RetrogeneDB ID: retro_cjac_1382

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:19290576..19290799(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COA5
• Ensembl ID: ENSCJAG00000007139
• Aliases: None
• Description: cytochrome c oxidase assembly factor 5 [Source:HGNC Symbol;Acc:33848]

Sequence

>retro_cjac_1382
ATGCTCCAATACTATGAGGACAAGCTGGAGGGTGGCACATACGCATACCCGAAGGAAGACCTGGGCATGTGTCTACTGCT
GTCGGACTATGTGATCCAGGAAGGGAAATCCCCTCAGCGGTGTTTGAAGGAAGGATACTGCAAAGCTTTGAAATACTCAT
TTTTTTGAGGGTAAAAGATCAATGTTGGATACCAGGGTAAGATTCAGAGGAAGAAAAGGATAT

Alignment

ORF - retro_cjac_1382 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.33 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPQYYEDKPEGGACSGLREDLGLCLLQSDCVIQEGKSPRECLKEGYCKALKYSFF-ECKRSTLDTRARFR
          M.QYYEDK.EGG......EDLG.CLL.SD.VIQEGKSP..CLKEGYCKALKYSFF.E.KRS.LDTR.RFR
Retrocopy MLQYYEDKLEGGTYAYPKEDLGMCLLLSDYVIQEGKSPQRCLKEGYCKALKYSFF>EGKRSMLDTRVRFR

Parental  GRKGY
          GRKGY
Retrocopy GRKGY

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	2.86 RPM
SRP051959_heart	0.00 RPM	2.03 RPM
SRP051959_kidney	0.02 RPM	2.93 RPM
SRP051959_liver	0.00 RPM	3.14 RPM
SRP051959_lung	0.00 RPM	2.72 RPM
SRP051959_lymph_node	0.00 RPM	3.77 RPM
SRP051959_skeletal_muscle	0.00 RPM	3.54 RPM
SRP051959_spleen	0.00 RPM	3.17 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1382 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1382 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1382 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007139	1 retrocopy	retro_cjac_1382 ,
Cavia porcellus	ENSCPOG00000009263	1 retrocopy	retro_cpor_270,
Equus caballus	ENSECAG00000004183	1 retrocopy	retro_ecab_295,
Echinops telfairi	ENSETEG00000013626	1 retrocopy	retro_etel_757,
Felis catus	ENSFCAG00000004424	1 retrocopy	retro_fcat_201,
Homo sapiens	ENSG00000183513	1 retrocopy	retro_hsap_204,
Gorilla gorilla	ENSGGOG00000006019	1 retrocopy	retro_ggor_278,
Myotis lucifugus	ENSMLUG00000013167	2 retrocopies	retro_mluc_1336, retro_mluc_1760,
Monodelphis domestica	ENSMODG00000001197	1 retrocopy	retro_mdom_1413,
Nomascus leucogenys	ENSNLEG00000001998	1 retrocopy	retro_nleu_1854,
Ochotona princeps	ENSOPRG00000002972	3 retrocopies	retro_opri_1198, retro_opri_1203, retro_opri_391,
Pongo abelii	ENSPPYG00000012085	1 retrocopy	retro_pabe_435,
Pan troglodytes	ENSPTRG00000012267	1 retrocopy	retro_ptro_340,
Pteropus vampyrus	ENSPVAG00000001578	1 retrocopy	retro_pvam_460,
Sorex araneus	ENSSARG00000006275	1 retrocopy	retro_sara_61,