RetrogeneDB ID: retro_cjac_1626

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 18:6526052..6526258(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000006453
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HMGN3
• Ensembl ID: ENSCJAG00000010800
• Aliases: None
• Description: high mobility group nucleosomal binding domain 3 [Source:HGNC Symbol;Acc:12312]

Sequence

>retro_cjac_1626
ATGCAGATGAGAAAGTCTCCGGAGAATACAGAGGGCAAAGACGGATCCAAGTAACTAAACAGGAGCCCAGAAAATTGTCT
TCCAGATTGTCAGCAAAACCTGCTCCACCGAAACCTGAACCCAAACCAAGAAAAATATCTGCTAAGAAAGAACCTGGAGC
AAAGCTTAGCAGAGGTGTTAAAGAGAAGAATGAAGGAAAGCTGGAA

Alignment

ORF - retro_cjac_1626 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.57 %
• Parental protein coverage: 69.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPKRKSPENAEGKDGSK-VTKQEPTRRSARLSAKPAPPKPEPKPRKTSAKKEPGAKISRGAKGKKEEKQE
          M..RKSPEN.EGKDGSK.VTKQEP...S.RLSAKPAPPKPEPKPRK.SAKKEPGAK.SRG.K.K.E.K.E
Retrocopy MQMRKSPENTEGKDGSK<VTKQEPRKLSSRLSAKPAPPKPEPKPRKISAKKEPGAKLSRGVKEKNEGKLE

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	3.66 RPM
SRP051959_heart	0.00 RPM	29.94 RPM
SRP051959_kidney	0.00 RPM	19.24 RPM
SRP051959_liver	0.02 RPM	11.78 RPM
SRP051959_lung	0.02 RPM	7.69 RPM
SRP051959_lymph_node	0.02 RPM	3.20 RPM
SRP051959_skeletal_muscle	0.00 RPM	9.30 RPM
SRP051959_spleen	0.04 RPM	10.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1626 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1626 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1626 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011031	1 retrocopy	retro_amel_1920,
Bos taurus	ENSBTAG00000001422	2 retrocopies	retro_btau_1524, retro_btau_1558,
Canis familiaris	ENSCAFG00000002809	1 retrocopy	retro_cfam_1013,
Choloepus hoffmanni	ENSCHOG00000007015	1 retrocopy	retro_chof_2241,
Callithrix jacchus	ENSCJAG00000010800	2 retrocopies	retro_cjac_1626 , retro_cjac_819,
Mustela putorius furo	ENSMPUG00000018092	1 retrocopy	retro_mputfur_1164,
Otolemur garnettii	ENSOGAG00000016487	1 retrocopy	retro_ogar_190,
Pongo abelii	ENSPPYG00000016791	1 retrocopy	retro_pabe_421,