RetrogeneDB ID: retro_cjac_3981

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286464.1:53172..53322(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000032565
• Aliases: None
• Description: None

Sequence

>retro_cjac_3981
CTTTGTAGGCCCTAAGCTTCCTCAAGTGGAGATTTCCAGGCCTACTTTCTGCCTCCCAGTGGCCTTGACAAGCCCAGCTC
TGGCCTCCCTGCAGCCTCCCCAGGACCAGCTGCTGCCTGGCAGTGGTTTCCCCAGGCCAAGTTCCTGCCT

Alignment

ORF - retro_cjac_3981 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.82 %
• Parental protein coverage: 80.95 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLRTQTASSQALQAHLLPPSGLDKPSSYWPAAASAGPAPASQWPLQAQLIP
          L.R....SS...QA..LPPSGLDKPSS..P.AAS.GPA.A.QW..QA...P
Retrocopy LCRP*ASSSGDFQAYFLPPSGLDKPSSGLP-AASPGPAAAWQWFPQAKFLP

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	0.00 RPM
SRP051959_heart	0.00 RPM	0.00 RPM
SRP051959_kidney	0.00 RPM	0.00 RPM
SRP051959_liver	0.00 RPM	0.00 RPM
SRP051959_lung	0.00 RPM	0.02 RPM
SRP051959_lymph_node	0.00 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.00 RPM
SRP051959_spleen	0.00 RPM	0.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3981 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3981 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3981 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000032565	2 retrocopies	retro_cjac_2871, retro_cjac_3981 ,
Gorilla gorilla	ENSGGOG00000027883	1 retrocopy	retro_ggor_2012,
Pongo abelii	ENSPPYG00000019993	5 retrocopies	retro_pabe_1730, retro_pabe_3198, retro_pabe_3218, retro_pabe_3220, retro_pabe_3562,