RetrogeneDB ID: retro_chof_2457

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_77687:5947..6300(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCHOG00000000689
• Aliases: None
• Description: None

Sequence

>retro_chof_2457
CAGCCCGCCAAGGTGGCGAACATTCAACTTCCGCCTGAAGTAAATCGGCTTTTGTCTATAAGAAATTTGCCATATAAAAT
CATAGTTGAAGAAATGTATGATATATTTGGGAAATATGGACATATTTGTCAAATCAGAGTAGGGAACACACCTGAAACTG
GAGGAACAGCTTATGTAGTCTACGAAGACATCTTTGATGCAAGAATGCTGGTGATCGCCTATCAGGATTCAATGTTTGTA
ACAGATGCATGGTTTTTTAATATAATGCCAACAGAGCATTTCAGAAGATGGACACAAAAAAGGAGGAGGAGTAGCTGAAG
CTTCTCAAGGAGAAATACGGCATCAATGAAGAT

Alignment

ORF - retro_chof_2457 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.5 %
• Parental protein coverage: 95.2 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QAAKRANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDA-KN
          Q.AK.ANI.LPPEVNR.L.IRNLPYKI..EEMYDIFGKYG.I.QIRVGNTPET.GTAYVVYEDIFDA.KN
Retrocopy QPAKVANIQLPPEVNRLLSIRNLPYKIIVEEMYDIFGKYGHICQIRVGNTPETGGTAYVVYEDIFDA<KN

Parental  ACDHLSGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGINTD
          A.D.LSGFNVCNR...V..YNANRAFQKMDTKK.EE.LKLLKEKYGIN.D
Retrocopy AGDRLSGFNVCNR-CMVF*YNANRAFQKMDTKKEEE*LKLLKEKYGINED

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_2457 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 17 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002786	1 retrocopy	retro_amel_1594,
Bos taurus	ENSBTAG00000003407	1 retrocopy	retro_btau_606,
Choloepus hoffmanni	ENSCHOG00000000689	3 retrocopies	retro_chof_1217, retro_chof_2457 , retro_chof_351,
Callithrix jacchus	ENSCJAG00000007716	2 retrocopies	retro_cjac_2632, retro_cjac_487,
Dasypus novemcinctus	ENSDNOG00000007148	1 retrocopy	retro_dnov_1313,
Equus caballus	ENSECAG00000015618	1 retrocopy	retro_ecab_733,
Felis catus	ENSFCAG00000031365	1 retrocopy	retro_fcat_247,
Homo sapiens	ENSG00000115128	1 retrocopy	retro_hsap_1773,
Myotis lucifugus	ENSMLUG00000002473	1 retrocopy	retro_mluc_1529,
Macaca mulatta	ENSMMUG00000001282	1 retrocopy	retro_mmul_1262,
Mustela putorius furo	ENSMPUG00000013957	1 retrocopy	retro_mputfur_882,
Nomascus leucogenys	ENSNLEG00000000815	1 retrocopy	retro_nleu_2806,
Otolemur garnettii	ENSOGAG00000004468	1 retrocopy	retro_ogar_2877,
Pongo abelii	ENSPPYG00000012603	2 retrocopies	retro_pabe_1098, retro_pabe_1461,
Pan troglodytes	ENSPTRG00000011709	1 retrocopy	retro_ptro_1187,
Sorex araneus	ENSSARG00000011902	1 retrocopy	retro_sara_638,
Tupaia belangeri	ENSTBEG00000012532	5 retrocopies	retro_tbel_1722, retro_tbel_3076, retro_tbel_3766, retro_tbel_3886, retro_tbel_829,