RetrogeneDB ID: retro_cjac_3003

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:88966135..88966333(-)
• Located in intron of: ENSCJAG00000004690

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000010726
• Aliases: None
• Description: None

Sequence

>retro_cjac_3003
ATGGATAGCAGCCATGTGCAGCCTGTCAAGTTGGCCAGGGTCACCAAGGTCCTGGGCAGGACCCGTTCTCAGTGCACGCA
GGTGCGCATGGAATTTATGGACGACATGAGCTGCTCCAGCATCCGCAATGTAAAAGGCCCCGTGCGCAAGGGCGACTTGC
TGACCCTGTTGGAGTCCCAGCGAGAGGCCCGGAGGTTA

Alignment

ORF - retro_cjac_3003 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.88 %
• Parental protein coverage: 98.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDTSRVQPIKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLESEREARRL
          MD.S.VQP.KLARVTKVLGRT.SQ..CTQVR.EFMDD.S.S.IRNVKGPVR.GD.LTLLES.REARRL
Retrocopy MDSSHVQPVKLARVTKVLGRTRSQ--CTQVRMEFMDDMSCSSIRNVKGPVRKGDLLTLLESQREARRL

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	0.07 RPM	50.76 RPM
SRP051959_heart	0.02 RPM	58.23 RPM
SRP051959_kidney	0.35 RPM	57.99 RPM
SRP051959_liver	0.00 RPM	66.82 RPM
SRP051959_lung	0.02 RPM	73.66 RPM
SRP051959_lymph_node	0.02 RPM	99.04 RPM
SRP051959_skeletal_muscle	0.02 RPM	84.05 RPM
SRP051959_spleen	0.00 RPM	83.51 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3003 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3003 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3003 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010726	12 retrocopies	retro_cjac_1404, retro_cjac_1744, retro_cjac_1893, retro_cjac_195, retro_cjac_23, retro_cjac_2516, retro_cjac_2582, retro_cjac_3003 , retro_cjac_339, retro_cjac_4170, retro_cjac_551, retro_cjac_715,
Gorilla gorilla	ENSGGOG00000024725	2 retrocopies	retro_ggor_1052, retro_ggor_95,