RetrogeneDB ID: retro_cjac_660

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:11328608..11329061(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000036835
• Aliases: None
• Description: None

Sequence

>retro_cjac_660
CAAGAACTACTTGTTGAGGAGCATGGGGAGAAGAAGTCCCAGGTGGCACAGCTCCTAGGGAATGTTCACGCTGCCCTGAA
GCCGTTTTCAGTAAAATTCAATGAGATCACAGATCCCGATAAAAAGCAGATGCTCTAACAGATTCAGCACACAGCGAAGC
TTGCCACGGAGCTGCTTGAGAAAGCTGTGTAGTACAGACTTGGAAAGAAAGCCAACAGCTGTGTGCAAGGATTGTTGGAG
GAGGCCAAGGATTTGCTTTCTGAGTTGCTGGATTCTGCATTCTGGAGTCAGGTGACTGGCAATTTCATTTTCTCCAAACT
GCCCAAGTTCTGGGATGGGGAGTTCCACAAATACATGGAAGCTCTGAATCTCCTCTCTCTGGATGTTTTAACCAGAGTTA
GTGTGTATATGCCAGAAACTGTGAATTTTGACCAAAAGATTGTGGACAATGGT

Alignment

ORF - retro_cjac_660 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.82 %
• Parental protein coverage: 54.87 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QNHLFRQYREKRPEAAQLLEDVQAALMPFLVKLNETTDADKKQMLERIRHAVQLATEPLEKAVQSRLTGE
          Q..L.....EK....AQLL..V.AAL.PF.VK.NE.TD.DKKQML..I.H...LATE.LEKAV..RL.G.
Retrocopy QELLVEEHGEKKSQVAQLLGNVHAALKPFSVKFNEITDPDKKQML*QIQHTAKLATELLEKAV*YRL-GK

Parental  EVTSRVEVLLEEAKDLLSDWLDSTLGSDVTDNSIFSELPKFWEGEFHRDMEALNVLPPDVLTRVSEYVPE
          ...S.V..LLEEAKDLLS..LDS...S.VT.N.IFS.LPKFW.GEFH..MEALN.L..DVLTRVS.Y.PE
Retrocopy KANSCVQGLLEEAKDLLSELLDSAFWSQVTGNFIFSKLPKFWDGEFHKYMEALNLLSLDVLTRVSVYMPE

Parental  IVNFVQKIVDNG
          .VNF.QKIVDNG
Retrocopy TVNFDQKIVDNG

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	0.29 RPM
SRP051959_heart	0.02 RPM	0.18 RPM
SRP051959_kidney	0.02 RPM	0.04 RPM
SRP051959_liver	0.00 RPM	0.26 RPM
SRP051959_lung	0.00 RPM	0.16 RPM
SRP051959_lymph_node	0.00 RPM	0.14 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.09 RPM
SRP051959_spleen	0.00 RPM	0.19 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_660 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_660 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_660 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	ENSCJAG00000036835	1 retrocopy	retro_cjac_660 ,