RetrogeneDB ID: retro_chof_1813

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_391721:234..751(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRR11
• Ensembl ID: ENSCHOG00000012284
• Aliases: None
• Description: proline rich 11 [Source:HGNC Symbol;Acc:25619]

Sequence

>retro_chof_1813
CCTCCACATCCTCCTCTACCTCCTTCTGCACCACCAATAGCACCTTTACTGCTCAGAAAAGCAGAGTGCAATAAAGCACT
TCAGGCTGAGCCTTTAAAAAAAGACAGACCCATGCAAATACAGTTAAAGATCTCCTGTCTGTGAAATTTAAAAAGACCCA
GAGTTTTGATGAAAAGAGGAAGCTTGTACCATCACTGTAGGCACCGAATCCTGTAGTTACCATCTCTGATCTGCAACGTG
TTACCTTGAAACATAACTCCAAAGTGTTATCAACTCATGTTACAAATGTCTTAATTACCCCTGATAAAAGCCAGATAGAT
CTGCAGAGACTATTGAGAAAAGTCAATATAAAGAGGACCCAGGTGGAACCCCTCTTACCGATAAAGAAAATATGGAAACA
GGAGCTGGACCAACCCCAATAATGACCCAAGCCTTGAGGAGAAAGTTTCAGGTGGCTCACCCAAGAAGTCCACCTCAAAC
TCTGCCACTTTCTACAGGCAGCTTTGATGAACAAAAC

Alignment

ORF - retro_chof_1813 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.86 %
• Parental protein coverage: 66.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PPPPPLPPPAPPIAPLLLRKADRTKALQAEPLKKDGPMQI-TVKDLLTVKLKKTQSFDEKRKLVPSPKAP
          PP.PPLPP.APPIAPLLLRKA...KALQAEPLKKD.PMQI.TVKDLL.VK.KKTQSFDEKRKLVPS..AP
Retrocopy PPHPPLPPSAPPIAPLLLRKAECNKALQAEPLKKDRPMQI<TVKDLLSVKFKKTQSFDEKRKLVPSL*AP

Parental  KPLVTVSDLQRVTLKPNSKVLSTRVTNVLITPGKSQIDLRKLLRKVNVERS-PGGTPLTNKENMETGTGL
          .P.VT.SDLQRVTLK.NSKVLST.VTNVLITP.KSQIDL..LLRKVN..R..PGGTPLT.KENMETG.G.
Retrocopy NPVVTISDLQRVTLKHNSKVLSTHVTNVLITPDKSQIDLQRLLRKVNIKRT<PGGTPLTDKENMETGAGP

Parental  TPIMTQALRRKFQLAHPRSPTQALPLSTSSFDEQN
          TPIMTQALRRKFQ.AHPRSP.Q.LPLST.SFDEQN
Retrocopy TPIMTQALRRKFQVAHPRSPPQTLPLSTGSFDEQN

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_1813 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012284	2 retrocopies	retro_chof_1813 , retro_chof_294,
Mustela putorius furo	ENSMPUG00000015240	1 retrocopy	retro_mputfur_1231,
Otolemur garnettii	ENSOGAG00000005839	1 retrocopy	retro_ogar_414,