RetrogeneDB ID: retro_cjac_3637

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01191139.1:2684..3020(+)
• 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_3637
GAAAGAAAGAAAACAGAAGAAGGAAGGAAGGAAGAAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGA
AGGAAGGAAAAAAGGAAGGAAAAAAGGAAGGAAAAAAGGAAGGAAAAAAGGAAGGAAAGAAGGAAGGAAGGAAGGAAGGA
AGGAGGGAAGAAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAAAAAGGAAGGAAAAAAGGAAGGA
AAGAAGGAAGGAAGGAAGGAAGGAAGGAGGGAAGGAAGGAAGGAAGGAAGGAGGGAAGGAAGGAAGGAAGGAAGGAAGGA
AGGAAGGAAGACAGGC

Alignment

ORF - retro_cjac_3637 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.83 %
• Parental protein coverage: 69.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ERGRKEGGREREGEEGKREGRREGGKEGRKKERKRER-EREKERERERERERERE-ERKERKRKKERKRK
          ER...E.GR..E..EG..EGR.EG.KEGRKK.RK..R.E..KE...ER..E...E..R.ERK......RK
Retrocopy ERKKTEEGRKEERKEGRKEGRKEGRKEGRKKGRKKGR<EKRKEKRKERRKEGRKE<RREERKEGRKEGRK

Parental  EGRKEGKRERERER-KEGRKEGRFEEERKEGRKEGRKEGRKEGRKEG
          EGRKE...E...ER.KEGRKEGR..E.RKEGR.EGRKEGRKEGRK.G
Retrocopy EGRKEKRKEKRKER<KEGRKEGR-REGRKEGRREGRKEGRKEGRKTG

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	0.00 RPM
SRP051959_kidney	0.00 RPM	0.00 RPM
SRP051959_liver	0.00 RPM	0.00 RPM
SRP051959_lung	0.00 RPM	0.00 RPM
SRP051959_lymph_node	0.00 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_3637 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3637 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3637 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,