RetrogeneDB ID: retro_chof_32

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_451215:42..858(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000000249
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000006397
• Aliases: None
• Description: None

Sequence

>retro_chof_32
ATCCCAGAATCCAACAATAGCGTGTATACTTCCTTCATGAAGTCTCATCGCTGCTATGACCTGATTCCCACAAGCTCCAA
ATTGGTTGTATTTGATACTTCCCTACAGGTGAAGAAAGCTTTCTTTGCTTTGGTGACTAATGGTGTACGAGCTGCCCCTT
TGTGGGATAGTAAGAAGCAAAGTTTTGTGGGCATGCTGACCATCACCGATTTCATCAATATCCTGCACCGCTACTATAAA
TCAGCTTTGGTACAGATCTATGAGCTAGAAGAACACAAGATAGAAACTTGGAGAGAGGTGTACCTACAGGACTCCTTTAA
ACCACTTGTCTGCATTTCTCCTAATGCCAGCTTGTTTGATGCTGTATCTTCATTAATTCGAAACAAGATCCACAGACTGC
CAGTTATTGACCCGGAATCAGGCAACACCTTGTACATCCTTACCCACAAGCGCATCCTCAAGTTCCTCAAATTGTTTATC
ACCGAGTTTCCCAAGCCAGAGTTCATGTCCAAGTCTCTGGAAAAGCTGCAGATTGGCACCTATGCCAGCATTGCTATGGT
CCGTACTACCACCCCTGTCTATGTGGCTCTGGGCATCTTTGTGCAGCACAGAGTCTCTGCCCTGCCAGTGGTGGATGAGA
AAGGGCGTGTGGTGGACATCTACTCCAAGTTTGATGTTATCAATCTTGCAGCAGAAAAGACCTACAACAACTTAGATGTG
TCCGTAACCAAAGCCCTGCAACATAGATCACACTACTTTGAGGGTGTCCTCAAGTGCTATCTGCACGAGACTCTGGAAAC
CATCATCAACAGGCTG

Alignment

ORF - retro_chof_32 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100.0 %
• Parental protein coverage: 64.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PESNNSVYTSFMKSHRCYDLIPTSSKLVVFDTSLQVKKAFFALVTNGVRAAPLWDSKKQSFVGMLTITDF
          PESNNSVYTSFMKSHRCYDLIPTSSKLVVFDTSLQVKKAFFALVTNGVRAAPLWDSKKQSFVGMLTITDF
Retrocopy PESNNSVYTSFMKSHRCYDLIPTSSKLVVFDTSLQVKKAFFALVTNGVRAAPLWDSKKQSFVGMLTITDF

Parental  INILHRYYKSALVQIYELEEHKIETWREVYLQDSFKPLVCISPNASLFDAVSSLIRNKIHRLPVIDPESG
          INILHRYYKSALVQIYELEEHKIETWREVYLQDSFKPLVCISPNASLFDAVSSLIRNKIHRLPVIDPESG
Retrocopy INILHRYYKSALVQIYELEEHKIETWREVYLQDSFKPLVCISPNASLFDAVSSLIRNKIHRLPVIDPESG

Parental  NTLYILTHKRILKFLKLFITEFPKPEFMSKSLEKLQIGTYASIAMVRTTTPVYVALGIFVQHRVSALPVV
          NTLYILTHKRILKFLKLFITEFPKPEFMSKSLEKLQIGTYASIAMVRTTTPVYVALGIFVQHRVSALPVV
Retrocopy NTLYILTHKRILKFLKLFITEFPKPEFMSKSLEKLQIGTYASIAMVRTTTPVYVALGIFVQHRVSALPVV

Parental  DEKGRVVDIYSKFDVI
          DEKGRVVDIYSKFDVI
Retrocopy DEKGRVVDIYSKFDVI

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_32 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006964	2 retrocopies	retro_amel_1722, retro_amel_406,
Choloepus hoffmanni	ENSCHOG00000006397	1 retrocopy	retro_chof_32 ,
Callithrix jacchus	ENSCJAG00000020827	2 retrocopies	retro_cjac_3045, retro_cjac_3892,
Felis catus	ENSFCAG00000000091	1 retrocopy	retro_fcat_1730,
Myotis lucifugus	ENSMLUG00000011156	2 retrocopies	retro_mluc_2417, retro_mluc_451,
Oryctolagus cuniculus	ENSOCUG00000008409	1 retrocopy	retro_ocun_829,
Sus scrofa	ENSSSCG00000000185	1 retrocopy	retro_sscr_210,
Tursiops truncatus	ENSTTRG00000004730	1 retrocopy	retro_ttru_497,