RetrogeneDB ID: retro_cjac_2923

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:103642848..103643426(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SIRT5
• Ensembl ID: ENSCJAG00000019802
• Aliases: None
• Description: sirtuin 5 [Source:HGNC Symbol;Acc:14933]

Sequence

>retro_cjac_2923
GCCCCGCACCTCGCCACCACCAAATGTGAGGCCCTGCTAGGCACACAGGGCCACTGGGGCATGATCATGACAGAACATCC
ATGGGTGGCACCCCAGGCTGGCACCAAGAACCTTCTAGAAATCCATCCTAGCTTATGTTAAACTCCATGTACCTTTTGTG
GAGTGGTGTGTGAGAATTACAAGAGTCCGGTTTGTCCACCTTTATTATGAGTAGGTGCTCCAGTACCTGGAACGCAAGAT
GCCAGAATCCCAGTTGAGAAACTTCCCCGGTGTTAAGAGGCAGAGAGCAGGGGGTGCTGCAACTTCAGCCCTGTGGTTAG
GCGAAAACCTGGATCCTGCCATTCCGGAGGAGGCTGACAGAGAGCTCACCCTTGTGACTATGTCTAGTGGCATGCATTCC
CCCTGTGGTGTAACCAACCGCTGTGTTTGCCCACCCGAAGTCTGCCAGGGGAGTGCCAGTGACCGAATTTAACATGGAGA
CCACCCCAGCCATGAGAAAATTCAGGCTTCATTTTCAAGAACGCTGTGGTAGGGTGCTTCCTGAAGCCCCTGCTGGTCAT
GGAAATGAAACTGTTTCT

Alignment

ORF - retro_cjac_2923 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.59 %
• Parental protein coverage: 62.9 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AGHRAIAECEARLGKQGRRVMVITQNIDELHRKAGTKNLLEIHGELIETRCTSCGVVAENYRSPIVSALS
          A.H.A...CEA.LG.QG...M..T.........AGTKNLLEIH..L..T.CT.CGVV.ENY.SP....L.
Retrocopy APHLATTKCEALLGTQGHWGMIMTEH-PWVAPQAGTKNLLEIHPSLC*TPCTFCGVVCENYKSPVCPPLL

Parental  GRGAPEPGTQDANIPVEKLPRCEEAD-CGGLLRPHVVWFGENLDPAILEEVDGELA-HCD-LCLVVGTSS
          ..GAP.PGTQDA.IPVEKLPRC.EA...GG.......W.GENLDPAI.EE.D.EL...CD.LCLV.....
Retrocopy *VGAPVPGTQDARIPVEKLPRC*EAE>AGGAATS-ALWLGENLDPAIPEEADRELT<PCD<LCLVACIPP

Parental  VVYPAAMFAPQVAARGVPVAEFNMETTPATNRFRFHFQGPCGTTLPEALAPHENETIS
          VV.P.A.FA....ARGVPV.EFNMETTPA...FR.HFQ..CG..LPEA.A.H.NET.S
Retrocopy VV*PTAVFAHPKSARGVPVTEFNMETTPAMRKFRLHFQERCGRVLPEAPAGHGNETVS

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	1.69 RPM
SRP051959_heart	0.09 RPM	1.70 RPM
SRP051959_kidney	0.07 RPM	1.62 RPM
SRP051959_liver	0.06 RPM	2.45 RPM
SRP051959_lung	0.07 RPM	1.45 RPM
SRP051959_lymph_node	0.00 RPM	0.55 RPM
SRP051959_skeletal_muscle	0.07 RPM	1.27 RPM
SRP051959_spleen	0.13 RPM	1.37 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2923 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2923 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2923 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019802	1 retrocopy	retro_cjac_2923 ,
Erinaceus europaeus	ENSEEUG00000005650	1 retrocopy	retro_eeur_209,
Homo sapiens	ENSG00000124523	1 retrocopy	retro_hsap_167,
Macropus eugenii	ENSMEUG00000008671	1 retrocopy	retro_meug_733,
Nomascus leucogenys	ENSNLEG00000000843	1 retrocopy	retro_nleu_977,
Pan troglodytes	ENSPTRG00000017736	1 retrocopy	retro_ptro_158,
Tursiops truncatus	ENSTTRG00000007786	1 retrocopy	retro_ttru_944,