RetrogeneDB ID: retro_cjac_3478

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01181319.1:4154..4444(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000015697
• Aliases: None
• Description: None

Sequence

>retro_cjac_3478
TCCTCGGCATCCCTCTGTCCCAGCCACAGCTCAGGACACCCCTCTGCAGGAACAAGCCTGGTGGGCTGCCTGGAACCTGG
ACCCGTCTAGCGGCCGCCCTGCTGCTGCTGGCTGTGGGCTGCTTCCTGGCCATGTGGCAGCTCCAGCATCAAGGCAGCCC
GACAGGAAGACTGGGCTCCATGGCCCCTCCACCCAGCGGACACTCCCATGGCCCTGGCATTTAACATCACGGTGCCATCA
TCAACCCTGCAGGTCAATCATGCTGGCAGCGGCTCGGGGGAGGGAGGGTC

Alignment

ORF - retro_cjac_3478 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 68.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TSEALVPNPWRPQDSSG-NKAGGLPGTWARLVAALLLLAMGCFLAMWQLQHQGSPTGGLGSMAPPPSGHS
          .S..L.P.......S.G.NK.GGLPGTW.RL.AALLLLA.GCFLAMWQLQHQGSPTG.LGSMAPPPSGHS
Retrocopy SSASLCPSHSSGHPSAG<NKPGGLPGTWTRLAAALLLLAVGCFLAMWQLQHQGSPTGRLGSMAPPPSGHS

Parental  HGPGVYHHGAIISPAGQAWSCLLPGGNV
          HGPG..HHGAII.PAGQ.....L.GG.V
Retrocopy HGPGI*HHGAIINPAGQSCWQRLGGGRV

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	0.04 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_3478 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3478 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3478 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015697	1 retrocopy	retro_cjac_3478 ,