RetrogeneDB ID: retro_cjac_819

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:126268718..126268942(-)
• Located in intron of: ENSCJAG00000016951

Retrocopy information

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

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_819
ATGCCAAAGAGAAAGTCTCCAAAGAATGCAGAGGGCAAAGATGGATCGAAAGTAACTAACAGGAGCCCACAAGATGGTCT
GCCAGATTGTCAGCGAAACCTGCTCCACCAAAACCTGAACCCAAACCAAGAAACACATCTGCTAAGAAAGAACCTGGAGC
AAAGATTAGCAGAGGTGCTAAAGGGAAGAAGGAGGAAAAGCAGGAAGCTGGAAAGGAAGGCACA

Alignment

ORF - retro_cjac_819 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.42 %
• Parental protein coverage: 75.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPKRKSPENAEGKDGSKVTK-QEPTRRSARLSAKPAPPKPEPKPRKTSAKKEPGAKISRGAKGKKEEKQE
          MPKRKSP.NAEGKDGSKVT..QEPTR.SARLSAKPAPPKPEPKPR.TSAKKEPGAKISRGAKGKKEEKQE
Retrocopy MPKRKSPKNAEGKDGSKVTN<QEPTRWSARLSAKPAPPKPEPKPRNTSAKKEPGAKISRGAKGKKEEKQE

Parental  AGKEGT
          AGKEGT
Retrocopy AGKEGT

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	0.16 RPM	3.66 RPM
SRP051959_heart	0.25 RPM	29.94 RPM
SRP051959_kidney	0.09 RPM	19.24 RPM
SRP051959_liver	0.26 RPM	11.78 RPM
SRP051959_lung	0.20 RPM	7.69 RPM
SRP051959_lymph_node	0.11 RPM	3.20 RPM
SRP051959_skeletal_muscle	0.00 RPM	9.30 RPM
SRP051959_spleen	0.17 RPM	10.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_819 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_819 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_819 has 0 orthologous retrocopies within eutheria group .

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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,