RetrogeneDB ID: retro_cjac_3106

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:1648077..1648664(-)
• Located in intron of: ENSCJAG00000009008

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000034550
• Aliases: None
• Description: None

Sequence

>retro_cjac_3106
TGTGTGCACGTGCATGTGTGCATGTGTGCCTGCGTGTGTGTGTGTGCGTGCGTGTGTGCACGTGTTGTGTGCGTGTGTGC
GTGCATGTGTGCATGTGTGCGTGCGTGTCTGTGTGCGTGTGTGCGTGCGTGTGTTCACGTGTTGTGTGCTTGTGCGTGCG
TGTGTGCATGTGTGTGTGCGCGTGCGTGTGTGTCTGTGTTGTGCGTGTGCATGTGCACGTGCGTGTGTGCATGTGTGCGT
GCGTGTGTGTCTGTGTGTGTGTGTGCGTGCGTGCACGTGTTGTGTGCGTGTGCGTGCGTGTGCATGTGTGCGTCTGTGTG
TGTGCATGTGTGCACGTGCGTGTGTGCATGTGTGCATGCATGTCTGTGTGTGTGTGTGTGCGTGCGTGTGTGCACGTGTT
GTGTGCGTGTGTGCACGTGTTGTGTGCGTGTGTCTGTGTGTGCGTGCGTGTGCGTGTGTGCATGTGTGCACGTGCGTGTG
CATGTGTGCGTGCATGTGTGTGCGTGTGCGCATGTGTGCGTGCGTGTCTGTGTGTGTGCATGTGTGCGTGCGTGTGTCTG
TGTGCGTGTGTGCACGTGTGTGTGTGC

Alignment

ORF - retro_cjac_3106 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.63 %
• Parental protein coverage: 99.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  CVCVCVCVCVCVCLCVCVCVSVSVCVCVCVCVCVSVCVCVCVCVCVSVC-VSVCVSVCVCLCECVCLCV-
          CV.V.VC.C.CVC.C.CVC..V.VCVC.C.C.CV..C.C.CV..CV.V..V..CV.VC.C.C.CVC.CV.
Retrocopy CVHVHVCMCACVCVCACVCARV-VCVCACMCACVRACLCACVRACVHVL<VCLCVRVCMCVCACVCVCV>

Parental  CVCVCVCVCVCVLCVCVLNVCACMCVSVIGVSVCECECMCFCM-MCEHVCVCICVCAYVCICVNVCL--L
          CVC.C.CVC.CV...CV..VC.C.CV.V.....C.C.C...C...C.HV.VC.C.C..VC.CV..C...L
Retrocopy CVCMCTCVCACVRA-CV-SVCVCACVHVLCACACVCMCASVCV<ACVHVRVCMCACMSVCVCVRACVHVL

Parental  CACV---CVCVCVCDRVCVCTCMSVCICAACVRVCVCKCVCVYLYMCVCICTCVCACVYMHVYVC
          CACV...C.CVCVC.RV.VC.C...C.C...VR.CVC.C.CV....CVC.C.CVC.C...HV.VC
Retrocopy CACVHVLCACVCVCVRVRVCMCARACAC---VRACVCVCACVRACLCVCMCACVCLCACVHVCVC

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	0.02 RPM	0.00 RPM
SRP051959_heart	0.00 RPM	0.00 RPM
SRP051959_kidney	0.00 RPM	0.02 RPM
SRP051959_liver	0.00 RPM	0.02 RPM
SRP051959_lung	0.05 RPM	0.00 RPM
SRP051959_lymph_node	0.05 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_3106 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3106 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3106 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	ENSCJAG00000034550	1 retrocopy	retro_cjac_3106 ,