RetrogeneDB ID: retro_cjac_3728

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01197316.1:601..961(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000010339
• Aliases: None
• Description: None

Sequence

>retro_cjac_3728
AAAGAGGGAAGGAAGGAAAGGAAGGGAAAGAAGGGAGAGAAGGAAGGGAAGGGCGGGAATGGAAAAAAGGGAAGAAGGGA
GGGAGGGAGGGAGGGAAGGAAGGGAGGAAGAGGAAGGGAAGAAGGGAAGGAGGGAAGGAAGGAAGGAAAGGAAAGGAAGA
GAAGGAAGGGAAAAAGGGAAAGAAAGGAAGGAAGGAAGAAGGCAGGAAGGAGGAAGAGAAGGAAGGGAGGGAGGGAGGAA
GAGAGGGAGGGAAGGATGGAAGGAAGAAGGAAGGAGGAAGGAAATGAAGGCAGGAAGGAAAGGAAGGAAGGAAGGAAGGA
AGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA

Alignment

ORF - retro_cjac_3728 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.6 %
• Parental protein coverage: 73.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KEGRKGRERGRKEGGREREGEEGKREGRREGGKEGRKKERKREREREKERE-REREREREREERKE-RKR
          KEGRK..ER..K.G..E..G..GK..GRREGG.EGRK..R.RE...E...E..ER.R.....ERKE.RK.
Retrocopy KEGRK--ERKGKKGEKEGKGGNGKK-GRREGGREGRKGGRGREEGKEGRKEGKERKRRKGKRERKEGRKK

Parental  KKERKRKEGRKEGKRERERE--RKEGRKEGRFEEERKEGRKEGRKEGRKEGRKEG
          ...RKR..G..E..RE...E..RKE...EGR...ERKEGRKEGRKEGRKEGRKEG
Retrocopy AGRRKRRKGGREEEREGRMEGRRKEEGNEGR--KERKEGRKEGRKEGRKEGRKEG

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	0.00 RPM
SRP051959_heart	0.07 RPM	0.00 RPM
SRP051959_kidney	0.13 RPM	0.00 RPM
SRP051959_liver	0.04 RPM	0.00 RPM
SRP051959_lung	0.44 RPM	0.00 RPM
SRP051959_lymph_node	0.32 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.07 RPM	0.00 RPM
SRP051959_spleen	0.29 RPM	0.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3728 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3728 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3728 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010339	9 retrocopies	retro_cjac_1356, retro_cjac_2297, retro_cjac_2882, retro_cjac_3255, retro_cjac_3637, retro_cjac_3700, retro_cjac_3728 , retro_cjac_386, retro_cjac_420,