RetrogeneDB ID: retro_cjac_2358

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:99791753..99792520(+)
• Located in intron of: ENSCJAG00000001507

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCUN1D1
• Ensembl ID: ENSCJAG00000005148
• Aliases: None
• Description: DCN1, defective in cullin neddylation 1, domain containing 1 [Source:HGNC Symbol;Acc:18184]

Sequence

>retro_cjac_2358
AACAAGTTGAAATCATCGCAGAAGGGTAAAGTTTGTCAGGTTATGATCTTCACACAATCTAGTGAAAAAGCAGCAGCAAA
TTGTATATTTCAAAATGACTGGAAGTTAGACGCAACAGACAATTTTTGCCAAAATTCCCACTTCATATATGAGAGAGTGT
AAAATGATCATTAGACAGGAAGAAGTTAAAACAACTGTACAATAGATACAAAGTTCCTCAAGATGAGAATACAATTGGAA
TAGATGGTACACAGCAGTTCTGTGATGACCTGGCACTCAATCCAGCCAGCATTAGTGTGTTGATTATTGCATGGGGTTCA
GAGCAGCAACACAGTGTGAGTTCTCCAAACAGGAGTTCATGGATGGCATGACAGAATTAGGATGTGATAACACAGAAAAA
CTAAAGGCCCAGAAATCCAAGACGGAACAAGAATTGAAAGAACCAGAATGATTTAATGATTTTTAACAGTTTACTTTTAA
TTTTGCAAAGAATCTAGGACAAAAAGGATTAGATCTAGAAATGGCCATTTCCTACTAGAACTCAGTGCTAAGTGGAAGAT
ATAAATTCTTAGATTTATGGAATAACTTTTTGTTGGAACATCATAAACGATCAATACCAAAAGACATTTGGAATTCTTTT
AGACCTCAGTACAATGATTGCAGATGACATGCCTAATTATGATGAAGAAGGAGCATGGCCTGTTCTTATCGATGACTTTG
TGGAATGTGCACACCCTCAAACTGCTGGGACCAAATGTACAACAGTG

Alignment

ORF - retro_cjac_2358 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.61 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NKLKSSQKDKVRQFMIFTQSSEKTAVSCLSQNDWKLDVATDNFFQNPE-LYIRESVKGSLDRKKLEQLYN
          NKLKSSQK.KV.Q.MIFTQSSEK.A..C..QNDWKLD.ATDNF.QN...L.I.ESVK.SLDRKKL.QLYN
Retrocopy NKLKSSQKGKVCQVMIFTQSSEKAAANCIFQNDWKLD-ATDNFCQNSH<LHI*ESVK*SLDRKKLKQLYN

Parental  RYKDPQDENKIGIDGIQQFCDDLALDPASISVLIIAWK-FRAATQCEFSKQEFMDGMTELGCDSIEKLKA
          RYK.PQDEN.IGIDG.QQFCDDLAL.PASISVLIIAW..FRAATQCEFSKQEFMDGMTELGCD..EKLKA
Retrocopy RYKVPQDENTIGIDGTQQFCDDLALNPASISVLIIAWG<FRAATQCEFSKQEFMDGMTELGCDNTEKLKA

Parental  QIPKMEQELKEPARFKDFYQFTFNFAKNPGQKGLDLEMAIAYWNLVLNGRFKFLDLWNKFLLEHHKRSIP
          Q..K.EQELKEP..F.DF.QFTFNFAKN.GQKGLDLEMAI.Y.N.VL.GR.KFLDLWN.FLLEHHKRSIP
Retrocopy QKSKTEQELKEPE*FNDF*QFTFNFAKNLGQKGLDLEMAISY*NSVLSGRYKFLDLWNNFLLEHHKRSIP

Parental  KDTWN-LLLDFSTMIADDMSNYDEEGAWPVLIDDFVEFARPQIAGTKSTTV
          KD.WN.LL.D.STMIADDM.NYDEEGAWPVLIDDFVE.A.PQ.AGTK.TTV
Retrocopy KDIWN>LL-DLSTMIADDMPNYDEEGAWPVLIDDFVECAHPQTAGTKCTTV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP051959_colon	0.60 RPM	31.95 RPM
SRP051959_heart	0.51 RPM	27.40 RPM
SRP051959_kidney	0.53 RPM	32.37 RPM
SRP051959_liver	0.45 RPM	27.16 RPM
SRP051959_lung	0.99 RPM	28.06 RPM
SRP051959_lymph_node	1.07 RPM	24.06 RPM
SRP051959_skeletal_muscle	0.28 RPM	30.38 RPM
SRP051959_spleen	0.67 RPM	30.36 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2358 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2358 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2358 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
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 ,
Callithrix jacchus	ENSCJAG00000018601	1 retrocopy	retro_cjac_3959,
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,