RetrogeneDB ID: retro_cjac_2800

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:31880782..31881377(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000021887
• Aliases: None
• Description: None

Sequence

>retro_cjac_2800
CTTTTTTCTTACTCACCTCTCCTTGTATGTTTTACCACCAGTATTGTCTCCCAGTTGCTGTGGAACCTAAAAGGACCTGC
CAGAACAATCATATTCCTGGGTTGTGCCATCCAGCTCTATATCTCCCTGGGCTCCACTGAGTGCGTTCTGGCTGTAATGA
CTTTTGATCGCTATGCAGCAGTTTGCAAACCTCTCCACTCTACAGCTGTGACGAACTCACGGCTGTGCCACACTCTGGCA
GTGGTTGCGTGGCTGAGTGGAGTGGGAAACACTCTGATCCAGGGCACTGTCACCCTCAAGCTGCCTCACTGTGGACCCTG
GTGGCTCCACCATTTCTTCTGTGAGGTACCTCCATGATTAAGCTCGCCTGTGTAGACGTTCACGATAACAAGGTCCAGCT
GTTCGTTGGTTCGTTGATCTTGCTCCTCCTGCCCTTAGCACTGATATTGCTGTCCTATAGACAATAGCCAAGGTGGCCAT
GAAGATCAAGTCAGTCCAGGCCTCGTGCAAAGCCCTGGGGACATGTGGCTCCCATTCGATGGTAGTGTCCCTCTTCTAAG
GGACCATCACAGCTGTTTACATCCAGCCCAAGAGT

Alignment

ORF - retro_cjac_2800 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.41 %
• Parental protein coverage: 66.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LANLSFLDMCFTTGSVPQMLYNLWGPDKTISYVGCAIQLYFVLALGGVECVLLAVMAYDRYAAVCKALHY
          L...S.L..CFTT..V.Q.L.NL.GP..TI...GCAIQLY....LG..ECVL.AVM..DRYAAVCK.LH.
Retrocopy LFSYSPLLVCFTTSIVSQLLWNLKGPARTIIFLGCAIQLY--ISLGSTECVL-AVMTFDRYAAVCKPLHS

Parental  TVIMHPRLCGQLASVAWLSGFGNSLIMAPQTLMLPRCGHRRVHHFLCEVP-ALLKLSCVDTTANEAELFL
          T.....RLC..LA.VAWLSG.GN.LI....TL.LP.CG....HHF.CEVP....KL.CVD...N...LF.
Retrocopy TAVTNSRLCHTLAVVAWLSGVGNTLIQGTVTLKLPHCGPWWLHHFFCEVP<SMIKLACVDVHDNKVQLFV

Parental  VSVLFHLIPLTLILISYA-FIVQAVLRIQSAEGRQKAFGTCGSHLIVVSLFYGTATSMYLQPPS
          .S....L.PL.LIL.SY...I......I.S.....KA.GTCGSH..VVSLF.GT.T..Y.QP.S
Retrocopy GSLILLLLPLALILLSYR<TIAKVAMKIKSVQASCKALGTCGSHSMVVSLF*GTITAVYIQPKS

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	0.02 RPM
SRP051959_heart	0.05 RPM	0.11 RPM
SRP051959_kidney	0.00 RPM	0.00 RPM
SRP051959_liver	0.00 RPM	0.00 RPM
SRP051959_lung	0.00 RPM	0.13 RPM
SRP051959_lymph_node	0.00 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.07 RPM
SRP051959_spleen	0.00 RPM	0.06 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2800 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2800 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2800 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	ENSCJAG00000021887	1 retrocopy	retro_cjac_2800 ,