RetrogeneDB ID: retro_chof_328

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_7401:9928..10166(-)
• Located in intron of: ENSCHOG00000002617

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000013008
• Aliases: None
• Description: None

Sequence

>retro_chof_328
ATGGCCAACCCTATGCAACTACTGGCAAAGATCTTTAAAGGAATTTTAGTAGCTGAAGTTATGGGCATTTTTGGAGCTTA
TTTTTTGTTTAATAAAATGAACACAAGCCAAGATTTCAGGCGAACAATGAGCAAAAAAACCTCCCTTCATCTTGGAAATT
TAATACAAATCCCTTGAACATTCTGGAATGTGCAGAACCAGACAGCAAAATCAAGAAAAATGGATGAACAGCAAAAAC

Alignment

ORF - retro_chof_328 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.25 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MARTMEPLAKKIFKAILVAEVMGIFGAYFLFNKMNTSQDFRETMSKKF-PFILEVYYKSLEHSGMYEIRE
          MA..M..LAK.IFK.ILVAEVMGIFGAYFLFNKMNTSQDFR.TMSKK..PFILE..YKSLEHSGM...R.
Retrocopy MANPMQLLAK-IFKGILVAEVMGIFGAYFLFNKMNTSQDFRRTMSKKT>PFILEI*YKSLEHSGMCRTRQ

Parental  QDQEKWMNSKN
          Q.QEKWMNSKN
Retrocopy QNQEKWMNSKN

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_328 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 11 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017579	1 retrocopy	retro_amel_629,
Choloepus hoffmanni	ENSCHOG00000013008	2 retrocopies	retro_chof_328 , retro_chof_49,
Felis catus	ENSFCAG00000023228	2 retrocopies	retro_fcat_1289, retro_fcat_1750,
Homo sapiens	ENSG00000218739	2 retrocopies	retro_hsap_2312, retro_hsap_4294,
Gorilla gorilla	ENSGGOG00000025368	2 retrocopies	retro_ggor_1755, retro_ggor_2869,
Mus musculus	ENSMUSG00000062691	2 retrocopies	retro_mmus_426, retro_mmus_509,
Pongo abelii	ENSPPYG00000029876	2 retrocopies	retro_pabe_2045, retro_pabe_3499,
Pan troglodytes	ENSPTRG00000033858	2 retrocopies	retro_ptro_1687, retro_ptro_2911,
Rattus norvegicus	ENSRNOG00000040303	2 retrocopies	retro_rnor_1144, retro_rnor_973,
Sus scrofa	ENSSSCG00000020689	2 retrocopies	retro_sscr_328, retro_sscr_434,
Tursiops truncatus	ENSTTRG00000006884	7 retrocopies	retro_ttru_1069, retro_ttru_1866, retro_ttru_1946, retro_ttru_274, retro_ttru_526, retro_ttru_57, retro_ttru_832,