RetrogeneDB ID: retro_chof_190

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_426:210743..210959(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUMO1
• Ensembl ID: ENSCHOG00000009739
• Aliases: None
• Description: small ubiquitin-like modifier 1 [Source:HGNC Symbol;Acc:12502]

Sequence

>retro_chof_190
GATAGCAGTGAGATTCACTTCAAGGTAAAATGACAAAACATCTCAAAGAAACTCAAGGAATTATACTGTCAAAGATGGGG
AGTTCCAATGAATTCACTCAGGTTTCTCTTTGAAGGTCAGAGAATTGCTGATAATCACACTCCAAAAGAACTGGGAATGG
AGGAAGAAGATGCGATTGAAGTATATCAGGAACAAACAAGGGGTCATTCAACAGTT

Alignment

ORF - retro_chof_190 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.54 %
• Parental protein coverage: 51.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DSSEIHFKVK-MTTHLK-KLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTGG
          DSSEIHFKVK.MT.HLK.KLKE.YCQR.GVPMNSLRFLFEGQRIADNHTPKELGMEEED.IEVYQEQT.G
Retrocopy DSSEIHFKVK<MTKHLK>KLKELYCQRWGVPMNSLRFLFEGQRIADNHTPKELGMEEEDAIEVYQEQTRG

Parental  HSTV
          HSTV
Retrocopy HSTV

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_190 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 16 parental genes, and 59 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013225	5 retrocopies	retro_amel_1068, retro_amel_233, retro_amel_236, retro_amel_315, retro_amel_49,
Bos taurus	ENSBTAG00000009859	6 retrocopies	retro_btau_112, retro_btau_1512, retro_btau_1705, retro_btau_357, retro_btau_363, retro_btau_499,
Canis familiaris	ENSCAFG00000012431	8 retrocopies	retro_cfam_1226, retro_cfam_1253, retro_cfam_139, retro_cfam_1815, retro_cfam_1912, retro_cfam_2048, retro_cfam_386, retro_cfam_985,
Choloepus hoffmanni	ENSCHOG00000009739	2 retrocopies	retro_chof_190 , retro_chof_2068,
Choloepus hoffmanni	ENSCHOG00000010239	1 retrocopy	retro_chof_2468,
Felis catus	ENSFCAG00000031005	6 retrocopies	retro_fcat_1520, retro_fcat_218, retro_fcat_26, retro_fcat_472, retro_fcat_6, retro_fcat_862,
Loxodonta africana	ENSLAFG00000022855	5 retrocopies	retro_lafr_111, retro_lafr_1148, retro_lafr_189, retro_lafr_540, retro_lafr_951,
Myotis lucifugus	ENSMLUG00000007504	2 retrocopies	retro_mluc_1346, retro_mluc_188,
Macaca mulatta	ENSMMUG00000005240	7 retrocopies	retro_mmul_1108, retro_mmul_2035, retro_mmul_2081, retro_mmul_313, retro_mmul_373, retro_mmul_450, retro_mmul_855,
Mustela putorius furo	ENSMPUG00000000335	2 retrocopies	retro_mputfur_257, retro_mputfur_33,
Mus musculus	ENSMUSG00000026021	5 retrocopies	retro_mmus_1594, retro_mmus_2129, retro_mmus_2135, retro_mmus_252, retro_mmus_2962,
Nomascus leucogenys	ENSNLEG00000006997	4 retrocopies	retro_nleu_277, retro_nleu_384, retro_nleu_855, retro_nleu_865,
Otolemur garnettii	ENSOGAG00000030345	1 retrocopy	retro_ogar_215,
Pongo abelii	ENSPPYG00000013083	3 retrocopies	retro_pabe_11, retro_pabe_1830, retro_pabe_775,
Pan troglodytes	ENSPTRG00000012817	1 retrocopy	retro_ptro_119,
Sarcophilus harrisii	ENSSHAG00000011968	1 retrocopy	retro_shar_375,