RetrogeneDB ID: retro_chof_669

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_133455:1911..2336(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB8B
• Ensembl ID: ENSCHOG00000007196
• Aliases: None
• Description: RAB8B, member RAS oncogene family [Source:HGNC Symbol;Acc:30273]

Sequence

>retro_chof_669
GTGCAGAAGATCTGCCTCCGTTTTCGTTTTTTTGGATGATCCTTCAATACCACCTTTATTTCCACCGTAGGAACAGCTTT
AAGATCAAAACAGTTGTATTACAAGGAATGAAGATCAAGCTATGGATATGGGAAAGGCAGGCCAGGAGCGATTTCACACC
ATCACAACCTCTTATGACAGAGGAGCTATGGATAGCATGCTAGTATATGACATCATAAATGGTAAAAGTTTTGAAAACAT
TAAATAGCCTAGAAATATAGATGAGCATGCCAATGAAGATGTGGAAAGCATGTTACTAGGAAACACATGTGATATGGATG
ATAAAAGAGTTGTACCTAAAGGAAAAGGAGAAGAGATTGCAAAGGAGCATGGTATGAGATTTTTTTGAGACTAGTGCAAA
AGCAAATATAAACATCGAGAAGGCA

Alignment

ORF - retro_chof_669 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.64 %
• Parental protein coverage: 69.08 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VGKTCLLFRFSEDAFNTTFISTIGI-DFKIRTIELDGKKIKLQIWDT-AGQERFRTITTAYYRGAMGIML
          V.K.CL.FRF....FNTTFIST.G...FKI.T..L.G.KIKL.IW...AGQERF.TITT.Y.RGAM..ML
Retrocopy VQKICLRFRFFG*SFNTTFISTVGT<SFKIKTVVLQGMKIKLWIWER<AGQERFHTITTSYDRGAMDSML

Parental  VYDITNEKSFDNIKNWIRNIEEHASSDVERMILGNKCDMNDKRQVSKERGEKLAIDYGIK-FLETSAKSS
          VYDI.N.KSF.NIK...RNI.EHA..DVE.M.LGN.CDM.DKR.V.K..GE..A...G...F.ETSAK..
Retrocopy VYDIINGKSFENIK-*PRNIDEHANEDVESMLLGNTCDMDDKRVVPKGKGEEIAKEHGMR>FFETSAKAN

Parental  TNVEEA
          .N.E.A
Retrocopy INIEKA

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_669 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007196	3 retrocopies	retro_chof_1996, retro_chof_475, retro_chof_669 ,
Dasypus novemcinctus	ENSDNOG00000023965	3 retrocopies	retro_dnov_1191, retro_dnov_1981, retro_dnov_23,
Microcebus murinus	ENSMICG00000007113	1 retrocopy	retro_mmur_503,
Sorex araneus	ENSSARG00000005217	2 retrocopies	retro_sara_366, retro_sara_725,