RetrogeneDB ID: retro_cjac_3394

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01177894.1:6662..6863(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000032772
• Aliases: None
• Description: None

Sequence

>retro_cjac_3394
CACATCCTCCCCAGCTCACACACAGGCACACACACGTGCACACACATACATACACATGCACACGCACACATACACATGTG
TGGCACACATGCACATGCACACACACACAAATGCCCTCACACGTGTACACACACATGCACATGTGCACACATGCACATGC
ACATAAACGCACACACACATGCACATGCACTCACACACACA

Alignment

ORF - retro_cjac_3394 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.73 %
• Parental protein coverage: 63.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HTCMHALTHADTPTHIHTHAHVKPLTTYTHVHAHTHTNTCTHTHKHTCTHMHAHTHAHIHAHARTHT
          H......T...T.THIHTHAH.......TH.HAHTH....T.TH..TC.HMH.H..AH.HAHA.THT
Retrocopy HILPSSHTGTHTCTHIHTHAHAHIHMCGTHAHAHTHKCPHTCTHTCTCAHMHMHINAHTHAHALTHT

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	0.88 RPM
SRP051959_kidney	0.00 RPM	0.27 RPM
SRP051959_liver	0.00 RPM	0.00 RPM
SRP051959_lung	0.00 RPM	0.13 RPM
SRP051959_lymph_node	0.00 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.02 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_3394 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3394 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3394 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000032772	1 retrocopy	retro_cjac_3394 ,