RetrogeneDB ID: retro_cjac_655

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:201653581..201653956(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000004761
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NUDT3
• Ensembl ID: ENSCJAG00000015243
• Aliases: None
• Description: nudix (nucleoside diphosphate linked moiety X)-type motif 3 [Source:HGNC Symbol;Acc:8050]

Sequence

>retro_cjac_655
ATGATGAAGCTCAAGTCGAACCAGACCCGCACCTATGATGGCGATGGCTACAAGAAGCAGGCCGCATGCCTGTGTTTCCG
CAGCGAGAGCGAGGAGGAGGTGCTACTCGTGAGCAGTAGTTGCCATCCAGACAGGTGGATTGTCTCTGGAGGAGGCATGG
AGCCCCAGGAGGAGCCAAGTGTGGCAGCAGTTCGTGAAGTCTGTGAGGAGGCTGCAGTAAAAGGGACATTGGGAAGATTA
GTTGGAATTTTTGAGAACCGGGAGAGAAAGCACAGGACGTATGTCTATGTGCTCATTGTCACTGAAGTGCTGGAAGACTG
GGAAGACTCAGTGAACATTGGAAGGAAGAGGGAATGGTTTAAAATAGAAGACGCT

Alignment

ORF - retro_cjac_655 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.2 %
• Parental protein coverage: 72.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMKLKSNQTRTYDGDGYKKRAACLCFRSESEEEVLLVSSSRHPDRWIVPGGGMEPEEEPSVAAVREVCEE
          MMKLKSNQTRTYDGDGYKK.AACLCFRSESEEEVLLVSSS.HPDRWIV.GGGMEP.EEPSVAAVREVCEE
Retrocopy MMKLKSNQTRTYDGDGYKKQAACLCFRSESEEEVLLVSSSCHPDRWIVSGGGMEPQEEPSVAAVREVCEE

Parental  AGVKGTLGRLVGIFENQERKHRTYVYVLIVTEVLEDWEDSVNIGRKREWFKIEDA
          A.VKGTLGRLVGIFEN.ERKHRTYVYVLIVTEVLEDWEDSVNIGRKREWFKIEDA
Retrocopy AAVKGTLGRLVGIFENRERKHRTYVYVLIVTEVLEDWEDSVNIGRKREWFKIEDA

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	0.04 RPM	10.49 RPM
SRP051959_heart	0.07 RPM	12.17 RPM
SRP051959_kidney	0.07 RPM	11.96 RPM
SRP051959_liver	0.04 RPM	9.18 RPM
SRP051959_lung	0.07 RPM	15.16 RPM
SRP051959_lymph_node	0.09 RPM	14.79 RPM
SRP051959_skeletal_muscle	0.02 RPM	9.98 RPM
SRP051959_spleen	0.13 RPM	16.85 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_655 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_655 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_655 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015243	1 retrocopy	retro_cjac_655 ,
Otolemur garnettii	ENSOGAG00000034590	1 retrocopy	retro_ogar_646,