RetrogeneDB ID: retro_chof_1780

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_381806:2..847(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000003829
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: OGFRL1
• Ensembl ID: ENSCHOG00000002600
• Aliases: None
• Description: opioid growth factor receptor-like 1 [Source:HGNC Symbol;Acc:21378]

Sequence

>retro_chof_1780
GGCTTGAACTTTTATGCTAAAGAACTAACTACATATGAAATTGAGGAATTCAAAAAAACAAAAGAAGCAATTAGAAGATT
TCCCTGGCTTATAAAATGATGTTAGAATTTTTTGGAATAAAGCTGATTGATAAAACTGGAAATGTGGCCCGTGCTGTTAA
CTGGCAGGAAAGGTTTCAGCATCTGAATGAATCCCAGCACAACTATTTAAGAATCACCCGTATTCTTAAAAGCCTTGGTG
AACTTGGATATGAAAGTTTTAAATCTCCCCTTGTAAAATTTATTCTTCATGAGGCTCTTGTGGAAAATACTCTTCCCAAT
ATTAAGCAGAGTGCTCTGGAGTATTTTGTTTATACAATTAGAGACAGAAGAGAAAGGAGAAAGCTCCTCCGATTTGCTCA
GAAACATTACACGCCCTCAGAGAATTTTATCTGGGGACCACCTAGAAAAGAACAGTCAGAGGGAAGCAAAGCCCCGAAAA
CACCTGCCCCTCCGGCCTCCGGTCACAACAGTCAAACTTCTATGCATAAAAAATCCAAGGACACCAAAAATTCCTCCTCA
GCTGTTCATTTGAATAGCAAAACAGCAGAAGAAAAAAAATTGGCACCTAAAGAGCTTAGGAAACAGACAGACAAGCCCAG
AGCAGAGCCCAACGATGAAGCTGCCAAGCCAAGAAACAGTGAGAAGGACAGTAATGCTGAAAATTCGAATTTTCAGTCAG
AAAAAACAATGGACGATCCCAAAGAGAAAAAGGAGAGTGTACCCCCTTCTGAAAAAGAAAGTGAAAATCATAACAAAGAA
CCTGAAAATCCTGGGAATACAAGTCCCCATGATGACATATTTATT

Alignment

ORF - retro_chof_1780 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.11 %
• Parental protein coverage: 75.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GLNFYAKELTTYEIEEFKKTKEAIRRF-LLAYKMMLEFFGIKLIDKTGNVARAVNWQERFQHLNESQHNY
          GLNFYAKELTTYEIEEFKKTKEAIRRF..LAYKMMLEFFGIKLIDKTGNVARAVNWQERFQHLNESQHNY
Retrocopy GLNFYAKELTTYEIEEFKKTKEAIRRF<SLAYKMMLEFFGIKLIDKTGNVARAVNWQERFQHLNESQHNY

Parental  LRITRILKSLGELGYESFKSPLVKFILHEALVENTLPNIKQSALEYFVYTIRDRRERRKLLRFAQKHYTP
          LRITRILKSLGELGYESFKSPLVKFILHEALVENTLPNIKQSALEYFVYTIRDRRERRKLLRFAQKHYTP
Retrocopy LRITRILKSLGELGYESFKSPLVKFILHEALVENTLPNIKQSALEYFVYTIRDRRERRKLLRFAQKHYTP

Parental  SENFIWGPPRKEQSEGSKAPKTPAPPASSHNSQTSMHKKSKDSKNSSSAVHLNSKTAEEKKLAPKELRKQ
          SENFIWGPPRKEQSEGSKAPKTPAPPAS.HNSQTSMHKKSKD.KNSSSAVHLNSKTAE...LAPKELRKQ
Retrocopy SENFIWGPPRKEQSEGSKAPKTPAPPASGHNSQTSMHKKSKDTKNSSSAVHLNSKTAEXXXLAPKELRKQ

Parental  TDKPRAEPNDEAAKPRNSEKDSNAENSNFQSEKTMDNPKEKKESVPPSEKESENHNKDPENPGNTSPHDD
          TDKPRAEPNDEAAKPRNSEKDSNAENSNFQSEKTMD.PKEKKESVPPSEKESENHNK.PENPGNTSPHDD
Retrocopy TDKPRAEPNDEAAKPRNSEKDSNAENSNFQSEKTMDDPKEKKESVPPSEKESENHNKEPENPGNTSPHDD

Parental  ILL
          I..
Retrocopy IFI

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_1780 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002600	1 retrocopy	retro_chof_1780 ,
Callithrix jacchus	ENSCJAG00000003635	1 retrocopy	retro_cjac_2757,
Myotis lucifugus	ENSMLUG00000007329	1 retrocopy	retro_mluc_870,