RetrogeneDB ID: retro_cjac_3801

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01202197.1:2..271(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000019733
• Aliases: None
• Description: None

Sequence

>retro_cjac_3801
GGGGGCAACCTTGGGGAGAAACAAAATGTTCTCCTCTCCAGAAAAGGGGCGAGAGACACAGACCCAACCCCAACGGCTCT
CGGCCCAGGGGACTAAACTAGGTCAGTCGTCCCTGTTCAACGAGTCGGAAACCAGAGCAGCAGCTCGGACTCGGAGGTGG
AGAGGCGCCGCAGCCCGCTCGGGACACTTTCCAGAAGCCGTGGGACTATTTCGCTCAAGTGAGAGCCCCAGGACGGCGCG
TTCTTAAAGGACTCTCCTACCCTGGGTAC

Alignment

ORF - retro_cjac_3801 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.1 %
• Parental protein coverage: 61.04 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GDDLGANDELI-PFQDEGGEEQEPSSDSASAQRDLDEV-KSSLVNESE-NQSSSSDSEAERR-PQPARDT
          G..LG.......P.Q..G..E........S..R.L..V..SSL.NESE.NQSSSSDSE.ERR.PQPARDT
Retrocopy GGNLGEKQNVL<PLQKRG--ERHRPNPNGSRPRGLN*V<QSSLFNESE<NQSSSSDSEVERR<PQPARDT

Parental  FQKPRDYFAEVRRPQDGAFFKGPPYPGY
          FQKP.DYFA.VR.P......KG..YPGY
Retrocopy FQKPWDYFAQVRAP-GRRVLKGLSYPGY

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	0.07 RPM
SRP051959_heart	0.00 RPM	0.56 RPM
SRP051959_kidney	0.00 RPM	0.16 RPM
SRP051959_liver	0.00 RPM	0.32 RPM
SRP051959_lung	0.00 RPM	0.28 RPM
SRP051959_lymph_node	0.00 RPM	0.16 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.26 RPM
SRP051959_spleen	0.00 RPM	0.40 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3801 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3801 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3801 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019733	2 retrocopies	retro_cjac_371, retro_cjac_3801 ,