RetrogeneDB ID: retro_chof_1728

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_369366:410..1041(+)
• Located in intron of: None

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_1728
AACAAGATGTAATTATTGCAGAAGGATAAAGTTCTTGAGTTTATAATTTTCACCAAGTCTAGTGAACAAACAGCAGTAAG
TTGTTTATGTCAAAATACAGACTTGAAGTTAGATATTGCAATGGATGTTTTTTCCCAAAAACCTGAAATTAATATATAAG
AGTGTAAAAGAATATTTTGATAGAAAGAATTTGGAACAACTGTGCAAGGGATACAAAGATCCCCAAGATGAAAATAAAAG
TGGAATAAATAGTAGATAGCAGATCTGTGTTGATTGGGACTCAATCATGCCAGCAATAGTGTGTTGGGTATTGATTACTG
CATGGAAATCTGGAAACACAACATGGCATGAGTTCTCCAAACCAGAGTGCATGGATGGCATGACAGAATTAGGATGTGAC
TGGGCAGAAAAACCAAACTACCCAATCCCAAGATGGAACAAGAATAGGAAGAAACAGAATGATTTGAGATTTTTACCAGT
TTACTTTTAACTTACATAGAATCCAGGTCAAAAAGAATTAGATCTAGAAATGGCCATTGCTTACTGGAATTTAGTGTATA
GTGGAAAATTTTAATTCTTAGATTTATGGAATAAAATTTTGTTGGAACATCATAAACAATCAATATGGAAA

Alignment

ORF - retro_chof_1728 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.04 %
• Parental protein coverage: 81.18 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  NKLKSSQKDKVRQFMIFTQSSEKTAVSCLSQN-DWKLDVATDNFFQ-NPELYIRESVKGSLDRKKLEQLY
          NK....QKDKV..F.IFT.SSE.TAVSCL.QN.D.KLD.A.D.F.Q.N..L.I..SVK...DRK.LEQL.
Retrocopy NKM*LLQKDKVLEFIIFTKSSEQTAVSCLCQNTDLKLDIAMDVFSQ>NLKL-IYKSVKEYFDRKNLEQLC

Parental  NRYKDPQDENKIGIDGIQQFCDDL-ALDPASII-VLIIAWKFRAATQCEFSKQEFMDGMTELGCDSIE-K
          ..YKDPQDENK.GI....Q.C.D.....PA....VLI.AWK....T..EFSK.E.MDGMTELGCD..E.K
Retrocopy KGYKDPQDENKSGINSR*QICVDWDSIMPAIVCWVLITAWKSGNTTWHEFSKPECMDGMTELGCDWAE<K

Parental  LKAQIPKMEQELKEPGRFK-DFYQFTFNFAK-NPGQKGLDLEMAI-YWNLVLNGRFKFLDLWNK-FLEHH
          .K...PKMEQE..E...F..DFYQFTFN....NPGQK.LDLEMAI.YWNLV..G.F.FLDLWNK..LEHH
Retrocopy TKLPNPKMEQE*EETE*FE<DFYQFTFNLHR<NPGQKELDLEMAIAYWNLVYSGKF*FLDLWNKILLEHH

Parental  KRSIPK
          K.SI.K
Retrocopy KQSIWK

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_1728 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,