RetrogeneDB ID: retro_cjac_3540

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01183655.1:2741..3039(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000037406
• Aliases: None
• Description: None

Sequence

>retro_cjac_3540
TTCTTTTTGATAATGTCTTGCTCTGTCACCCAGGCTGGAGTGCAGTGGCACAATCTCAGCTTACTACAACCTCCACCTCC
CGGGTTTAAGTGATTCTCCCACCTCAGCCTCCCAAGTAGTTGGGATTACAGGCACCCACAACCATGCCCTGCTCATTTTT
GTATTTTTGTAGAGACATGTTTTCACCATGTTGGCAAGGCTGGTCTTGACTACTAATCTCAGATCGTCTGCCTGCCTCAG
CCTCACAAAGTGCTGGGATTACAGGCATCAGCCACCATGCCCAGACAGTCTTATTCTT

Alignment

ORF - retro_cjac_3540 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.76 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FFETGSHSVTQAGVQWRDLGSLQPPPPGFKQFCCLSLPSSWDYRRAPPRPANFCI-FSKDRVSSCWPGWS
          FF...S.SVTQAGVQW..L..LQPPPPGFK.F..LSLPSSWDYR...P.PA.FCI.F..D..S.CW.GWS
Retrocopy FFLIMSCSVTQAGVQWHNLSLLQPPPPGFK*FSHLSLPSSWDYRHPQPCPAHFCI<FCRDMFSPCWQGWS

Parental  -RSLDLRISGFLSLPKCWDYRREPPRPAIIFL
          .....LR.S..LSL.KCWDYR..PP.P....L
Retrocopy <LTTNLRSSACLSLTKCWDYRHQPPCPDSLIL

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	0.09 RPM
SRP051959_heart	0.00 RPM	0.58 RPM
SRP051959_kidney	0.00 RPM	0.09 RPM
SRP051959_liver	0.00 RPM	0.00 RPM
SRP051959_lung	0.00 RPM	0.21 RPM
SRP051959_lymph_node	0.00 RPM	0.11 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.11 RPM
SRP051959_spleen	0.00 RPM	0.11 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3540 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3540 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3540 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000037406	10 retrocopies	retro_cjac_3399, retro_cjac_3402, retro_cjac_3421, retro_cjac_3540 , retro_cjac_3565, retro_cjac_3590, retro_cjac_3621, retro_cjac_3687, retro_cjac_3718, retro_cjac_3798,