RetrogeneDB ID: retro_chof_25

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_89766:444..1416(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCHOG00000004108
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000009239
• Aliases: None
• Description: None

Sequence

>retro_chof_25
GCCACCGAAGGACCCTGTCATGTGCCCAAACCAGCTATCTTTGACATGATCAATAAGGCAAAATGGGAAGCCTGGAACGC
CCTTGGTAGCTTACCCAAGGACACGGCCAGGCAGAACTATGTGGATTTGGTGTCCAGTTTGGGTTCGCCATCTGAATTCT
CTGGCCACGTGAAGCCTGCTGCAGACAGGAGCCAGGCTGGATATGAAACCCTGCTGGTGACCTCAGAGGATGGCATCACA
AAGATCACGCTAAACCGTCCCACCAAAAAAAATGCCATCAGCACCCAGATGTATCAAGAAATTATGCTTGCACTTGAGGC
CGCAGGCGAGGATGACTCAGCCATAACCATTGTCACAGGAAATGGTGACTATTATAGTAGTGGGAACGATCTGAATAACT
TCGCTGATGTTCACCCTAGTGAGGCAGAGGAGAAATCTAAGAGTGCTGCCATCTTACTGAGGGAATTTGTAAGCCATTTT
ATAGATTTTCCTAAGCCTCTGATTGCAGTGGTGAATGGTCCAGCTGTGGGAATCACCGTCACCCTTCTAGGGCTTTTTGA
TTTGGTGTATGCGTCCGACAAGGCGACATTTCATACTCCTTTTAGTCACCTCAGCCAGTGTCCGGAAGGATGTTCCTCTT
ACGTTTTTCCGAAGATAATGGGCTCAGTCAAGGCAACTGAGATGCTTGTTTTTGGAAAGAAGTTAACAGCCAGAGAAGCA
TGTGCTCAAGGACTCGTTAATGAAGTATTTCCTGATAGCACTTTCCAAAAAGAAGTTTGGGCCAGGCTGAAAGCATATTC
AAAGCTCCCACCAAATGCCATGAGAATTTCAAAACAGGTAATCCGAAATAGAGAGAAAGAAAAGCTACATGCTGTTAATT
TGGAAGAATGCAACATCCTCCAGGAAAGATGGCAGTCAGAGGAATGCCTGAACGCGATCATGAACGTCTTATCCAAAAGA
GCAAAACTGTGA

Alignment

ORF - retro_chof_25 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.21 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ATEGPCHVPKPAIFDMINKAKWEAWNALGSLPKDTARQNYVDLVSSLGSPSESSGHVKPAADRSQAGYET
          ATEGPCHVPKPAIFDMINKAKWEAWNALGSLPKDTARQNYVDLVSSLGSPSE.SGHVKPAADRSQAGYET
Retrocopy ATEGPCHVPKPAIFDMINKAKWEAWNALGSLPKDTARQNYVDLVSSLGSPSEFSGHVKPAADRSQAGYET

Parental  LLVTSEDGITKITLNRPTKKNAISTQMYQEIMLALEAAGKDDSAITIVTGNGDYYSSGNDLNNFADFHPS
          LLVTSEDGITKITLNRPTKKNAISTQMYQEIMLALEAAG.DDSAITIVTGNGDYYSSGNDLNNFAD.HPS
Retrocopy LLVTSEDGITKITLNRPTKKNAISTQMYQEIMLALEAAGEDDSAITIVTGNGDYYSSGNDLNNFADVHPS

Parental  EAEEKSKSAAILLREFVGHFIDFPKPLIAVVNGPAVGITVTLLGLFDLVYASDKATFHTPFSHLGQCPEG
          EAEEKSKSAAILLREFV.HFIDFPKPLIAVVNGPAVGITVTLLGLFDLVYASDKATFHTPFSHL.QCPEG
Retrocopy EAEEKSKSAAILLREFVSHFIDFPKPLIAVVNGPAVGITVTLLGLFDLVYASDKATFHTPFSHLSQCPEG

Parental  CSSYIFPKIMGSVKATEMLVFGKKLTAREACAQGLVNEVFPDSTFQKEVWARLKAYSKLPPNAMRISKQV
          CSSY.FPKIMGSVKATEMLVFGKKLTAREACAQGLVNEVFPDSTFQKEVWARLKAYSKLPPNAMRISKQV
Retrocopy CSSYVFPKIMGSVKATEMLVFGKKLTAREACAQGLVNEVFPDSTFQKEVWARLKAYSKLPPNAMRISKQV

Parental  IRNREKEKLHAVNLEECNILQERWQSEECRNAIMNFLSKRTKL
          IRNREKEKLHAVNLEECNILQERWQSEEC.NAIMN.LSKR.KL
Retrocopy IRNREKEKLHAVNLEECNILQERWQSEECLNAIMNVLSKRAKL

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_25 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009409	1 retrocopy	retro_cfam_536,
Choloepus hoffmanni	ENSCHOG00000009239	1 retrocopy	retro_chof_25 ,
Choloepus hoffmanni	ENSCHOG00000011787	1 retrocopy	retro_chof_525,
Procavia capensis	ENSPCAG00000008568	1 retrocopy	retro_pcap_71,
Rattus norvegicus	ENSRNOG00000016369	1 retrocopy	retro_rnor_1179,
Tupaia belangeri	ENSTBEG00000015862	2 retrocopies	retro_tbel_2398, retro_tbel_814,