RetrogeneDB ID: retro_cjac_3718

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01196893.1:11..301(-)
• 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_3718
TTTTTCAAACGGAGTTTTGCTTTTGTTACCCAGGCTACACTGCAATGGTGCGATCTCAGCTCACGGCAACCTCTGCCTCC
CCAGGTTCAAGGGATTCTCCTGCCCCAGCCTCCCAGGTAGCTGGGATCACAGGCATGCACCACCATGCCCGGCTAATTTT
GTATTTTAGTAGAGACAGGGTTTATTCATATTGGTCAGGCTGGTCTTGAACTCCTGACCTCAGGTGATCTGCCTGCCTTG
GCCTCCCAAAGTGCTGGGATTACAGGTATGAGCCACCGCGCCTGGCCTTG

Alignment

ORF - retro_cjac_3718 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63. %
• Parental protein coverage: 97. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FFETGSHSVTQAGVQWRDLGSLQPPPPG-FKQFCCLSLPSSWDYRRAPPRPANF-CI-FSKDRVSSCWPG
          FF......VTQA..QW.DL.S.QP.PP..FK.F.C.SLP.SWD.R.APP.PANF.CI.FS.DRV.S.W.G
Retrocopy FFKRSFAFVTQATLQWCDLSSRQPLPPQ>FKGFSCPSLPGSWDHRHAPPCPANF<CI<FSRDRVYSYWSG

Parental  WSRSLDLRISGFLSLPKCWDYRREPPRPAI
          WS...DLR.S..L.LPKCWDYR.EPPR.A.
Retrocopy WS*TPDLR*SACLGLPKCWDYRYEPPRLAL

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	0.24 RPM	0.09 RPM
SRP051959_heart	0.16 RPM	0.58 RPM
SRP051959_kidney	0.20 RPM	0.09 RPM
SRP051959_liver	0.13 RPM	0.00 RPM
SRP051959_lung	0.31 RPM	0.21 RPM
SRP051959_lymph_node	0.37 RPM	0.11 RPM
SRP051959_skeletal_muscle	0.04 RPM	0.11 RPM
SRP051959_spleen	0.46 RPM	0.11 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3718 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3718 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3718 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,