RetrogeneDB ID: retro_cjac_3551

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01184246.1:10836..11064(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000017243
• Aliases: None
• Description: None

Sequence

>retro_cjac_3551
TTATTATTGAGATGGGGTCTCACTCTGTCACTCAGGCTGGAGTGCAGTGGCACAGTCATGGTCACCACAGCCTTGACCTC
CAGGGTCAAGTGATCTTCAGCCTCAGCCTCCTAAAGAGCTGGAACTACAGGTGCATGCCACCATACTTGGCTAATTTTTT
AATTTTAATTTTAATTTGGTAGAGATGGGGTCTCACTGTGTTGCCTAGGTTGGTATGGAACTCCTCAG

Alignment

ORF - retro_cjac_3551 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.5 %
• Parental protein coverage: 76.77 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LFLRWSLTLSPKLECSGTIL-AHCNLRLQ-GSSD-SPASASQVAGITGTRHHAWLIF-ISYWLHRNGVSL
          L.LRW.LTLS..LECSGT....H..L.LQ.GSSD.S.ASAS..AG.TG..HH.WLIF.......R.GVSL
Retrocopy LLLRWGLTLSLRLECSGTVM<GHHSLDLQ<GSSD<SSASAS*RAGTTGACHHTWLIF*F*F*FGRDGVSL

Parental  YCPGWSAMAQ
          .C.GW....Q
Retrocopy CCLGWYGTPQ

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	0.11 RPM	0.02 RPM
SRP051959_heart	0.05 RPM	0.00 RPM
SRP051959_kidney	0.00 RPM	0.02 RPM
SRP051959_liver	0.02 RPM	0.00 RPM
SRP051959_lung	0.05 RPM	0.02 RPM
SRP051959_lymph_node	0.05 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.02 RPM	0.00 RPM
SRP051959_spleen	0.11 RPM	0.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3551 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3551 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3551 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017243	14 retrocopies	retro_cjac_3381, retro_cjac_3429, retro_cjac_3433, retro_cjac_3484, retro_cjac_3486, retro_cjac_3498, retro_cjac_3539, retro_cjac_3551 , retro_cjac_3593, retro_cjac_3642, retro_cjac_3714, retro_cjac_3722, retro_cjac_3765, retro_cjac_3800,
Callithrix jacchus	ENSCJAG00000033715	2 retrocopies	retro_cjac_3382, retro_cjac_3516,
Callithrix jacchus	ENSCJAG00000036730	3 retrocopies	retro_cjac_3670, retro_cjac_3747, retro_cjac_3777,