RetrogeneDB ID: retro_chof_1323

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_2624:1872..2330(+)
• Located in intron of: None

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_1323
CGCTTTGTTCCGAGGGTCTGCTGCTGATACTATCACCACTCTCTGCGCTCCGCAGCACCCCATCCCGCCTGACCTAATAA
AGCCCTCAGCCTGGGATACAAGGCCAAGCAAGTCTATGTCATCCATAGGATTTGAGTGTGCCACGGTGGCCGCAAACTCC
CGCTTCCTAAGGGTGCAACCTATGGCAAGCCTGTCTGTCATGGTGTCCACCAGCTGAAGTTTGCTCTAAGCCTTCAGTCT
GTTGCTGAGGAGCAAGCTGGACACCACAGTAGGGTGCTGAGACCCTGAATTCTTACTGGGTTGGTGAAGATTCCACATAC
AAATTCTTTGCGTTTATCCTCATTGATTCATTCCATAAAACTCTCAGAGGAAATCTTGACAACCAGTGGATCACCAAGCC
AGTTCACAGGCACAGAGAGAAGTGTGGGCTGATGACTGCAGGCTGCAAAAGCCGTGGC

Alignment

ORF - retro_chof_1323 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.39 %
• Parental protein coverage: 89.02 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RFLLRVRCWQYRQLSALHRAPRPTRPDKARRLGYKAKQGYVIYRIRVRRGGRKRPVPKGATYGKPVHHGV
          RF..RV.C..Y...S....AP.P..P.KA..LGYKAKQ.YVI.RI.V..GGRK.P.PKGATYGKPV.HGV
Retrocopy RFVPRVCC*YYHH-SLRSAAPHPA*PNKALSLGYKAKQVYVIHRI*VCHGGRKLPLPKGATYGKPVCHGV

Parental  NQLKFARSLQSVAEERAGRHCGALR-VLNSYWVGEDSTYKFFEVILIDPFHKAIRRNPDTQWITKPVHKH
          .QLKFA.SLQSVAEE.AG.H...LR..LNSYWVGEDSTYKFF..ILID.FHK..R.N.D.QWITKPVH.H
Retrocopy HQLKFALSLQSVAEEQAGHHSRVLR<TLNSYWVGEDSTYKFFAFILIDSFHKTLRGNLDNQWITKPVHRH

Parental  REMRGLTSAGRKSRG
          RE..GL..AG.KSRG
Retrocopy REKCGLMTAGCKSRG

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_1323 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,