RetrogeneDB ID: retro_chof_76

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_1440:16904..17185(+)
• Located in intron of: ENSCHOG00000001932

Retrocopy information

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

Parental gene information

• Parental gene symbol: LAMTOR5
• Ensembl ID: ENSCHOG00000013405
• Aliases: None
• Description: late endosomal/lysosomal adaptor, MAPK and MTOR activator 5 [Source:HGNC Symbol;Acc:17955]

Sequence

>retro_chof_76
GGCAGGATGGCAGAGACCTTGGTGCAACAAATTGGAGGACAAGATGAAGAATCTATCCATTATTGGAGTCCTAGGCAAAG
ATTCACAGGGACTTAATCTGGGCTGCCATGGGGACCTTGTCAGATAAGCATGTTGGAGTAATATCTGTTTTAGTCCAGTC
AACAATTAAGCTAACGTCTGTCCCCACTGATATTCCTGTGATATATCTAGAATCAGATAATGTGACCATTATGATCCAGA
AACAGGATGGCATCACAATGGCAGTGCTCCAAATAGCCTCT

Alignment

ORF - retro_chof_76 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.53 %
• Parental protein coverage: 61.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GGMEETLEQH-LEDTMKNPSIVGVLCTDSQGLNLGCRG-TLSDEHAGVISVLAQQAAKLTSDPTDIPVVC
          G.M.ETL.Q..LED.MKN.SI.GVL..DSQGLNLGC.G.TLSD.H.GVISVL.Q...KLTS.PTDIPV..
Retrocopy GRMAETLVQQ>LEDKMKNLSIIGVLGKDSQGLNLGCHG>TLSDKHVGVISVLVQSTIKLTSVPTDIPVIY

Parental  LESDNGNIMIQKHDGITVAVHKMAS
          LESDN..IMIQK.DGIT.AV...AS
Retrocopy LESDNVTIMIQKQDGITMAVLQIAS

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_76 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 6 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011504	2 retrocopies	retro_amel_118, retro_amel_974,
Bos taurus	ENSBTAG00000014970	3 retrocopies	retro_btau_1505, retro_btau_1755, retro_btau_71,
Choloepus hoffmanni	ENSCHOG00000013405	3 retrocopies	retro_chof_2428, retro_chof_76 , retro_chof_910,
Macaca mulatta	ENSMMUG00000015023	4 retrocopies	retro_mmul_164, retro_mmul_2452, retro_mmul_440, retro_mmul_499,
Sus scrofa	ENSSSCG00000006807	1 retrocopy	retro_sscr_986,
Ictidomys tridecemlineatus	ENSSTOG00000003401	5 retrocopies	retro_itri_1196, retro_itri_154, retro_itri_198, retro_itri_587, retro_itri_86,