RetrogeneDB ID: retro_cjac_3539

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01183636.1:4960..5187(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000017243
• Aliases: None
• Description: None

Sequence

>retro_cjac_3539
TTGTTTTAAAGATGGAGTCTCACTCTGTTATACAGGCTGGAGTGTAGTGGCACAATCTTGGCTCACTACAACTTACACTT
CCCAAGTTCAAGTAGTTCTCCTGCCTCAGCCTCCTGAGTAGCTGGAATTCCAAATACTACCACCATACCCAGCTAATTTT
TTTTTTTTTTTTTTTTTTTTGTATTTTTAGTAGAGACAGTGTTTCACTATCTTGGCCACGCTGGTCT

Alignment

ORF - retro_cjac_3539 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.44 %
• Parental protein coverage: 72.73 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LFLRWSLTLSPKLECSGTILAHCNLRLQGSSDSPASASQVAGITGTR-HHAWLIFISYW----LHRNGVS
          LF.RWSLTL...LECSGTILAH.NL....SS.SPASAS.VAGI..T..HH..LIF..........R..VS
Retrocopy LF*RWSLTLLYRLECSGTILAHYNLHFPSSSSSPASAS*VAGIPNTT<HHTQLIFFFFFFFCIFSRDSVS

Parental  LYCPGWS
          L..P.WS
Retrocopy LSWPRWS

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	0.02 RPM
SRP051959_heart	0.00 RPM	0.00 RPM
SRP051959_kidney	0.04 RPM	0.02 RPM
SRP051959_liver	0.02 RPM	0.00 RPM
SRP051959_lung	0.02 RPM	0.02 RPM
SRP051959_lymph_node	0.05 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.00 RPM
SRP051959_spleen	0.02 RPM	0.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3539 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3539 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3539 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017243	14 retrocopies	retro_cjac_3381, retro_cjac_3429, retro_cjac_3433, retro_cjac_3484, retro_cjac_3486, retro_cjac_3498, retro_cjac_3539 , retro_cjac_3551, retro_cjac_3593, retro_cjac_3642, retro_cjac_3714, retro_cjac_3722, retro_cjac_3765, retro_cjac_3800,
Callithrix jacchus	ENSCJAG00000033715	2 retrocopies	retro_cjac_3382, retro_cjac_3516,
Callithrix jacchus	ENSCJAG00000036730	3 retrocopies	retro_cjac_3670, retro_cjac_3747, retro_cjac_3777,