RetrogeneDB ID: retro_cjac_2666

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:130451175..130451413(-)
• Located in intron of: ENSCJAG00000013483

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000032817
• Aliases: None
• Description: None

Sequence

>retro_cjac_2666
ACACATATACCAACACACCTACACATGCACACACATACACCTACACATATGTACAACACACACGCACACACACCTACATA
CAGACATGCCTACATATATGAAACACACATGCACACACACTAACACACACCTACATACATGCAGCCACACATGCATACAT
ACTGACACACACCTACACATGTGCTCACACCTACATACCAAGACATACCTACACAGGCACACACATACCAACACACAC

Alignment

ORF - retro_cjac_2666 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.57 %
• Parental protein coverage: 75. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  THADTHLHTLHTCLHTPTHTY-TQTRTHLHTHADTQTRPHTCTDTSTCTHAQTHR--HAQTHLHTCTHRH
          TH..THLH..HT..HTPTH.Y.T.T.THLHT...T....HTCT.T.T..H...H...H..THLH.C.H.H
Retrocopy THIPTHLH-MHT--HTPTHMY>THTHTHLHTDMPTYMK-HTCTHTNTHLHTCSHTCIHTDTHLHMCSHLH

Parental  THRHRHRHIHTHAH
          T....HRH.HT..H
Retrocopy TKTYLHRHTHTNTH

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	0.09 RPM
SRP051959_heart	0.00 RPM	0.40 RPM
SRP051959_kidney	0.00 RPM	0.07 RPM
SRP051959_liver	0.00 RPM	0.00 RPM
SRP051959_lung	0.02 RPM	0.52 RPM
SRP051959_lymph_node	0.00 RPM	0.05 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.13 RPM
SRP051959_spleen	0.00 RPM	0.02 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2666 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2666 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2666 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000032817	1 retrocopy	retro_cjac_2666 ,