RetrogeneDB ID: retro_cjac_3789

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01201525.1:691..1164(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000012916
• Aliases: None
• Description: None

Sequence

>retro_cjac_3789
GGAGGCTCTATAATAGGAAGCTGTGGATCAGAATATGACTACTTTTATTCTGATGAGGAAGCAATAGAAGCTGACAATGA
GGGTTATGCTGAGCCCAGTGATAAGAAAATGAAGATGACACGGAATCAAATATTAGGACTAATACAGGCTGGGCAGATGC
CATGGCTGCAGTCCTCAACAAGAAAACTCCTGAAAGTAAACCTACTATTCTGGTCAAAAATAAGAAGCTGGAAAAGGAAA
AAGAAAAGTTAAAGCAAGAAAAACAAGAGAAAATAAAACAGCGTGATAAGTGGATGGAGTGGGAAATGATATGCAGAGTA
AAGCCAGATGTTGTCTAAGACAAGGAGACAGAGAGAAATATTCAGCGAATTGCAAGGAGGGGTGTGGTGCAATTATTTAA
TGCTGTTCACAAACATCAAAAGAACGTTGATGAGAAGGTTAAAGAAGCTGAAAGCTCTACTAGAAAGCAAACT

Alignment

ORF - retro_cjac_3789 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.02 %
• Parental protein coverage: 56.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GSDSEGSSGPEYDDFYSDEEAIEADNESDAEPHDE-ENEDDAESNPGTNMGWADAMAKVLNKKTPESKPT
          G....GS.G.EYD.FYSDEEAIEADNE..AEP.D..ENEDD.ESN..TN.GWADAMA.VLNKKTPESKPT
Retrocopy GGSIIGSCGSEYDYFYSDEEAIEADNEGYAEPSDK<ENEDDTESNIRTNTGWADAMAAVLNKKTPESKPT

Parental  ILVKNKKLEKEKEKLKQERQEKIKQRDKRMEWEMMCRVKPDVVQDKETERNLQRIATRGVVQLFNAVQKH
          ILVKNKKLEKEKEKLKQE.QEKIKQRDK.MEWEM.CRVKPDVV.DKETERN.QRIA.RGVVQLFNAV.KH
Retrocopy ILVKNKKLEKEKEKLKQEKQEKIKQRDKWMEWEMICRVKPDVV*DKETERNIQRIARRGVVQLFNAVHKH

Parental  QKNVDEKVKEAGSSIRKRT
          QKNVDEKVKEA.SS.RK.T
Retrocopy QKNVDEKVKEAESSTRKQT

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	4.33 RPM
SRP051959_heart	0.00 RPM	7.12 RPM
SRP051959_kidney	0.00 RPM	6.79 RPM
SRP051959_liver	0.00 RPM	6.91 RPM
SRP051959_lung	0.02 RPM	6.75 RPM
SRP051959_lymph_node	0.00 RPM	5.91 RPM
SRP051959_skeletal_muscle	0.00 RPM	7.64 RPM
SRP051959_spleen	0.00 RPM	5.61 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3789 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3789 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3789 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000174	1 retrocopy	retro_chof_1961,
Callithrix jacchus	ENSCJAG00000012916	2 retrocopies	retro_cjac_3789 , retro_cjac_455,
Mus musculus	ENSMUSG00000001305	1 retrocopy	retro_mmus_3531,
Oryctolagus cuniculus	ENSOCUG00000017863	4 retrocopies	retro_ocun_1738, retro_ocun_820, retro_ocun_962, retro_ocun_992,
Ictidomys tridecemlineatus	ENSSTOG00000001244	1 retrocopy	retro_itri_1554,
Tarsius syrichta	ENSTSYG00000012715	1 retrocopy	retro_tsyr_2006,