RetrogeneDB ID: retro_chof_260

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_5761:35765..36300(-)
• Located in intron of: ENSCHOG00000008364

Retrocopy information

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

Parental gene information

• Parental gene symbol: RABGGTB
• Ensembl ID: ENSCHOG00000009456
• Aliases: None
• Description: Rab geranylgeranyltransferase, beta subunit [Source:HGNC Symbol;Acc:9796]

Sequence

>retro_chof_260
GGCACACAACATAAGGTTGTTGTTATCAAGCTAGTTGCACCTGTCATCCTATTAGTGGAGAAACATGCAGATTATAGTGC
ATCCTATGGCTTAAAAAAAGATGATTATGAATATTGTATGTCTGAATATTTGAGAATGAGTGGCATCTACTGGGTCTCAG
TAATGAATCTCATGGGACGTCATCACATGAATAGACAGGAAATTCTAACATTTATTAAATTGTGCCAACATGAGTGTGGT
GGAGTAAGTTTAAATATTGGACGTAATCTTTTGTACATGCTTAGTGCTGTATAGATTCTTACTCTGTATGATAGTGTTAA
TATTATTGATGCAAATAAAGATGTGAAGTATGTACAAAGTCTACAAAAAGAAGATAGGTTTTTTGCTGGAGACATTTAAG
GAAAAATTGATACAAGATTTTCTTTCTGTGTGGTGGCAACTCCGGCTCTAGTGGGGAAGCTAGATGCTATAACTTTGTGG
AAATGCAATTGATTTTGTTTTGTCCTACATGAAATTTGATGGTGGATTAACCTGT

Alignment

ORF - retro_chof_260 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.32 %
• Parental protein coverage: 54.98 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GTPQKDVVIKPDAPGTLLVEKHADYIASYGSKKDDYEYCMSEYLRMSGIYWGLTVMDLMGQLHRMNREEI
          GT..K.VVIK..AP..LLVEKHADY.ASYG.KKDDYEYCMSEYLRMSGIYW...VM.LMG..H.MNR.EI
Retrocopy GTQHKVVVIKLVAPVILLVEKHADYSASYGLKKDDYEYCMSEYLRMSGIYW-VSVMNLMGR-HHMNRQEI

Parental  LTFIKSCQHECGGISASIGHDPHLLYTLSAVQILTLYDSINVIDVNKVVEYVQSLQKEDGSFAGDIWGEI
          LTFIK.CQHECGG.S..IG....LLY.LSAV.ILTLYDS.N.ID.NK.V.YVQSLQKED..FAGDI.G.I
Retrocopy LTFIKLCQHECGGVSLNIGRN--LLYMLSAV*ILTLYDSVNIIDANKDVKYVQSLQKEDRFFAGDI*GKI

Parental  DTRFSFCAVATLALLGKLDAINVEK-AIDFVLSCMNFDGGFGC
          DTRFSFC.VAT.AL.GKLDAI...K.AIDFVLS.M.FDGG..C
Retrocopy DTRFSFCVVATPALVGKLDAITLWK>AIDFVLSYMKFDGGLTC

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_260 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000011052	1 retrocopy	retro_acar_155,
Canis familiaris	ENSCAFG00000020392	1 retrocopy	retro_cfam_2104,
Choloepus hoffmanni	ENSCHOG00000009456	2 retrocopies	retro_chof_1851, retro_chof_260 ,
Mus musculus	ENSMUSG00000038975	1 retrocopy	retro_mmus_1030,
Otolemur garnettii	ENSOGAG00000007665	1 retrocopy	retro_ogar_1089,
Sorex araneus	ENSSARG00000007392	1 retrocopy	retro_sara_207,
Ictidomys tridecemlineatus	ENSSTOG00000021824	1 retrocopy	retro_itri_484,
Tursiops truncatus	ENSTTRG00000014126	3 retrocopies	retro_ttru_1391, retro_ttru_1767, retro_ttru_214,