RetrogeneDB ID: retro_cjac_1017

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:23480141..23480329(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACBD7
• Ensembl ID: ENSCJAG00000009249
• Aliases: None
• Description: acyl-CoA binding domain containing 7 [Source:HGNC Symbol;Acc:17715]

Sequence

>retro_cjac_1017
GATGAAAAACTAAAAGAATGCTATGGACTTTACAAACAAGCTATAACTGGAAACATTAATAGTGAGTATCTGGGAATGCT
GGGTTTAAAGGGCAAGGCCGAATGGGAAGCATGGAACCTCCAAGAAGGTTGTCAGTGGAAGACGCAGTGAGTGCCTCTAT
TTGTAAGGCAAATGAGCCAATAGAAAAA

Alignment

ORF - retro_cjac_1017 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.62 %
• Parental protein coverage: 71.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DGELRDLYGLYKQATIGDINIECPGMLDLKGKAKWEAWNLQKG-LSTEDAMTAYISKAKELIEK
          D..L...YGLYKQA..G.IN.E..GML.LKGKA.WEAWNLQ.G.LS.EDA..A.I.KA.E.IEK
Retrocopy DEKLKECYGLYKQAITGNINSEYLGMLGLKGKAEWEAWNLQEG<LSVEDAVSASICKANEPIEK

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	0.02 RPM
SRP051959_heart	0.00 RPM	0.00 RPM
SRP051959_kidney	0.00 RPM	0.04 RPM
SRP051959_liver	0.02 RPM	0.00 RPM
SRP051959_lung	0.00 RPM	0.08 RPM
SRP051959_lymph_node	0.00 RPM	0.02 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.02 RPM
SRP051959_spleen	0.02 RPM	0.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1017 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1017 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1017 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1669
Pan troglodytes	retro_ptro_1132
Gorilla gorilla	retro_ggor_1257
Pongo abelii	retro_pabe_1376
Macaca mulatta	retro_mmul_1577

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009249	1 retrocopy	retro_cjac_1017 ,
Callithrix jacchus	ENSCJAG00000021436	1 retrocopy	retro_cjac_954,
Felis catus	ENSFCAG00000027337	1 retrocopy	retro_fcat_683,
Homo sapiens	ENSG00000176244	2 retrocopies	retro_hsap_1501, retro_hsap_1669,
Gorilla gorilla	ENSGGOG00000015777	3 retrocopies	retro_ggor_1152, retro_ggor_1257, retro_ggor_625,
Macaca mulatta	ENSMMUG00000010587	2 retrocopies	retro_mmul_1577, retro_mmul_2141,
Nomascus leucogenys	ENSNLEG00000012353	2 retrocopies	retro_nleu_1147, retro_nleu_1720,
Pongo abelii	ENSPPYG00000002111	2 retrocopies	retro_pabe_1252, retro_pabe_1376,
Pan troglodytes	ENSPTRG00000041316	3 retrocopies	retro_ptro_1018, retro_ptro_1132, retro_ptro_530,
Pteropus vampyrus	ENSPVAG00000007153	1 retrocopy	retro_pvam_649,