RetrogeneDB ID: retro_cjac_2527

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:64991904..64992285(+)
• Located in intron of: ENSCJAG00000009042

Retrocopy information

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

Parental gene information

• Parental gene symbol: BRI3
• Ensembl ID: ENSCJAG00000015227
• Aliases: None
• Description: brain protein I3 [Source:HGNC Symbol;Acc:1109]

Sequence

>retro_cjac_2527
ATAGACCACGGGCTTCTGCTGCAGGAGTGGCTGCCCACCTACAACCTAGGGGCCGGCCAGGTCGACGGCGCGTGCAGCCC
GCATGGCTATGGTGCCATCTTGCTGCCCACCCCTTCCCACTGCCTGCCCTCCCCTTACCTCATCACAGGAATACCCACCC
ACCACCCCAGGGTCTACAATTGCCACAGCCGGACTATTACTCGGTACCCTGCCAATGCCATCATCATCATGGGAGGCTGT
CACGTCTGCAGGGTCGGGGTGCTGGAGGACTGCTTCACTTTCCTAGGAATCCTCCTGGCCATCATCCTGTTCCCCTTTGG
ATTCATCTGCTGATTTGCCTTGAGGAAGCAAAGATGCCCCAACTTCGGAGAAGACTTTGCT

Alignment

ORF - retro_cjac_2527 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.02 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDHKPLLQERPPAYNLEAGQGDYACGPHGYGAIPAAPPPP--PYPYLVTGIPTHHPRVYNIHSRTVTRYP
          .DH..LLQE..P.YNL.AGQ.D.AC.PHGYGAI....P....P.PYL.TGIPTHHPRVYN.HSRT.TRYP
Retrocopy IDHGLLLQEWLPTYNLGAGQVDGACSPHGYGAILLPTPSHCLPSPYLITGIPTHHPRVYNCHSRTITRYP

Parental  ANSIVVVGGCPVCRVGVLEDCFTFLGIFLAIILFPFGFICCFALRKRRCPNCGATFA
          AN.I...GGC.VCRVGVLEDCFTFLGI.LAIILFPFGFIC.FALRK.RCPN.G..FA
Retrocopy ANAIIIMGGCHVCRVGVLEDCFTFLGILLAIILFPFGFIC*FALRKQRCPNFGEDFA

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	9.98 RPM
SRP051959_heart	0.00 RPM	21.07 RPM
SRP051959_kidney	0.04 RPM	14.93 RPM
SRP051959_liver	0.00 RPM	20.95 RPM
SRP051959_lung	0.00 RPM	12.48 RPM
SRP051959_lymph_node	0.00 RPM	8.29 RPM
SRP051959_skeletal_muscle	0.00 RPM	23.28 RPM
SRP051959_spleen	0.00 RPM	17.65 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2527 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2527 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2527 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015227	1 retrocopy	retro_cjac_2527 ,
Homo sapiens	ENSG00000164713	3 retrocopies	retro_hsap_1095, retro_hsap_1811, retro_hsap_195,
Gorilla gorilla	ENSGGOG00000009646	1 retrocopy	retro_ggor_205,
Microcebus murinus	ENSMICG00000002888	1 retrocopy	retro_mmur_372,
Macaca mulatta	ENSMMUG00000013275	2 retrocopies	retro_mmul_1248, retro_mmul_849,
Otolemur garnettii	ENSOGAG00000000638	1 retrocopy	retro_ogar_63,
Pongo abelii	ENSPPYG00000025815	3 retrocopies	retro_pabe_1484, retro_pabe_50, retro_pabe_910,
Pan troglodytes	ENSPTRG00000019436	1 retrocopy	retro_ptro_698,
Tursiops truncatus	ENSTTRG00000015705	2 retrocopies	retro_ttru_706, retro_ttru_91,