RetrogeneDB ID: retro_cjac_792

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:70176211..70176886(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACAD11
• Ensembl ID: ENSCJAG00000003027
• Aliases: None
• Description: acyl-CoA dehydrogenase family, member 11 [Source:HGNC Symbol;Acc:30211]

Sequence

>retro_cjac_792
AGAACTCAAAATACTTCTGGCTCCAGACACAAAAAGCACAGCATGATTCTTGTTCCCATGAACACACCTGGAGTAGAATT
AATAAGACCTTGGTCAGTTTTTGTCTACACAGATAATTTTCATGGAGGACATTTTGAGATCCATTTAAATCAACTGCGAG
TTCCTGACACAAATCTAATACAAGGTGAAGGCAGTGGATATGAAATTTCCCAAAGCTGCCTTGGACCTGGCAGAATCCAC
CAATGTATGAGAACAATAGGTTTGGTGGAGCATGCTTTGCAGATCATGTGTTAGCAGGCAACACAAAGGGTAGCCTTTAA
GAAGTTGTTTGCACATGAGGTTGTGGCTCACTGGATTGCTGAAAGCCGCATTGCCATTGAGAAGATTCACTTGTTGACTC
TGAAAGCCACTCACAGCATAGACACTCTGGGCAGTGCTGGTGCTAGGAAGGAGATTGCAGTGATCAAAGTGGCTGCCCCA
CGGGCTGACTGCAAAATCACTGACCGAGCCATCTAGGTGTTCGGAGGTGCTGGTGTTTCCCAGGATTACCTTCTGGCCAA
CATATATGCTTTAACCCAAGTTTTGCATTTAGCAGACGGACCTGACAAAGTTTACCTCTCAGCAATTGCAACAATGGAGC
TGCAGGACCAAGCCAAAGGGCAGACAGCCAAGATG

Alignment

ORF - retro_cjac_792 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.42 %
• Parental protein coverage: 57.8 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RTQNTSVSRHKKHSMILVPMSTPGVELIRPLSVFGYTDNFHGGHFEIHFNQVRVPATNLILGEGRGFEIS
          RTQNTS.SRHKKHSMILVPM.TPGVELIRP.SVF.YTDNFHGGHFEIH.NQ.RVP.TNLI.GEG.G.EIS
Retrocopy RTQNTSGSRHKKHSMILVPMNTPGVELIRPWSVFVYTDNFHGGHFEIHLNQLRVPDTNLIQGEGSGYEIS

Parental  QGRLGPGRIHHCMRTIGLAERALQIMCERATQRVAFKKKLFAHETVAHWIAESRIAIEKIRLLTLKAAHN
          Q..LGPGRIH.CMRTIGL.E.ALQIMC..ATQRVAF.KKLFAHE.VAHWIAESRIAIEKI.LLTLKA.H.
Retrocopy QSCLGPGRIHQCMRTIGLVEHALQIMC*QATQRVAF-KKLFAHEVVAHWIAESRIAIEKIHLLTLKATHS

Parental  IDTLGSAGARKEIAMIKVAAPRAVCRIIDWAIQVCGGAGVSQDYPLANMYAVTRALRIADGPDEVHLSAI
          IDTLGSAGARKEIA.IKVAAPRA.C.I.D.AI.V.GGAGVSQDY.LAN.YA.T..L..ADGPD.V.LSAI
Retrocopy IDTLGSAGARKEIAVIKVAAPRADCKITDRAI*VFGGAGVSQDYLLANIYALTQVLHLADGPDKVYLSAI

Parental  ATMELQDQAQELTARM
          ATMELQDQA...TA.M
Retrocopy ATMELQDQAKGQTAKM

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	10.49 RPM
SRP051959_heart	0.00 RPM	6.14 RPM
SRP051959_kidney	0.00 RPM	14.42 RPM
SRP051959_liver	0.04 RPM	15.81 RPM
SRP051959_lung	0.00 RPM	8.08 RPM
SRP051959_lymph_node	0.00 RPM	6.64 RPM
SRP051959_skeletal_muscle	0.02 RPM	4.76 RPM
SRP051959_spleen	0.00 RPM	7.37 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_792 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_792 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_792 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003027	1 retrocopy	retro_cjac_792 ,