RetrogeneDB ID: retro_cjac_3486

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01181589.1:9206..9479(+)
• 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_3486
TTGTTTTTAAGATGGTGTCTCACCATTGTCTCCCAGGCTAGAGTGCAATGGCATGATCTTGGCTCACTGCAACCTCCACG
CCTCCAGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTTAGTAGCTGGGATTACAGGTGTGTGCCACCACGCCTGGCTAAT
TTTATGTCTTTTTTTTTTTTTTTTTTTTTTAGTAGAGATGGGGTGTCACCATGTTGGTCAGGCTGGTCTCAAACTCCTGA
CCTTGTTATCTGCCCGCCTGGGCCTCCCAAAGT

Alignment

ORF - retro_cjac_3486 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.84 %
• Parental protein coverage: 90.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LFLRWSLT-LSPKLECSGTILAHCNLRLQ-GSSDSPASASQVAGITGTRHHAWLIFISYWLHRNGVSLYC
          LFLRW.LT.LSP.LEC.G.ILAHCNL....GSS.SPASAS.VAGITG..HHAWLI..........V...C
Retrocopy LFLRWCLT>LSPRLECNGMILAHCNLHAS>GSSNSPASASLVAGITGVCHHAWLILCLFFFFFFLVEMGC

Parental  PGWSAMAQSQLTATSA-AWIIQA
          ..........LT..SA.AW..Q.
Retrocopy HHVGQAGLKLLTLLSA>AWASQS

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	0.02 RPM
SRP051959_heart	0.00 RPM	0.00 RPM
SRP051959_kidney	0.00 RPM	0.02 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	0.02 RPM	0.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3486 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3486 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3486 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,