RetrogeneDB ID: retro_chof_1462

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_30007:793..1168(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COMMD10
• Ensembl ID: ENSCHOG00000008311
• Aliases: None
• Description: COMM domain containing 10 [Source:HGNC Symbol;Acc:30201]

Sequence

>retro_chof_1462
TTCAGTTTAGAACAGGCAGCGTTTCCCAAAGTGAGGCCAGGAGCTTTGCAGCAGCGGTTAGAGGATGTTCATCTTAGGCA
AGACAAGGCCGAAACATCTGTCCAGGCTTGGTCTCCTATGGGTCAGGAAACAGCTGAAAAGTTCAGGCAGAGAAGCCTGG
CTCCTCACAGGCTAGAGACAGTAGGAGGGCAGCTGAGCCTTCAAATGGCTCCCTCTGCTCCAGCAAATCTAAAATCTCCC
CAAGCTTTGTTACGGCTAGGAGGGAGAAATGGAGATTCAAAGAGCCTGGAGAAAGCTCTTATGGAATTCAGTCACAAGTT
GCTGCTTCATTTCTACAACAAGCTAGAGACCACACAAGCACAGCTGGGTTCCCTT

Alignment

ORF - retro_chof_1462 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.8 %
• Parental protein coverage: 61.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FILEQAVYHNVKPAALQQQLQNIHLRQEKAEPFVIAWSTMGQETVEKFRQRILAPPRLETVGWQLNLQMA
          F.LEQA....V.P.ALQQ.L...HLRQ.KAE..V.AWS.MGQET.EKFRQR.LAP.RLETVG.QL.LQMA
Retrocopy FSLEQAAFPKVRPGALQQRLEDVHLRQDKAETSVQAWSPMGQETAEKFRQRSLAPHRLETVGGQLSLQMA

Parental  HSAQANLKSPQAVLQLGVSNEDSKSLEKVLMEFSHKELFDFYNKLETIQAQLDSL
          .SA.ANLKSPQA.L.LG..N.DSKSLEK.LMEFSHK.L..FYNKLET.QAQL.SL
Retrocopy PSAPANLKSPQALLRLGGRNGDSKSLEKALMEFSHKLLLHFYNKLETTQAQLGSL

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_1462 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008311	2 retrocopies	retro_chof_1462 , retro_chof_1585,
Cavia porcellus	ENSCPOG00000020474	1 retrocopy	retro_cpor_337,
Loxodonta africana	ENSLAFG00000011885	1 retrocopy	retro_lafr_142,
Microcebus murinus	ENSMICG00000006173	2 retrocopies	retro_mmur_1132, retro_mmur_607,
Myotis lucifugus	ENSMLUG00000010780	1 retrocopy	retro_mluc_2087,
Sarcophilus harrisii	ENSSHAG00000001698	1 retrocopy	retro_shar_261,
Tupaia belangeri	ENSTBEG00000004061	1 retrocopy	retro_tbel_3381,