RetrogeneDB ID: retro_chof_475

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_113227:4379..4783(-)
• 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_475
TATGATTGTTTATTCAGGTCACTTCTGATTGTCGACTCTGGGGTTGGAAAGCCTTGCCTCCTTCTTACGTCTGCAGATGA
TGCATACACAGAAAGCTGCATCAGCACAATTGGTGCGGAATTCAAAATAACAACTATAGAGTTAGGTGGGAAAACAATCA
AGCTTCAAATATGGCACACAGCAGGCCAAGAAAGATTTTAAACAATCATCTCCAGTCACTACAGAGGAGCACATGGCATC
ACAGTTGTGTATGATGTGACAGATCAGGAGTCCTTCAATAATGTTAAACAGTGGCTGGAGAAAATAGATCATTATGTCAG
TGAAACATCAGTAAGTTGTTGGTAGGGAACAAATGTGATTTGACCAGTAAAAATAAAAAATGTCGTAGACAACGCAACAG
CAAA

Alignment

ORF - retro_chof_475 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.94 %
• Parental protein coverage: 64.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YDYLFKLLLIGDSGVGKTCLLFRFSEDAFNTTFISTIGIDFKIRTIELDGKKIKLQIWDTAGQERFRTIT
          YD.LF..LLI.DSGVGK.CLL.....DA.....ISTIG..FKI.TIEL.GK.IKLQIW.TAGQERF.TI.
Retrocopy YDCLFRSLLIVDSGVGKPCLLLTSADDAYTESCISTIGAEFKITTIELGGKTIKLQIWHTAGQERF*TII

Parental  TAYYRGAMGIMLVYDITNEKSFDNIKNWIRNIEEHASS-DVERMILGNKCDMNDK-RQVSKERGEK
          ...YRGA.GI..VYD.T...SF.N.K.W...I....S.........GNKCD...K.......R..K
Retrocopy SSHYRGAHGITVVYDVTDQESFNNVKQWLEKIDHYVSE<NISKLLVGNKCDLTSKNKKCRRQRNSK

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_475 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,