RetrogeneDB ID: retro_chof_1828

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_39800:12703..13054(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTX3
• Ensembl ID: ENSCHOG00000010893
• Aliases: None
• Description: metaxin 3 [Source:HGNC Symbol;Acc:24812]

Sequence

>retro_chof_1828
GCTTATGCCAAGTTTTCTGGTGCACCCTTGAAAGTCAGTGCCATAGATAACACCTGGAGAGGTTCAAGAAGACATTTACC
ATTGTTGACAACTGAAGGCAATATTGTTTCTCAGCCAGCAAAAATACTAAACTTTTTAAGAAAACAGAAATATAATGCTG
ATTATGGACTCTCAGCAAAACATGGGGCAGATACCCTGGCTTACATTGCTCTCCTTGAAGAGAAGCTTCTTCCTGCAGTG
CCTCACACATTCTGGGTTGAGAGTGACAATTACTTTTCTATAACAATGCCATGGTTTGCTTCATGAATTCCTTTTCCCTT
GAGTTTGATCCTGCCTGGAAGAATGTCTAGA

Alignment

ORF - retro_chof_1828 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.45 %
• Parental protein coverage: 81.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AYAKFSGAPLKVSVIDNTWRGSTGDLPLLTTEDNIVSQPAKILNFLRKQKYNADYELSAKQGADTLAYIA
          AYAKFSGAPLKVS.IDNTWRGS...LPLLTTE.NIVSQPAKILNFLRKQKYNADY.LSAK.GADTLAYIA
Retrocopy AYAKFSGAPLKVSAIDNTWRGSRRHLPLLTTEGNIVSQPAKILNFLRKQKYNADYGLSAKHGADTLAYIA

Parental  LLEEKLLPAVLHTFWVESDNYFSITKPWFASRIPFPLSLILPGRMSR
          LLEEKLLPAV.HTFWVESDNYFSIT.PWFAS.IPFPLSLILPGRMSR
Retrocopy LLEEKLLPAVPHTFWVESDNYFSITMPWFAS*IPFPLSLILPGRMSR

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_1828 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009655	1 retrocopy	retro_chof_2429,
Choloepus hoffmanni	ENSCHOG00000010893	1 retrocopy	retro_chof_1828 ,
Callithrix jacchus	ENSCJAG00000019700	1 retrocopy	retro_cjac_2994,
Macaca mulatta	ENSMMUG00000021104	1 retrocopy	retro_mmul_489,
Vicugna pacos	ENSVPAG00000009404	1 retrocopy	retro_vpac_626,