RetrogeneDB ID: retro_chof_2299

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_64458:1012..1503(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WDR82
• Ensembl ID: ENSCHOG00000000774
• Aliases: None
• Description: WD repeat domain 82 [Source:HGNC Symbol;Acc:28826]

Sequence

>retro_chof_2299
GTGTTGGCTTTGTCCATGTCACTTGTGGATGATACGTTTATTTCTGGGTCTCTCGATAAAACCATTCATCTTTGGGATCT
CCACTCTCCTAACTGCCAGGGCCTCATGCATCTACAGGGCAAACCAGTTTGCTCTTTTGATTGAGAAGGGTTAATTTTTC
TGTAGGTGTCAATTCCAAAATGGTCAAACTTTATGCCTTCATTCTTTTGATAAGGGGCCATTTGCCACCTTTAAGATGCT
AACTGATTGGACTTGTAAGTGGACAGGACTGAATTTCAGCAATCATGGCAAGTTTATCCTCTTCTCCACCAACAGCAGCT
TCATCCATCCCATTGATAGCATTCAAGGGAGTGGTGATGCATACATTTGGGGGTTATGCCAACAGCAAAGCTGTCACACT
GGAGGCCTCGTTTACTCCAGACTCCCAGTTTATCATGATTATTTCAGAGGATGGCAAGATCAATGTTTGGAATGGAGAGG
GTGGTATAAAA

Alignment

ORF - retro_chof_2299 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.83 %
• Parental protein coverage: 56.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VVALSMSPVDDTFISGSLDKTIRLWDLRSPNCQGLMHLQGKPVCSFDPEGLI-FAAGVNSEMVKLYD-LR
          V.ALSMS.VDDTFISGSLDKTI.LWDL.SPNCQGLMHLQGKPVCSFD.EGLI.F..GVNS.MVKLY..L.
Retrocopy VLALSMSLVDDTFISGSLDKTIHLWDLHSPNCQGLMHLQGKPVCSFD*EGLI<FSVGVNSKMVKLYA<LH

Parental  SFDKGPFATFKMQYDRTCEWTGLKFSNDGKLILISTNGSFIRLID-AFKGVVMHTFGGYANSKAVTLEAS
          SFDKGPFATFKM..D.TC.WTGL.FSN.GK.IL.STN.SFI..ID.AFKGVVMHTFGGYANSKAVTLEAS
Retrocopy SFDKGPFATFKMLTDWTCKWTGLNFSNHGKFILFSTNSSFIHPID>AFKGVVMHTFGGYANSKAVTLEAS

Parental  FTPDSQFIMIGSEDGKIHVWNGESGIK
          FTPDSQFIMI.SEDGKI.VWNGE.GIK
Retrocopy FTPDSQFIMIISEDGKINVWNGEGGIK

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_2299 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.

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000774	1 retrocopy	retro_chof_2299 ,
Callithrix jacchus	ENSCJAG00000006114	1 retrocopy	retro_cjac_3022,
Homo sapiens	ENSG00000164091	2 retrocopies	retro_hsap_2816, retro_hsap_419,
Loxodonta africana	ENSLAFG00000028309	1 retrocopy	retro_lafr_639,
Macropus eugenii	ENSMEUG00000009280	1 retrocopy	retro_meug_1207,
Macaca mulatta	ENSMMUG00000008234	2 retrocopies	retro_mmul_339, retro_mmul_511,
Monodelphis domestica	ENSMODG00000011614	4 retrocopies	retro_mdom_1259, retro_mdom_144, retro_mdom_219, retro_mdom_398,
Nomascus leucogenys	ENSNLEG00000007104	2 retrocopies	retro_nleu_1016, retro_nleu_1195,
Otolemur garnettii	ENSOGAG00000016032	1 retrocopy	retro_ogar_1314,
Pongo abelii	ENSPPYG00000013812	2 retrocopies	retro_pabe_185, retro_pabe_300,
Rattus norvegicus	ENSRNOG00000048441	3 retrocopies	retro_rnor_1003, retro_rnor_1109, retro_rnor_1152,