RetrogeneDB ID: retro_chof_40

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_33290:3116..3830(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000000642
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000013497
• Aliases: None
• Description: None

Sequence

>retro_chof_40
ATGCTAGGCGGCTCCCTGGGCTCCAGGCTGTTGCGAAGTGTGGGTGGCATTCGCGGGCAGTTCGGGGTGCGGTGTGTCTG
CGAAGGTGGCGCAGCTATGGCGGCAGGGGAGAGCATGGCCCAGCAGATGGTCTGGGTGGACTTGGAGATGACAGGATTGG
ACATTGAGAAGGATCAGATTATTGAAATGGCCTGTCTGATTACTGACTCTGATCTCAACATTTTGGCGGAGGGTCCTAAC
CTGATTATAAAACAGCCAGATGAGTTGCTGGACAGCATGTCAGATTGGTGTAAGGAGCATCATGGGAAGTCTGGTCTTAC
CAAGGCAGTGAAGGAGAGTACAATTACATTGCAGCAGGCAGAGTATGAATTTCTGTCCTTTGTACGACAGCAGACTCCTC
CAGGGCTCTGTCCACTTGCAGGAAATTCAGTTCATGCAGATAAGAAGTTTCTTGACAAATATATGCCTCAGTTCATGAAA
CATCTTCATTATAGAATAATTGATGTGAGCACTGTTAAAGAGCTGTGCAGACACTGGTATCCAGAAGAATATGAATTTGC
ACCAAAGAAGGCTGCTTCTCGCAGGGCACTTGATGACATTAGTGAAAGCATCAAAGAACTTGAGTTTTACCGAAATAACA
TCTTTAAGAAAAAAACAGATGAAAAGAAGAGGAAAATTATAGAAAACGGGGAAAATGAGAAGACTGTGAGTTGA

Alignment

ORF - retro_chof_40 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.86 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLGGSLGSRLLRSVGGIRGQFGARGVCEGGAAMAAGESMAQRMVWVDLEMTGLDIEKDQIIEMACLITDS
          MLGGSLGSRLLRSVGGIRGQFG.R.VCEGGAAMAAGESMAQ.MVWVDLEMTGLDIEKDQIIEMACLITDS
Retrocopy MLGGSLGSRLLRSVGGIRGQFGVRCVCEGGAAMAAGESMAQQMVWVDLEMTGLDIEKDQIIEMACLITDS

Parental  DLNILAEGPNLIIKQPDELLDSMSDWCKEHHGKSGLTKAVKESTITLQQAEYEFLSFVRQQTPPGLCPLA
          DLNILAEGPNLIIKQPDELLDSMSDWCKEHHGKSGLTKAVKESTITLQQAEYEFLSFVRQQTPPGLCPLA
Retrocopy DLNILAEGPNLIIKQPDELLDSMSDWCKEHHGKSGLTKAVKESTITLQQAEYEFLSFVRQQTPPGLCPLA

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_40 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013497	1 retrocopy	retro_chof_40 ,
Callithrix jacchus	ENSCJAG00000012434	1 retrocopy	retro_cjac_1493,
Dipodomys ordii	ENSDORG00000011255	1 retrocopy	retro_dord_374,
Equus caballus	ENSECAG00000005988	1 retrocopy	retro_ecab_572,
Myotis lucifugus	ENSMLUG00000009030	1 retrocopy	retro_mluc_1861,
Monodelphis domestica	ENSMODG00000013913	1 retrocopy	retro_mdom_1575,
Tarsius syrichta	ENSTSYG00000002237	1 retrocopy	retro_tsyr_1177,