RetrogeneDB ID: retro_chof_1007

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_183365:2821..3388(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000006609
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000001689
• Aliases: None
• Description: None

Sequence

>retro_chof_1007
CGCCTGGACTTTGATTATAAGAAAGAAACGACAAAGGCAAGTTTCAGATGAAGAACTCCCGTCAAGCTCTGGAGAAAATT
CGATGAGTCTAAAGAAGTTGCTGAGTCAAGCATGTTCAATCTTCTAGAGATGGATATTGAACAGGTGAGCCAGCTCTCTG
CACTTGTACAAGCCCAGCTAGAGTACCACAAGCAGGCTGTGCAGATCCTGCAGCAAGTCACCGACAGACTGGAAGAAAGA
ATAAGACAAGCTTCATCTCAGCCTAGAAGGGAATATCAGCCTAAACCACGGATGAGCCTGGAATTCCCAACTGGGGATAG
TAGTCAGCCCAACGGGGGCCTTTCACACGCAAGCGCTCCCAAACCTGCAGGTGCCCTGATGGATCAGCCCTGTTGCCGAG
CTCTGTACGACTTTGAACCTGAAAATGAAGGCGAGCTGGGTTTTAAAGAGGGTGACATCATCACACTCACCAACCAAATT
GATGAGAACTGGTATGAGGGGATGCTTCATGGCCAGTCAGGCTTCTTCCCCATCAACTATGTGGAAATTCTGGTTCCCCT
GCCCCAT

Alignment

ORF - retro_chof_1007 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.76 %
• Parental protein coverage: 53.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RLDFDYKK-KRQGKIPDEEL-RQALEK-FDESKEVAESSMFNLLEMDIEQVSQLSALVQAQLEYHKQAVQ
          RLDFDYKK.KRQ....DEEL.RQALEK.FDESKEVAESSMFNLLEMDIEQVSQLSALVQAQLEYHKQAVQ
Retrocopy RLDFDYKK>KRQRQVSDEEL>RQALEK>FDESKEVAESSMFNLLEMDIEQVSQLSALVQAQLEYHKQAVQ

Parental  ILQQVTVRLEERIRQASSQPRREYQPKPRMSLEFPTGDSSQPNGGLSHASTPKPAGAPMDQPCCRALYDF
          ILQQVT.RLEERIRQASSQPRREYQPKPRMSLEFPTGDSSQPNGGLSHAS.PKPAGA.MDQPCCRALYDF
Retrocopy ILQQVTDRLEERIRQASSQPRREYQPKPRMSLEFPTGDSSQPNGGLSHASAPKPAGALMDQPCCRALYDF

Parental  EPENEGELGFKEGDIITLTNQIDENWYEGMLHGQSGFFPINYVEILVPLPH
          EPENEGELGFKEGDIITLTNQIDENWYEGMLHGQSGFFPINYVEILVPLPH
Retrocopy EPENEGELGFKEGDIITLTNQIDENWYEGMLHGQSGFFPINYVEILVPLPH

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_1007 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010823	1 retrocopy	retro_amel_1668,
Choloepus hoffmanni	ENSCHOG00000001689	2 retrocopies	retro_chof_1007 , retro_chof_24,
Macropus eugenii	ENSMEUG00000015197	1 retrocopy	retro_meug_523,
Macaca mulatta	ENSMMUG00000000273	1 retrocopy	retro_mmul_1264,
Pan troglodytes	ENSPTRG00000020792	1 retrocopy	retro_ptro_576,