RetrogeneDB ID: retro_cjac_1423

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:86934650..86935294(-)
• Located in intron of: None

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_1423
AACAAGTTGAAATAATCGCAGAAGGGTAAAGTTCATCAGTTAATGATCTTAACACAGTCTAGTGAAAAAACAGCAGTAAG
TCGTCTATCTCTAAATGACTGGCAGTGAGATGTTGCAACTGATAATTTCTTTCAAAATCCTGAGCTCTGTATATGAGAGA
GTGTAAAATGATCATTGGACAGGAAGATGTCAGAACAACTGACAATAGGTACAAACGTTCTCAAGATGAGAATGAAATTG
GAGTAGATGGTGTGCAGCAGTTCTACGATGACCTGGCACTCGATCCAGCCAGGATTAGTGTGTTGATTATTACATGGAAG
TTCACAGCAGCAATGCAGTGTGAGTTCTCCAAACAGGGGTTCATGGGTGGCATGACAGAAGAAGGACGTGACAGCATAGA
AAAACTAGAGGCCTAGATAACCAAGATGGAAGAAGAATTGAAAGAACCAGGAGAATTTAAGGATTTTTAATAGTTTACTT
TTAATTTTGCAAAGAATCCAGGACAAAAAGGATTAGATCTAGAAATGGTCATTGCATGCTGGAACTTAGTGCAGGATGGA
AAATTTAAGTTCTTAGAATTATGAAATAAATTTTTGTTGGAACATCATAAACGATCAATACCAAAAGATACTTGGAATCT
TCTT

Alignment

ORF - retro_cjac_1423 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.17 %
• Parental protein coverage: 83.33 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NKLKSSQKDKVRQFMIFTQSSEKTAVSCLSQNDWKLDVATDNFFQNPELYIRESVKGSLDRKKLEQLY-N
          NKLK.SQK.KV.Q.MI.TQSSEKTAVS.LS.NDW..DVATDNFFQNPEL.I.ESVK.SLDRK..EQL..N
Retrocopy NKLK*SQKGKVHQLMILTQSSEKTAVSRLSLNDWQ*DVATDNFFQNPELCI*ESVK*SLDRKMSEQLT<N

Parental  RYKDPQDENKIGIDGIQQFCDDLALDPASISVLIIAWKFRAATQCEFSKQEFMDGMTELGCDSIEKLKAQ
          RYK..QDEN.IG.DG.QQF.DDLALDPA.ISVLII.WKF.AA.QCEFSKQ.FM.GMTE.G.DSIEKL.A.
Retrocopy RYKRSQDENEIGVDGVQQFYDDLALDPARISVLIITWKFTAAMQCEFSKQGFMGGMTEEGRDSIEKLEA*

Parental  IPKMEQELKEPARFKDFYQFTFNFAKNPGQKGLDLEMAIAYWNLVLNGRFKFLDLWNKFLLEHHKRSIPK
          I.KME.ELKEP..FKDF..FTFNFAKNPGQKGLDLEM.IA.WNLV..G.FKFL.L.NKFLLEHHKRSIPK
Retrocopy ITKMEEELKEPGEFKDF**FTFNFAKNPGQKGLDLEMVIACWNLVQDGKFKFLEL*NKFLLEHHKRSIPK

Parental  DTWNLL
          DTWNLL
Retrocopy DTWNLL

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	0.00 RPM	31.95 RPM
SRP051959_heart	0.00 RPM	27.40 RPM
SRP051959_kidney	0.00 RPM	32.37 RPM
SRP051959_liver	0.00 RPM	27.16 RPM
SRP051959_lung	0.00 RPM	28.06 RPM
SRP051959_lymph_node	0.00 RPM	24.06 RPM
SRP051959_skeletal_muscle	0.00 RPM	30.38 RPM
SRP051959_spleen	0.00 RPM	30.36 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1423 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1423 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1423 has 0 orthologous retrocopies within eutheria group .

---

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,