RetrogeneDB ID: retro_chof_2096

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_4870:11517..11824(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000004496
• Aliases: None
• Description: None

Sequence

>retro_chof_2096
CCCCCAGCGCGGCTTAGAAGACATCGGATCCTGAAAGAAATCCGGGAATTGCAGAAGAGTGCAGCGCTATAGCAAAGAAC
CTGCCTTCCAGCCTCCTGGTAAAACAAATAGGTGCTGAATTCTCCCAAGGCCTGCACTTCCGTTGCAGGCCCAGGCCCCG
CTGGCCTGACAAGAGGCAGTGGAAACATTTCTAGTTCCTGTCTTCGAAGTCGCCCACCTCCTGTCTTTACATGCTGGCTG
CGGCACTCTTTTCCCAAAGGATGTGCAAATGGCAGGGAAGATCCAAGGCCTTCAAGAGGGACTGGGC

Alignment

ORF - retro_chof_2096 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.8 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PSPRRRRHRRGYQTLREIRKLQKSTNL-LIRRRPFSLLVREICTIFSRGVD-LNWQAQALLALQEAAETF
          P..R.RRHR.....L.EIR.LQKS..L......P.SLLV..I...FS.G...L..QAQA.LA.QEA.ETF
Retrocopy PPARLRRHR----ILKEIRELQKSAAL<IAKNLPSSLLVKQIGAEFSQGLH<LPLQAQAPLA*QEAVETF

Parental  LVHLFEDAYLLSLHAGRVTLFPKDVQLARRIRGIEQGLG
          LV..FE.A.LLSLHAG..TLFPKDVQ.A..I.G...GLG
Retrocopy LVPVFEVAHLLSLHAGCGTLFPKDVQMAGKIQGLQEGLG

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_2096 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 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000023938	1 retrocopy	retro_btau_947,
Choloepus hoffmanni	ENSCHOG00000004496	3 retrocopies	retro_chof_2096 , retro_chof_2448, retro_chof_4,
Ornithorhynchus anatinus	ENSOANG00000000516	1 retrocopy	retro_oana_72,
Otolemur garnettii	ENSOGAG00000024154	2 retrocopies	retro_ogar_3405, retro_ogar_3505,
Ictidomys tridecemlineatus	ENSSTOG00000025168	2 retrocopies	retro_itri_835, retro_itri_994,
Tarsius syrichta	ENSTSYG00000010334	1 retrocopy	retro_tsyr_2007,
Tursiops truncatus	ENSTTRG00000010278	2 retrocopies	retro_ttru_590, retro_ttru_784,