RetrogeneDB ID: retro_chof_1878

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_41308:12611..13043(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MALSU1
• Ensembl ID: ENSCHOG00000002338
• Aliases: None
• Description: mitochondrial assembly of ribosomal large subunit 1 [Source:HGNC Symbol;Acc:21721]

Sequence

>retro_chof_1878
ACTAGTCACGGGTTTAACATGGATGTGCTGGTTTCACTTCTGAGGCAAGAAAATGCAAAAGACATTTATATGATCAAATT
TCCTCTGGAGATGAAATATATAGATTACTTTTTGATTGGAGGAGGAACCTCCACCTGACATTTACACTCCATGGACTCCT
CCATTGTAAAAATGTACAAATACCTGAAAACTATAAGTGAGCCTTATGTTAAGATTGAAGACAAGGACGCTGATGACTGG
CTTTGTGTGGACTTTGGCAGGGTGGTGATTCTTTGAGAAACCAGAGAAGCCTATGAATTAGAGAAATTATGGACCCCGCA
TTCTTATGATGACCAGTTAGCTCAGATACCACCTGAGACATTGCCTGAAGACTTCATTCTTGGAATAGAAGACAACACCT
TATTCCTGACTCCTGTGAAGTTCAAGTGTGAA

Alignment

ORF - retro_chof_1878 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 99.31 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TSPKFNIDVLVSLLRQENAKDICVIKVPPEMKYTDYFVIGSATSTRHLHA----MAYIYKHLKCKSEPHV
          TS..FN.DVLVSLLRQENAKDI..IK.P.EMKY.DYF.IG..TST.HLH.........YK.LK..SEP.V
Retrocopy TSHGFNMDVLVSLLRQENAKDIYMIKFPLEMKYIDYFLIGGGTST*HLHSMDSSIVKMYKYLKTISEPYV

Parental  RIEGKNTDDWLCVDFGSMVIHLMLPETRETYELEKLWTLRSYDDQLAQIPPETLPEDFILGIEDTTLSLP
          .IE.K..DDWLCVDFG..VI...L.ETRE.YELEKLWT..SYDDQLAQIPPETLPEDFILGIED.TL.L.
Retrocopy KIEDKDADDWLCVDFGRVVI---L*ETREAYELEKLWTPHSYDDQLAQIPPETLPEDFILGIEDNTLFLT

Parental  PVEFKCE
          PV.FKCE
Retrocopy PVKFKCE

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_1878 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002338	1 retrocopy	retro_chof_1878 ,
Equus caballus	ENSECAG00000016105	1 retrocopy	retro_ecab_884,
Echinops telfairi	ENSETEG00000015566	1 retrocopy	retro_etel_574,
Loxodonta africana	ENSLAFG00000011921	1 retrocopy	retro_lafr_538,
Oryctolagus cuniculus	ENSOCUG00000008972	1 retrocopy	retro_ocun_621,
Otolemur garnettii	ENSOGAG00000017157	1 retrocopy	retro_ogar_2324,
Tursiops truncatus	ENSTTRG00000008920	1 retrocopy	retro_ttru_1715,