RetrogeneDB ID: retro_chof_2195

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_57582:9282..9566(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PQLC3
• Ensembl ID: ENSCHOG00000006017
• Aliases: None
• Description: PQ loop repeat containing 3 [Source:HGNC Symbol;Acc:28503]

Sequence

>retro_chof_2195
CTGCAGAAGTGGATCATAGATCTGGGAATGAATTTATGTACTTTCATTAGTGTGGCCAGGCAGTTTGCTCAACTCCAGTA
TGTGTGGAAGACAAGGGACTTGGGAGCTGTGACTGCTCTGACTTGGAGCCTTGCTTCATACACCTGAGTGACAAGAATAG
TAACAACTTTAATGACCACCAATGATCTTACAGTTCTTATACTTTTGTGATTATGCCGTCTTTAAATATCTGGGTAACAG
GTACAATACTTCACTATCACAAGAAAACCATGGTGAAGACTGAA

Alignment

ORF - retro_chof_2195 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.21 %
• Parental protein coverage: 91.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LQKWIIDLAMNLCTFISAASKFAQLQYLWKTRDSGAVSALTWSLASYTCATRIVTTLMTTNDLTILT-RF
          LQKWIIDL.MNLCTFIS.A..FAQLQY.WKTRD.GAV.ALTWSLASYT..TRIVTTLMTTNDLT.L...F
Retrocopy LQKWIIDLGMNLCTFISVARQFAQLQYVWKTRDLGAVTALTWSLASYT*VTRIVTTLMTTNDLTVLI<TF

Parental  VIMLALNIWVTATILHYRKKTTMKTE
          VIM..LNIWVT.TILHY.KKT..KTE
Retrocopy VIMPSLNIWVTGTILHYHKKTMVKTE

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_2195 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006017	3 retrocopies	retro_chof_1902, retro_chof_2195 , retro_chof_717,
Callithrix jacchus	ENSCJAG00000006801	1 retrocopy	retro_cjac_3969,
Dasypus novemcinctus	ENSDNOG00000015960	1 retrocopy	retro_dnov_2157,
Macropus eugenii	ENSMEUG00000009376	1 retrocopy	retro_meug_1167,
Mus musculus	ENSMUSG00000045679	2 retrocopies	retro_mmus_1352, retro_mmus_2875,