RetrogeneDB ID: retro_chof_248

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_5439:37328..37694(+)
• Located in intron of: ENSCHOG00000000796

Retrocopy information

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

Parental gene information

• Parental gene symbol: BLOC1S6
• Ensembl ID: ENSCHOG00000012059
• Aliases: None
• Description: biogenesis of lysosomal organelles complex-1, subunit 6, pallidin [Source:HGNC Symbol;Acc:8549]

Sequence

>retro_chof_248
CTTTCTCACTATTCATCAGATCTGCAGAGATCAAGCAAGTTCTCCAGGAACTCACACAAAACCAAGCTGTATTATTAAAT
ACACTGGAACAAGAGATTTCAAAATTTTAAAGAATGTCATTTTATGTTGGATATTAATGCTTTGTTCACTGAAGCTAAAC
ACTATCATACCAAGTTGGTGAATATAAGAAAACAAATGCTGATGCTTCATGAAAAGACATCAAAGTTTTAAAAAAACTTA
AATAAGAGAGAGAGCCCACTTAAACTGCAGCAGAAGAGGCAGAAAGAAGAGTTGGAAAGGGAGCAGCAATGAGAAAAGGA
AATTGAAAGAGAAAAGCAGTTAACTGCCAAACCAGCTAAAAGGACA

Alignment

ORF - retro_chof_248 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.42 %
• Parental protein coverage: 67.06 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LSHYLPDLQRS-KQALQELTQNQVVLLDTLEQEISKF-KECHSMLDINALFTEAKHYHTKLV--IKEMLM
          LSHY..DLQRS.KQ.LQELTQNQ.VLL.TLEQEISKF.KECH.MLDINALFTEAKHYHTKLV...K.MLM
Retrocopy LSHYSSDLQRS<KQVLQELTQNQAVLLNTLEQEISKF>KECHFMLDINALFTEAKHYHTKLVNIRKQMLM

Parental  LHEKTSK----LKKRALKLQQKRQ--KEELEREQQREKEIEREKQLTAKPAKRT
          LHEKTSK....L.KR...L.......KEELEREQQ.EKEIEREKQLTAKPAKRT
Retrocopy LHEKTSKF*KNLNKRESPLKLQQKRQKEELEREQQ*EKEIEREKQLTAKPAKRT

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_248 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 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012059	7 retrocopies	retro_chof_1342, retro_chof_20, retro_chof_2054, retro_chof_2102, retro_chof_211, retro_chof_248 , retro_chof_600,
Dasypus novemcinctus	ENSDNOG00000019785	5 retrocopies	retro_dnov_1687, retro_dnov_1885, retro_dnov_2009, retro_dnov_2411, retro_dnov_275,
Echinops telfairi	ENSETEG00000007378	1 retrocopy	retro_etel_404,
Gorilla gorilla	ENSGGOG00000013892	1 retrocopy	retro_ggor_2983,
Macropus eugenii	ENSMEUG00000012636	1 retrocopy	retro_meug_778,
Microcebus murinus	ENSMICG00000005595	1 retrocopy	retro_mmur_1610,
Monodelphis domestica	ENSMODG00000017628	2 retrocopies	retro_mdom_1673, retro_mdom_561,
Oryctolagus cuniculus	ENSOCUG00000017351	1 retrocopy	retro_ocun_1575,
Otolemur garnettii	ENSOGAG00000013706	1 retrocopy	retro_ogar_206,
Ochotona princeps	ENSOPRG00000007310	1 retrocopy	retro_opri_574,
Pan troglodytes	ENSPTRG00000007038	1 retrocopy	retro_ptro_2949,