RetrogeneDB ID: retro_chof_357

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_90:32619..32889(+)
• Located in intron of: ENSCHOG00000005439

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL15
• Ensembl ID: ENSCHOG00000001114
• Aliases: None
• Description: ribosomal protein L15 [Source:HGNC Symbol;Acc:10306]

Sequence

>retro_chof_357
CAGCTCTCTACTCTCCACAGGGCCCTGCTTTCCACCAGGCCTGATAAAGTGCACAGACTGGGATACAAGGTCAAGCAAGG
TTATGTCATCAATAGGATTCGAGTGCGTCGTGGTGGCCGCAAATGCCTGGTTCCTAAGGGTGCAACCTATGGCAAGCCTG
TCCATCATGGTGTTAACCAGTTGAAATTTGCTCGAAGCCTTCAGTCTGTTGCTGAGGAGTGAGCTGAATGCCACTGTGGG
GTGCTGAGAGTCCTGAATTCTTACTGGGTT

Alignment

ORF - retro_chof_357 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.44 %
• Parental protein coverage: 52.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QLSALHRAPRPTRPDKARRLGYKAKQGYVIYRIRVRRGGRKRPVPKGATYGKPVHHGVNQLKFARSLQSV
          QLS.LHRA...TRPDK..RLGYK.KQGYVI.RIRVRRGGRK..VPKGATYGKPVHHGVNQLKFARSLQSV
Retrocopy QLSTLHRALLSTRPDKVHRLGYKVKQGYVINRIRVRRGGRKCLVPKGATYGKPVHHGVNQLKFARSLQSV

Parental  AEERAGRHCGALRVLNSYWV
          AEE.A..HCG.LRVLNSYWV
Retrocopy AEE*AECHCGVLRVLNSYWV

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_357 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001114	6 retrocopies	retro_chof_1201, retro_chof_1253, retro_chof_1323, retro_chof_2246, retro_chof_357 , retro_chof_877,
Equus caballus	ENSECAG00000010157	1 retrocopy	retro_ecab_38,
Procavia capensis	ENSPCAG00000011995	1 retrocopy	retro_pcap_265,
Tursiops truncatus	ENSTTRG00000007244	5 retrocopies	retro_ttru_1305, retro_ttru_1358, retro_ttru_280, retro_ttru_920, retro_ttru_987,