RetrogeneDB ID: retro_chof_2095

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_48623:13213..13709(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBAC1
• Ensembl ID: ENSCHOG00000011350
• Aliases: None
• Description: UBA domain containing 1 [Source:HGNC Symbol;Acc:30221]

Sequence

>retro_chof_2095
CCAGCCCCACTCCCTTAAGGTGGCTGATGTCTCAGCAGAAGAAAAGAAAAAATAAGACCAGCAAGCTTCAGATAGAGATG
CTATATTCCCAACCACAGCCAAACTACCATTGTGCAACATGGACCCGGGCTTGGTACAACCCAACATGAGAGATTTCCAA
ATGAAACTCTGGAAAATCTTGGTATCTCTCATCGAGGTGGCACAAAAATTGTGAGCCCTGAACCCTAAAGCAGTTAAATT
ATTTAAGAAGGCAAATGCCATGTTGGATGATGATGAGAAAGTGCAAGTGGATTAAGCAATCTGCGCCAGCTCACGGAGAT
TGGCTTTCTGGAAGAGGAGAGCCGCGAAGGCCCTTCGGCTGAATGGCGTGTCAGCAACTCAGGCCATGGAGTGGTTATCT
GAGCATGGGAAGATCCAGCCAAACACACACCTCTTCCAAGCTGCGCCTCGCCAGAAGCGCCCGGAGCTGTGGGCAGCCTC
CTCCAAGGCTGCTGCT

Alignment

ORF - retro_chof_2095 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.06 %
• Parental protein coverage: 51.08 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  PSPVP-KMADVSAEEQKKQDQKAPDRDAIFQATANLPPCSMDREVAQPSMRDFQTELRKILVSLIEVAQK
          P.P.P.K.ADVSAEE.KK.DQ.A.DRDAIF..TA.LP.C.MD....QP.MRDFQ..L.KILVSLIEVAQK
Retrocopy PAPLP>KVADVSAEEKKK*DQQASDRDAIFPTTAKLPLCNMDPGLVQPNMRDFQMKLWKILVSLIEVAQK

Parental  LLALNPDAVELFKKANAMLDEDEEAHVDEAA-LRQLTEMGFPES-RAVKALRLSHMSVTQAMEWLIEHA-
          L.ALNP.AV.LFKKANAMLD.DE...VD.A..LRQLTE.GF.E..RA.KALRL...S.TQAMEWL.EH..
Retrocopy L*ALNPKAVKLFKKANAMLDDDEKVQVD*AI<LRQLTEIGFLEE>RAAKALRLNGVSATQAMEWLSEHG<

Parental  EDPTIDTPLPGHATPDVPGAA-VASSDAAS
          EDP...TPLP..A.P..PGA...ASS.AA.
Retrocopy EDPAKHTPLPSCASPEAPGAV>AASSKAAA

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_2095 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011350	2 retrocopies	retro_chof_2095 , retro_chof_541,