RetrogeneDB ID: retro_chof_906

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_166429:2968..3448(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NHLRC3
• Ensembl ID: ENSCHOG00000004789
• Aliases: None
• Description: NHL repeat containing 3 [Source:HGNC Symbol;Acc:33751]

Sequence

>retro_chof_906
ATTTTAAGGAACTTTGCTCTTCCTATTTCATGGATAACTGAAAACACTCTTTATCGGCTGGATGTGGGTTGGCCTAAGTA
TTCAGAAAACTTTACTGGGGCAACATTTTATGTCACAGTTGACTCCCTCAACGGATTGGTTTATGTAGGGCCAAGAAGGT
ATAGCATCCCAAAGGTGTTTGTGTTCACAGGATATTTTCTGTGAGCCTGGAATCTCACTGCAGACACACCTCATGGCATG
TGTGCAGCCAGCACATTACACGAGCAATCTGTCTGGATCATGGATGTAGGAAGTGGATCCTATGGTCATACTGTTAAAAA
ATGCAATTCCTTTGGTGATCTTGTTCAAGGCCTGGGTACCCCAAGCCAAAAAGGCACTGGTTTGAATCCCCCGCAGTTAG
ATAACCCTGCAGAATCACAGGTAGAGGACACAGGAGACATTTACATTGTAGAAGGAGATGGAGAGCTGAATAACAGATTG

Alignment

ORF - retro_chof_906 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.54 %
• Parental protein coverage: 51.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ILRNFALHVSWRTKNTLYRLDVDWPRYPEYFTGATFCVAVDPLSGLVYVAQRGDHLPKVLVFTQDGYFLR
          ILRNFAL..SW.T.NTLYRLDV.WP.Y.E.FTGATF.V.VD.L.GLVYV..R....PKV.VFT..GYFL.
Retrocopy ILRNFALPISWITENTLYRLDVGWPKYSENFTGATFYVTVDSLNGLVYVGPRRYSIPKVFVFT--GYFL*

Parental  AWNHTVDTPHGMFAASTLHEQSVWITDVGSGSFGHTVKKYSSFGDLVQVLGTPGKKGTGLNPLQFDNPAE
          AWN.T.DTPHGM.AASTLHEQSVWI.DVGSGS.GHTVKK..SFGDLVQ.LGTP..KGTGLNP.Q.DNPAE
Retrocopy AWNLTADTPHGMCAASTLHEQSVWIMDVGSGSYGHTVKKCNSFGDLVQGLGTPSQKGTGLNPPQLDNPAE

Parental  LYVEDTGDIYIVDGDGGLNNRL
          ..VEDTGDIYIV.GDG.LNNRL
Retrocopy SQVEDTGDIYIVEGDGELNNRL

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_906 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004789	1 retrocopy	retro_chof_906 ,