RetrogeneDB ID: retro_cjac_2302

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:187504803..187505062(-)
• Located in intron of: ENSCJAG00000014023

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000001349
• Aliases: None
• Description: None

Sequence

>retro_cjac_2302
AGTTGGCGAGGAAGATCAGCATATAGGCTTAGACCTAGAGGTCGGTCTCTGCAGCCTCCTGAGCTGCCTGGGCCTGTGCT
CGAGCCAGTGATGAACAGCCTCAGCAAGAGGCACCGCTGCCGGAAAGACAGGGCCCCGCCCCCGGCCAGGAGAGAGAGAA
GGACCCGGTGCTGCTGAGAGGCTCACGCTTGACTGGGAAGCGGATCTCGGGAGCCACCTCCAAGACTGGGATGAATGCAG
AGGAGGTCCTGGTGTCCGG

Alignment

ORF - retro_cjac_2302 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.75 %
• Parental protein coverage: 79.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SWRGRSTYR--PRPRSLQPPELTGTMLEP-SVEEPEEEKPPTESRDPTPDQKREDD-QGVAEIQVPDLEA
          SWRGRS.YR..PR.RSLQPPEL.G..LEP.S.E.P..E.P..E...P.P.Q.RE.D..G.AE....D.EA
Retrocopy SWRGRSAYRLRPRGRSLQPPELPGPVLEP<SDEQPQQEAPLPERQGPAPGQEREKD<PGAAERLTLDWEA

Parental  DLQELCQSKTGGECGDGPDVK
          DL....Q.....EC..GP.V.
Retrocopy DLGSHLQD--WDECRGGPGVR

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	0.00 RPM
SRP051959_heart	0.09 RPM	0.00 RPM
SRP051959_kidney	0.00 RPM	0.00 RPM
SRP051959_liver	0.00 RPM	0.04 RPM
SRP051959_lung	0.03 RPM	0.15 RPM
SRP051959_lymph_node	0.05 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.02 RPM	0.00 RPM
SRP051959_spleen	0.04 RPM	0.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2302 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2302 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2302 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_2422

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001349	1 retrocopy	retro_cjac_2302 ,
Nomascus leucogenys	ENSNLEG00000008241	1 retrocopy	retro_nleu_2846,