RetrogeneDB ID: retro_chof_2032

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_46036:5491..5977(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000005213
• Aliases: None
• Description: None

Sequence

>retro_chof_2032
GTGGTCACTGTTCTCCCAGCTCTGGCGTGGATGTTTGCTCTGTCAAGGGGCAGCCTTGTGTCCCCTTTGCTAGCGTGACA
TCATCCAGATGCTTCCACAGAGGAGACAGGCAGGCAGATTCTCAGAAAGACCTGATTGAAATCCCTTTGACTCCATCACA
GGAGTGAAGTGTAGGGTCCATAGAAACTGAGGAGCCCACCTGCTCTATGAGAGCAGAAGAAGGAGACAGTTGGAAAGCTG
CATGCTCTTTAGCCTCTTTGCTCTAGAATATCTGCACTACATGACAGAGAAGCAGCTAGATCCCTATGATCACCTGATTA
ATGGTTCAATAATGACTAGAACATTTACTCCAGGGCCATGGAGAAGCAAATCAGCCAAGGAATATTTGAGAATGAAGGGC
TGGCACTGCTGAGAGATTTTAGCAAAAACAGGAACAACAAGCAGAAACCAGGTGCCCCAGACATTGAATACCTCTTAGAA
AAGCCA

Alignment

ORF - retro_chof_2032 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.84 %
• Parental protein coverage: 98.19 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VFTVFSALARMLALSSRSQVSPLV-SVTSFRRFYRGDSPADSQKDMIEIPLPPWQERTDESLETKR-ARL
          V.TV..ALA.M.ALS..S.VSPL..SVTS.R.F.RGD..ADSQKD.IEIPL.P.QE....S.ET...A.L
Retrocopy VVTVLPALAWMFALSRGSLVSPLL<SVTSSRCFHRGDRQADSQKDLIEIPLTPSQE*SVGSIETEE<AHL

Parental  LYESRKRGMLENCILLSLFAKEYLHEMTEKQLNLYDRLINEP-SNDWDIYYWATEAKPAPEVFENEILTL
          LYESR.R..LE.C.L.SLFA.EYLH.MTEKQL..YD.LIN....ND..IY..A.E.......FENE.L.L
Retrocopy LYESRRRRQLESCMLFSLFALEYLHYMTEKQLDPYDHLINGS<NND*NIYSRAMEKQISQGIFENEGLAL

Parental  LRDFTKNKNKEQRLRAPDLEYLFEKP
          LRDF.KN.N..Q...APD.EYL.EKP
Retrocopy LRDFSKNRNNKQKPGAPDIEYLLEKP

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_2032 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005213	2 retrocopies	retro_chof_2032 , retro_chof_2340,
Monodelphis domestica	ENSMODG00000020366	1 retrocopy	retro_mdom_1118,