLPLPASKPSVPLPSPEPQISSPVQKEDT-SGKLQLRLSPAARNILDKHALDASQGTATGPRG-IFT
          KD.G.P.PASK.SVPLP.PEPQISSPV.KE.T..GKLQ..LSPAA.NI.DKHALDASQG..TGPRG.IFT
Retrocopy KDIGPPSPASKLSVPLPPPEPQISSPVKKEHT<TGKLQFHLSPAACNIQDKHALDASQGATTGPRG<IFT

Parental  KEDAVKLVELKQMGKIAESRQPQALPATP-AVPLPPQATAEPSYPRPLIPPVSTPGQPNALGTFTEIPAS
          KEDA.KLVELKQMGKI.ESR..QALP.TP.A.PLP.QATAEPS...PLI.PVSTPGQPNALGT.TEIPAS
Retrocopy KEDALKLVELKQMGKITESRPLQALPTTPAAAPLPTQATAEPSVSWPLISPVSTPGQPNALGTITEIPAS

Parental  NIRRVIAKRLTESKSTIPHAYATADCDLGAVLKVRQDLVKDDIKVSVNDFIIKAAAVTLK
          NI..VIAK.LTESKST.PHA.ATADCDLGAVLKVR.DLVKDDIKVSVNDFIIKAAAVTLK
Retrocopy NISTVIAKKLTESKSTVPHAHATADCDLGAVLKVREDLVKDDIKVSVNDFIIKAAAVTLK

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_2128 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003998	1 retrocopy	retro_chof_2128 ,
Choloepus hoffmanni	ENSCHOG00000013258	2 retrocopies	retro_chof_52, retro_chof_655,
Callithrix jacchus	ENSCJAG00000010888	1 retrocopy	retro_cjac_1425,
Mus musculus	ENSMUSG00000010914	1 retrocopy	retro_mmus_2937,