RetrogeneDB ID: retro_cjac_3742

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01198082.1:2459..3203(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000016605
• Aliases: None
• Description: None

Sequence

>retro_cjac_3742
CTGCTCCCGGGTCTAGTACAGCGCTGGCGCTATGGCAAGGTCTGCCTGGGCTCCTGCTCCACCTTCTCTTTTGGGGGCAG
TGACACACTGTCCGATGCTGCCTTTGAGCCTGTCTACTTGCTGGTAGACAAGGTGATCCGCTGGTTCAGAGTGGTGTTTG
TTGTGCTGGTGATTTTGCTGACAGGCTCCTTTGTGGCTGTCGCCTACCTGTGTGTCCTGCCTCTCATCCTCCGAACCTAT
TCAGTGCCACGACTCTGCTGGCATTTCTTCTCTGCCACCGGAATCTGATCCTCATTGTCTTCCGCTACTACCAGGCCATC
ACCGCTCCGCCTGGATACCCACCCCAGGGCAGGAATGATATTGCCATGGTCTCCATCTGTAAGAAATGCATTTACCCCAA
GCCAGCCAGAACGCACCACTGCAGCATCTGCAACAGGTGTGTGCTGAAGATGGATCATCACTGCCCCCGGCTAAAGAATT
GTGTGGGCCCCTATAACCATCGGTACTTCTTCTCTTTCTGCTTCTTCACGACTCTGGGCTGTGTCTACTGCAGCTATGGA
AGCTGGGACCTTTTCCGGGAGGCTTATGCTGCCATCGAGAAAATGAAGCAGCTTGACAAGAACAAACTACAGGCGGTTGC
CAACCAGACTTCCCACCAGGCCCCACCGCGCACCTTCTCCTTTCAAGAAAGGATGACTCATAGTAGTCATGGTGCTGCTG
ACATGGATGGAGTGCTCGGTGGTA

Alignment

ORF - retro_cjac_3742 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.6 %
• Parental protein coverage: 65.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LLRGLVQRWRYGKVCLRSLLYNSFGGSDTAVDAAFEPVYWLVDNVIRWFGVVFVVLVIVLTGSIVAIAYL
          LL.GLVQRWRYGKVCL.S....SFGGSDT..DAAFEPVY.LVD.VIRWF.VVFVVLVI.LTGS.VA.AYL
Retrocopy LLPGLVQRWRYGKVCLGSCSTFSFGGSDTLSDAAFEPVYLLVDKVIRWFRVVFVVLVILLTGSFVAVAYL

Parental  CVLPLILRTYSVPRLCWHFFYS-HWNLILIVFHYYQAITTPPGYPPQGRNDIAMVSICKKCIYPKPARTH
          CVLPLILRTYSVPRLCWHFF...H.NLILIVF.YYQAIT.PPGYPPQGRNDIAMVSICKKCIYPKPARTH
Retrocopy CVLPLILRTYSVPRLCWHFFSA<HRNLILIVFRYYQAITAPPGYPPQGRNDIAMVSICKKCIYPKPARTH

Parental  HCSICNRCVLKMDHHCPWLNNCVGHYNHRYFFSFCFFMTLGCVYCSYGSWDLFREAYAAIEKMKQLDKNK
          HCSICNRCVLKMDHHCP.L.NCVG.YNHRYFFSFCFF.TLGCVYCSYGSWDLFREAYAAIEKMKQLDKNK
Retrocopy HCSICNRCVLKMDHHCPRLKNCVGPYNHRYFFSFCFFTTLGCVYCSYGSWDLFREAYAAIEKMKQLDKNK

Parental  LQAVANQTYHQTPPPTFSFRERMTHKS-LVYL-WFLCSSV
          LQAVANQT.HQ.PP.TFSF.ERMTH.S..V.L.W..CS.V
Retrocopy LQAVANQTSHQAPPRTFSFQERMTHSS>MVLLTWMECSVV

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	0.02 RPM	6.10 RPM
SRP051959_heart	0.00 RPM	5.86 RPM
SRP051959_kidney	0.00 RPM	8.65 RPM
SRP051959_liver	0.02 RPM	6.93 RPM
SRP051959_lung	0.00 RPM	7.47 RPM
SRP051959_lymph_node	0.00 RPM	8.06 RPM
SRP051959_skeletal_muscle	0.02 RPM	6.97 RPM
SRP051959_spleen	0.04 RPM	7.61 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3742 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3742 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3742 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016605	2 retrocopies	retro_cjac_3503, retro_cjac_3742 ,
Rattus norvegicus	ENSRNOG00000046530	1 retrocopy	retro_rnor_2846,