RetrogeneDB ID: retro_cjac_420

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:76441584..76441964(+)
• 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_420
AAAGGAAGGAGGGAGGAGGAAGGAGGAAGGGTGGGAGGGAGAGAAGAAAGGAAGGAAGAAAAGGAGGGAAGAATGGAAGG
AGGGAGGGAGGGAAGGAGGGAAACAGGGAAGGAAGGAAGAAAAAGAGAAGGAAAGAAGGAAGGAAGGAGGGAAGGAAGGA
AAAGAGAGAATGAAGGAAGGAGGAAGGAAGGGAGGGAAAAGGGAAGGAAGGAAGAGAGGGAAAGAGGGAAGGAAGGAAGA
AACGAAGGAGGGGAGAGGGAGGGAAAGAGGGAAAGGAGGGAGGGAGGAAGGGAGGAAAAGAGGAAGGAAGAAAGGAAAGA
GGAATAAAGGAAGAGAAAGAAGGAAGGAAGGAAGGGAGGGAAAGAGGGAAGAAAGAAGGT

Alignment

ORF - retro_cjac_420 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.71 %
• Parental protein coverage: 75.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EGGKEGRKGRERGRKEGGREREGE-EGKREGRREGGKEGRKKERKRERERE---KEREREREREREREER
          .G..E...GR..GR.E...E.EG..EG.REGRRE.GKEGRK.E.K.E..RE....E.E..R...RE....
Retrocopy KGRREEEGGRVGGREERKEEKEGRMEGGREGRRETGKEGRKREGKKEGRREGRKRENEGRRKEGREKGRK

Parental  KERKRKKERKRKEGRKEGKRER-ERERKEGRKEGRFEEERKEGRKEGRKEGRKEGRKEG
          .ER.R.KE.....G..EGKRER.E..RK.G..EGR.E...KE..KEGRKEGR..G.KEG
Retrocopy EERERGKEGRNEGGEREGKRER<EGGRKGGKEEGRKERGIKE-EKEGRKEGRERGKKEG

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_420 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_420 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_420 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 ,