RetrogeneDB ID: retro_chof_1964

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_434869:574..913(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS10
• Ensembl ID: ENSCHOG00000006109
• Aliases: None
• Description: mitochondrial ribosomal protein S10 [Source:HGNC Symbol;Acc:14502]

Sequence

>retro_chof_1964
TTCAAACCTATACACATTGATGTTCCCAAGCATTTGACTAAGCCTGTGATAACCGTTTCTGATGAACCTGACACATTATA
TAAGCGCCTGTCAGTTTTAGTAAAAGGCCGATTGGACAGTTATGAATATTTTGTCATGCTTGCTGCTAAAGAACTTGGTA
TCTCTATTAAAGTACACGAACCTCCAAGGAAAATAGAGCTATTTACTCTTCTCAAATCAGTGCATATTTTCAAGATGCAC
AGAGTTCAGTATGAAATGAGAACACTTTACAGATGATTTGAGTTAGAACATCTAACTGGCAGCACAGCAGATGTCTACTT
GTATTATATTCATCGAAAC

Alignment

ORF - retro_chof_1964 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.34 %
• Parental protein coverage: 58. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FSNLHFDVPKDLTKPVITVSDEPDTLYKRLSVLVKGHDKAVLDSYEYFVMLAAKELGISIKVHEPPRKIE
          F...H.DVPK.LTKPVITVSDEPDTLYKRLSVLVKG.....LDSYEYFVMLAAKELGISIKVHEPPRKIE
Retrocopy FKPIHIDVPKHLTKPVITVSDEPDTLYKRLSVLVKGR----LDSYEYFVMLAAKELGISIKVHEPPRKIE

Parental  RFTLLKSVHIFK-HRVQYEMXXXXXXXXXEHLTGSTADVYLEYIQRN
          .FTLLKSVHIFK.HRVQYEM.........EHLTGSTADVYL.YI.RN
Retrocopy LFTLLKSVHIFKMHRVQYEMRTLYR*FELEHLTGSTADVYLYYIHRN

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_1964 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001638	1 retrocopy	retro_cfam_598,
Choloepus hoffmanni	ENSCHOG00000006109	1 retrocopy	retro_chof_1964 ,
Dasypus novemcinctus	ENSDNOG00000006067	1 retrocopy	retro_dnov_2007,
Macaca mulatta	ENSMMUG00000014661	1 retrocopy	retro_mmul_48,
Mus musculus	ENSMUSG00000034729	1 retrocopy	retro_mmus_1654,
Nomascus leucogenys	ENSNLEG00000004800	1 retrocopy	retro_nleu_1385,
Rattus norvegicus	ENSRNOG00000022609	1 retrocopy	retro_rnor_2284,
Tursiops truncatus	ENSTTRG00000014063	1 retrocopy	retro_ttru_1203,