RetrogeneDB ID: retro_chof_2008

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_45294:3548..3889(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZDHHC20
• Ensembl ID: ENSCHOG00000012155
• Aliases: None
• Description: zinc finger, DHHC-type containing 20 [Source:HGNC Symbol;Acc:20749]

Sequence

>retro_chof_2008
ACAATAGAATCATTCTGTGCACCCACATTTTCATATGGACCTGATGGAAATGGTTTCTCTCTTGGATACAGTAAAAACTG
GAGGCAAGTCTTTGGTGATGAAAAGAAATATTGGCTACTTCCAGTATTTTCAAGCTTGGGTGATGGTTGCAGTTTTCCAA
CTCACCTTTGGGGATGGACCCAGAACAAGCTTCTGTCACAAAGCAAAATAAACATGCCAGAAGTATTGGATCAAATCAAA
CTTTTCCTATCAAACCACTTACTGAATAAAAAAGAAACCAATTATTGGACAGTGAATCTCACTGGACAGAGAATGGATCT
GAAGAAGGCAGCATCATATCA

Alignment

ORF - retro_chof_2008 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.96 %
• Parental protein coverage: 51.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TIESFRAPTFSYGPDGNGFSLGYSKNWRQVFGDEKKYWLLPVFSSLGDGCSFPTRL-VGMDPEQASVTSQ
          TIESF.APTFSYGPDGNGFSLGYSKNWRQVFGDEKKYWLLPVFSSLGDGCSFPT.L..GMDPEQASVT.Q
Retrocopy TIESFCAPTFSYGPDGNGFSLGYSKNWRQVFGDEKKYWLLPVFSSLGDGCSFPTHL<LGMDPEQASVTKQ

Parental  NEYARSVGSNQTFPVKPLSE-SKNRLLDSESHWTENGSEEGSIRS
          N..ARS.GSNQTFP.KPL.E...N.LLDSESHWTENGSEEGSI.S
Retrocopy NKHARSIGSNQTFPIKPLTE*KRNQLLDSESHWTENGSEEGSIIS

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_2008 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012155	2 retrocopies	retro_chof_1627, retro_chof_2008 ,
Cavia porcellus	ENSCPOG00000011489	1 retrocopy	retro_cpor_303,
Equus caballus	ENSECAG00000016465	1 retrocopy	retro_ecab_683,
Homo sapiens	ENSG00000180776	1 retrocopy	retro_hsap_1211,
Gorilla gorilla	ENSGGOG00000000435	2 retrocopies	retro_ggor_1003, retro_ggor_943,
Macaca mulatta	ENSMMUG00000007373	1 retrocopy	retro_mmul_1288,
Pongo abelii	ENSPPYG00000005201	1 retrocopy	retro_pabe_1081,
Pan troglodytes	ENSPTRG00000005695	1 retrocopy	retro_ptro_829,
Tarsius syrichta	ENSTSYG00000003013	1 retrocopy	retro_tsyr_998,