RetrogeneDB ID: retro_cjac_1330

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:30641822..30642037(+)
• Located in intron of: ENSCJAG00000007622

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFB1
• Ensembl ID: ENSCJAG00000018067
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 1, 7kDa [Source:HGNC Symbol;Acc:7695]

Sequence

>retro_cjac_1330
TTGGGGTCTCCGGTCTCTGTTGCCACTGGACCTGCAGCGATCATGGTGAGCTTCCTTCAACTGTGTGGGACCAATGGGTT
CTTCCTTTTGCTCCTATGGGATTTATCCTTGGATGTTATCTTGACAGAAAGAATGATGAAAATCTAACTGCCTTCTGGAA
CAAGAGTATGTAAGATAAAAGGGAATTGAGACCCAATGAAGTATGTACCTGGAAG

Alignment

ORF - retro_cjac_1330 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.08 %
• Parental protein coverage: 67.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LGVPVAVATGPAAIMVNFLQL-LRDQWVVLFVPMGFVLGCYLDRKNDEKLTAFRNKSMLYKRELRPNEEY
          LG.PV.VATGPAAIMV.FLQL...DQWV..F.PMGF.LGCYLDRKNDE.LTAF.NKSM..KRELRPNE..
Retrocopy LGSPVSVATGPAAIMVSFLQL<VWDQWVLPFAPMGFILGCYLDRKNDENLTAFWNKSM*DKRELRPNEVC

Parental  TWK
          TWK
Retrocopy TWK

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	9.61 RPM
SRP051959_heart	0.02 RPM	23.71 RPM
SRP051959_kidney	0.00 RPM	19.21 RPM
SRP051959_liver	0.00 RPM	16.57 RPM
SRP051959_lung	0.02 RPM	7.58 RPM
SRP051959_lymph_node	0.11 RPM	9.29 RPM
SRP051959_skeletal_muscle	0.00 RPM	33.59 RPM
SRP051959_spleen	0.27 RPM	11.01 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1330 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1330 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1330 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014837	1 retrocopy	retro_amel_1060,
Callithrix jacchus	ENSCJAG00000018067	5 retrocopies	retro_cjac_1027, retro_cjac_1053, retro_cjac_1330 , retro_cjac_2586, retro_cjac_3294,
Homo sapiens	ENSG00000183648	2 retrocopies	retro_hsap_2646, retro_hsap_311,
Macaca mulatta	ENSMMUG00000022428	2 retrocopies	retro_mmul_1520, retro_mmul_538,
Nomascus leucogenys	ENSNLEG00000017129	1 retrocopy	retro_nleu_652,
Ochotona princeps	ENSOPRG00000012731	2 retrocopies	retro_opri_22, retro_opri_992,
Pongo abelii	ENSPPYG00000006076	1 retrocopy	retro_pabe_2325,
Pan troglodytes	ENSPTRG00000006649	2 retrocopies	retro_ptro_1782, retro_ptro_253,
Pteropus vampyrus	ENSPVAG00000015319	1 retrocopy	retro_pvam_642,
Tursiops truncatus	ENSTTRG00000008130	2 retrocopies	retro_ttru_1515, retro_ttru_830,
Vicugna pacos	ENSVPAG00000003502	2 retrocopies	retro_vpac_257, retro_vpac_39,