RetrogeneDB ID: retro_chof_2004

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_45069:4525..4773(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000000685
• Aliases: None
• Description: None

Sequence

>retro_chof_2004
ATGGCGTCGGCCACCCGCTTCATCCAGGGGCTGCAGAACTGTGCATCCAAGCAAGATCTGCAGGGAAGCTGCAAATGTGC
TACTAGGAGATCTCCAAGCAAACTCAGCCTCCTCCCAAGCTCCTGGTGGGCCCCAGCCACAAGCTCTCCAACAACTACTA
CTGCACTCGCGACGGCCACCGTGAAGCTGTCCCCCCCTCCGTCATCATGTCCTCACAGAAGGCACTGGTGTCAGGCAATG
CAGCAGAG

Alignment

ORF - retro_chof_2004 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.14 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASATRFIQRLRNWASGQDLQA-KLQLRYQEISKRTQPPPKLPVGPSHKLSNNYYCTRDGRREAVPPSVI
          MASATRFIQ.L.N.AS.QDLQ..KLQ..Y.EISK.TQPPPKL.VGPSHKLSNNYYCTRDG.REAVPPSVI
Retrocopy MASATRFIQGLQNCASKQDLQG<KLQMCY*EISKQTQPPPKLLVGPSHKLSNNYYCTRDGHREAVPPSVI

Parental  MSSQKALASGKPAE
          MSSQKAL.SG..AE
Retrocopy MSSQKALVSGNAAE

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_2004 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000685	1 retrocopy	retro_chof_2004 ,
Callithrix jacchus	ENSCJAG00000010709	2 retrocopies	retro_cjac_2942, retro_cjac_956,
Dipodomys ordii	ENSDORG00000012324	1 retrocopy	retro_dord_155,
Macropus eugenii	ENSMEUG00000015637	3 retrocopies	retro_meug_1487, retro_meug_149, retro_meug_587,
Rattus norvegicus	ENSRNOG00000006939	2 retrocopies	retro_rnor_1491, retro_rnor_1793,