RetrogeneDB ID: retro_chof_232

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: GeneScaffold_5093:23052..23826(-)
• Located in intron of: ENSCHOG00000002341

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCUN1D1
• Ensembl ID: ENSCHOG00000013358
• Aliases: None
• Description: DCN1, defective in cullin neddylation 1, domain containing 1 [Source:HGNC Symbol;Acc:18184]

Sequence

>retro_chof_232
AACAAGTTGAAATCATCGCAGAAGGATGAAGTTCGTCAGTTTATGATCTTCACACAGTCTAGTGAAAAAACAGCAGTAAG
TTGTCTGTCTCAAAATGACTGGAAGTTAGATGTTGCAACAGACAATTTTTTCCAAAATCCTGAACTTTATATACGAGAGA
GTGTAAAAGGATCGTTGGACAGAAAGAAATTAGAACAACTGTACAATAGATACAAAGATCCTCAAGATGAAAACAAAATT
GGAATAGATGGTATACAGCAGTTCTGTGATGACCTGGCACTCGATCCAGCCAGCATTAGTGTGTTGATTATTGCGTGGAA
GTTTAGAGCAGCAACACAGTGTGAATTCTCCAAACAGGAGTTTATGGACGGCATGACAGAATTAGGATGTGACAGCATAG
AAAAACTAAAGGCCCAGATACCCAAGATGGAACAAGAATTGAAAGAACCAGGACGATTTAAGGATTTTTACCAGTTTACT
TTTAATTTTGCAAAGAATCCAGGACAAAAAGGATTAGATCTAGAAATGGCCATTGCCTACTGGAATTTAGTGCTTAATGG
AAGATTTAAATTCTTAGACTTATGGAATAAATTTTTGTTGGAACATCATAAACGATCAATACCAAAAGATACCTGGAATC
TTCTTTTAGACTTCAGTACAATGATTGCAGATGACATGTCTAATTATGATGAAGAAGGAGCATGGCCTGTTCTTATTGAT
GACTTTGTGGAATTTGCACGCCCTCAAATTGCTGGGACAAAAAGTACAACAGTG

Alignment

ORF - retro_chof_232 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.67 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NKLKSSQKDKVRQFMIFTQSSEKTAVSCLSQNDWKLDVATDNFFQNPELYIRESVKGSLDRKKLEQLYNR
          NKLKSSQKD.VRQFMIFTQSSEKTAVSCLSQNDWKLDVATDNFFQNPELYIRESVKGSLDRKKLEQLYNR
Retrocopy NKLKSSQKDEVRQFMIFTQSSEKTAVSCLSQNDWKLDVATDNFFQNPELYIRESVKGSLDRKKLEQLYNR

Parental  YKDPQDENKIGIDGIQQFCDDLALDPASIIVLIIAWKFRAATQCEFSKQEFMDGMTELGCDSIEKLKAQI
          YKDPQDENKIGIDGIQQFCDDLALDPASI.VLIIAWKFRAATQCEFSKQEFMDGMTELGCDSIEKLKAQI
Retrocopy YKDPQDENKIGIDGIQQFCDDLALDPASISVLIIAWKFRAATQCEFSKQEFMDGMTELGCDSIEKLKAQI

Parental  PKMEQELKEPGRFKDFYQFTFNFAKNPGQKGLDLEMAI-YWNLVLNGRFKFLDLWNKF-LEHHKRSIPKD
          PKMEQELKEPGRFKDFYQFTFNFAKNPGQKGLDLEMAI.YWNLVLNGRFKFLDLWNKF.LEHHKRSIPKD
Retrocopy PKMEQELKEPGRFKDFYQFTFNFAKNPGQKGLDLEMAIAYWNLVLNGRFKFLDLWNKFLLEHHKRSIPKD

Parental  TWN-LLDFSTMIADDMSNYDEEGAWSVLIDDFVEFARPQIAGTKSTTV
          TWN.LLDFSTMIADDMSNYDEEGAW.VLIDDFVEFARPQIAGTKSTTV
Retrocopy TWNLLLDFSTMIADDMSNYDEEGAWPVLIDDFVEFARPQIAGTKSTTV

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_232 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 15 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007821	4 retrocopies	retro_chof_1022, retro_chof_1937, retro_chof_461, retro_chof_771,
Choloepus hoffmanni	ENSCHOG00000013358	14 retrocopies	retro_chof_1054, retro_chof_1129, retro_chof_1198, retro_chof_1373, retro_chof_1546, retro_chof_1728, retro_chof_2049, retro_chof_232 , retro_chof_2329, retro_chof_2369, retro_chof_2373, retro_chof_479, retro_chof_767, retro_chof_812,
Callithrix jacchus	ENSCJAG00000005148	2 retrocopies	retro_cjac_1423, retro_cjac_2358,
Cavia porcellus	ENSCPOG00000022086	4 retrocopies	retro_cpor_1289, retro_cpor_756, retro_cpor_758, retro_cpor_870,
Dasypus novemcinctus	ENSDNOG00000019073	2 retrocopies	retro_dnov_1494, retro_dnov_840,
Echinops telfairi	ENSETEG00000000166	1 retrocopy	retro_etel_1460,
Homo sapiens	ENSG00000043093	1 retrocopy	retro_hsap_3502,
Gorilla gorilla	ENSGGOG00000010767	1 retrocopy	retro_ggor_2368,
Macaca mulatta	ENSMMUG00000010552	1 retrocopy	retro_mmul_1782,
Mustela putorius furo	ENSMPUG00000002369	1 retrocopy	retro_mputfur_919,
Mus musculus	ENSMUSG00000027708	1 retrocopy	retro_mmus_1009,
Nomascus leucogenys	ENSNLEG00000005983	1 retrocopy	retro_nleu_793,
Otolemur garnettii	ENSOGAG00000000658	1 retrocopy	retro_ogar_3499,
Pan troglodytes	ENSPTRG00000015661	1 retrocopy	retro_ptro_2374,
Tarsius syrichta	ENSTSYG00000012276	1 retrocopy	retro_tsyr_669,