RetrogeneDB ID: retro_cjac_3503

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01182235.1:7750..8582(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000002373
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_3503
ATGCGAGGCCAGCGGAGCCTGCTGCTGGGCCCGGCCCGCCTCTGCCTCCACCTGCTTCTGCTGCTGGGCTGCAGGTGCCG
CTGTCCACCTCTGCTCCGGGGTCTAGTACAGCACTGGCGCTATGGCAAGGTCTGCCTGCACTCCCTGCTCCACCTCTCCT
TTGGGGGCAGTGACACCACTGTCGATGCTGCCTTTGAGCCTGTCTACTTGCTGGTAGACAAGGTGATCCGCTGGTTCAGA
GTGGTGTTTGTTGTGCTGGTGATTTTGCTGACAGGCTCCTTTGTGGCTGTCGCCTACCTGTGTGTCCTGCCTCTCATCCT
CCGAACCTATTCAGTGCCACGACTCTGCTGGCATTTCTTCTCTGCCACTGGAATCTGATCCTCATTGTCTTCCACTACTA
CCAGGCCATCACCGCTCTGCCTGGATACCCACCCCAGGGCAGGAATGATATTGCCATGGTCTCCATCTGTAAGAAATGCA
TTTACCCCAAGCCAGCCAGAACGCACCACTGCAGCATCTGCAACAGGTGTGTGCTGAAGATGGATCATCACTGCCCCCGG
CTAAAGAATTGTGCAGGCCCCTATAACCATCGGTACTTCTTCTCTTTCTGCTTCTTCACGACTCTGCTGTGTCTACTGCA
GCTATAGAAGCTGGGACCTTTTCCGGGAGGCTTATGCTGCCATCGAGAAAATGAAGCAGCTCGACAAGAACAAACTACAG
GCGGTTGCCAACCAGACTTCCCACCAGGCCCCACCGCGCACCTTCTCCTTTCGAGAAAGGATGACTCATAGTAGTCATGG
TGCTGCTGACATGGATGGAGTGCTCGGTGGTA

Alignment

ORF - retro_cjac_3503 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.12 %
• Parental protein coverage: 73.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MRGQRSLLLGPARLCLRLLLLLGYRRRCPPLLRGLVQRWRYGKVCLRSLLYNSFGGSDTAVDAAFEPVYW
          MRGQRSLLLGPARLCL.LLLLLG.R.RCPPLLRGLVQ.WRYGKVCL.SLL..SFGGSDT.VDAAFEPVY.
Retrocopy MRGQRSLLLGPARLCLHLLLLLGCRCRCPPLLRGLVQHWRYGKVCLHSLLHLSFGGSDTTVDAAFEPVYL

Parental  LVDNVIRWFGVVFVVLVIVLTGSIVAIAYLCVLPLILRTYSVPRLCWHFFYS-HWNLILIVFHYYQAITT
          LVD.VIRWF.VVFVVLVI.LTGS.VA.AYLCVLPLILRTYSVPRLCWHFF...HWNLILIVFHYYQAIT.
Retrocopy LVDKVIRWFRVVFVVLVILLTGSFVAVAYLCVLPLILRTYSVPRLCWHFFSA<HWNLILIVFHYYQAITA

Parental  PPGYPPQGRNDIAMVSICKKCIYPKPARTHHCSICNRCVLKMDHHCPWLNNCVGHYNHRYFFSFCFFMT-
          .PGYPPQGRNDIAMVSICKKCIYPKPARTHHCSICNRCVLKMDHHCP.L.NC.G.YNHRYFFSFC.F.T.
Retrocopy LPGYPPQGRNDIAMVSICKKCIYPKPARTHHCSICNRCVLKMDHHCPRLKNCAGPYNHRYFFSFC-FFT>

Parental  LGCVYCSYGSWDLFREAYAAIEKMKQLDKNKLQAVANQTYHQTPPPTFSFRERMTHKS-LVYL-WFLCSS
          L.CVYCSY.SWDLFREAYAAIEKMKQLDKNKLQAVANQT.HQ.PP.TFSFRERMTH.S..V.L.W..CS.
Retrocopy LCCVYCSYRSWDLFREAYAAIEKMKQLDKNKLQAVANQTSHQAPPRTFSFRERMTHSS>MVLLTWMECSV

Parental  V
          V
Retrocopy V

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	6.10 RPM
SRP051959_heart	0.04 RPM	5.86 RPM
SRP051959_kidney	0.04 RPM	8.65 RPM
SRP051959_liver	0.04 RPM	6.93 RPM
SRP051959_lung	0.07 RPM	7.47 RPM
SRP051959_lymph_node	0.07 RPM	8.06 RPM
SRP051959_skeletal_muscle	0.02 RPM	6.97 RPM
SRP051959_spleen	0.08 RPM	7.61 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3503 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3503 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3503 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,