RetrogeneDB ID: retro_cjac_3646

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01192191.1:2527..2784(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000034129
• Aliases: None
• Description: None

Sequence

>retro_cjac_3646
CTGAAAGGGCTCCATCCTCACCCTAGGGCCTTCCATATGTCATTTTAGATTATTTTGATTAGAAATGAAATGACCGACTG
GGCATGGTGGCTCATGCCTGTAATCCCAGTACTTTGGGAAGCCAGGGCAGGCAGATTACCCGAGGTCAGGAGTTCAAGAC
AAGACCGGCCAACATGGCGAAACCCTGTCTCTACCAAAAATACAAAAATTAGCTGGGTGTTGTGGTGAGTGCCTATAATT
CCAGCTACTCAGGAGGC

Alignment

ORF - retro_cjac_3646 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.67 %
• Parental protein coverage: 89.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LGSLQPVPPGFKRFSCLSLPSNWDYSWAWWCLPVIPALWEAKAGRSPEVRSSRSAWAMWRNPISTKNTKI
          L..L.P.P..F.......L..N....WAWW..PVIP.LWEA.AGR.PEVRSSR.....WRNP.STKNTKI
Retrocopy LKGLHPHPRAFHMSF*IILIRNEMTDWAWWLMPVIPVLWEARAGRLPEVRSSRQDRPTWRNPVSTKNTKI

Parental  R-LGVPGVVVHACNPSYLGG
          ..LGV...VV.A.N.SY.GG
Retrocopy S<LGV---VVSAYNSSYSGG

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	0.16 RPM
SRP051959_heart	0.00 RPM	0.02 RPM
SRP051959_kidney	0.00 RPM	0.02 RPM
SRP051959_liver	0.00 RPM	0.04 RPM
SRP051959_lung	0.00 RPM	0.10 RPM
SRP051959_lymph_node	0.00 RPM	0.30 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.04 RPM
SRP051959_spleen	0.00 RPM	0.13 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3646 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3646 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3646 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020103	14 retrocopies	retro_cjac_3387, retro_cjac_3463, retro_cjac_3466, retro_cjac_3471, retro_cjac_3522, retro_cjac_3527, retro_cjac_3574, retro_cjac_3575, retro_cjac_3586, retro_cjac_3699, retro_cjac_3705, retro_cjac_3737, retro_cjac_3750, retro_cjac_3753,
Callithrix jacchus	ENSCJAG00000034129	3 retrocopies	retro_cjac_3646 , retro_cjac_3740, retro_cjac_3780,
Gorilla gorilla	ENSGGOG00000023636	1 retrocopy	retro_ggor_688,