RetrogeneDB ID: retro_cjac_3843

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL284994.1:88777..89322(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAP1A
• Ensembl ID: ENSCJAG00000013392
• Aliases: None
• Description: RAP1A, member of RAS oncogene family [Source:HGNC Symbol;Acc:9855]

Sequence

>retro_cjac_3843
GAGTATAAGCTAGTGGTCCTTAGTTCAGGAGGCACTGGGAAGTTTGCTCTGACAGTTCAGTTAGTTCAGGGATTTTTTTT
TTTTTTTAAATATGACCCAATGATAGAGGATTTCTAAAGAAAGCAAGTTGAAATGGATTAACAGTGTATGCTAGAAATCC
TGGATACTGCAAAGACGAGCAACTTACAGCGATGAGGAATTTGTATATAAAGAATGGACAAAGTTTAACACTAGTATATT
CTATTATAGCTCAATCCACATTTAATGACTTACAGGACCCGAGGGAACAGATTTTACCGGTTAAGGGCACAGAATATGTT
CCAATGATTTTGTTTGGCCATAAATGTGACCTGGAAGATGAGTGAGTAGATGGCGAAAAAAAGAGCCAGAATTTGGCAAG
ACAATGGTGTCATTGCGCCTATGTAGAAACTTCTGCAAAGTCAAAGATCAATGTTAATGAGATGTTTTATGACCTGGTCA
GATGGATAAATAGAAAAACACCAGTGGAAAAGAAGAACCCTAAAAAGAAATCACATCTGCTTCTC

Alignment

ORF - retro_cjac_3843 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.63 %
• Parental protein coverage: 98.91 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EYKLVVLGSGGVGKSALTVQFVQGIFVE-KYDPTIEDSYRKQVEVDCQQCMLEILDTAGT-EQFTAMRDL
          EYKLVVL.SGG.GK.ALTVQ.VQG.F...KYDP.IED..RKQVE.D.Q.CMLEILDTA.T.EQ.TAMR.L
Retrocopy EYKLVVLSSGGTGKFALTVQLVQGFFFFFKYDPMIEDF*RKQVEMD*Q-CMLEILDTAKT<EQLTAMRNL

Parental  YMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTEDVPMILVGNKCDLEDERVVGKEQGQNLARQWCN
          Y.KNGQ...LVYSI.AQSTFNDLQD.REQIL.VK.TE.VPMIL.G.KCDLEDE.V.G....QNLARQWC.
Retrocopy YIKNGQSLTLVYSIIAQSTFNDLQDPREQILPVKGTEYVPMILFGHKCDLEDE*VDGEKKSQNLARQWCH

Parental  CAFLESSAKSKINVNEIFYDLVRQINRKTPVEKKKPKKKSCLLL
          CA..E.SAKSKINVNE.FYDLVR.INRKTPVEKK.PKKKS.LLL
Retrocopy CAYVETSAKSKINVNEMFYDLVRWINRKTPVEKKNPKKKSHLLL

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	16.55 RPM
SRP051959_heart	0.00 RPM	21.98 RPM
SRP051959_kidney	0.00 RPM	12.38 RPM
SRP051959_liver	0.00 RPM	14.66 RPM
SRP051959_lung	0.00 RPM	26.00 RPM
SRP051959_lymph_node	0.00 RPM	32.99 RPM
SRP051959_skeletal_muscle	0.02 RPM	15.46 RPM
SRP051959_spleen	0.00 RPM	23.61 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3843 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3843 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3843 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005384	1 retrocopy	retro_amel_1764,
Canis familiaris	ENSCAFG00000013686	1 retrocopy	retro_cfam_696,
Callithrix jacchus	ENSCJAG00000007261	3 retrocopies	retro_cjac_1435, retro_cjac_2371, retro_cjac_607,
Callithrix jacchus	ENSCJAG00000007630	1 retrocopy	retro_cjac_3313,
Callithrix jacchus	ENSCJAG00000013392	7 retrocopies	retro_cjac_1671, retro_cjac_2218, retro_cjac_3376, retro_cjac_3707, retro_cjac_3843 , retro_cjac_3844, retro_cjac_728,
Callithrix jacchus	ENSCJAG00000036517	1 retrocopy	retro_cjac_2400,
Dasypus novemcinctus	ENSDNOG00000007809	5 retrocopies	retro_dnov_101, retro_dnov_1617, retro_dnov_1764, retro_dnov_628, retro_dnov_94,
Equus caballus	ENSECAG00000016434	1 retrocopy	retro_ecab_99,
Erinaceus europaeus	ENSEEUG00000010446	2 retrocopies	retro_eeur_306, retro_eeur_361,
Echinops telfairi	ENSETEG00000016893	2 retrocopies	retro_etel_1196, retro_etel_176,
Homo sapiens	ENSG00000116473	1 retrocopy	retro_hsap_1364,
Myotis lucifugus	ENSMLUG00000010571	3 retrocopies	retro_mluc_2311, retro_mluc_2312, retro_mluc_2313,
Monodelphis domestica	ENSMODG00000001323	3 retrocopies	retro_mdom_1327, retro_mdom_139, retro_mdom_1777,
Mus musculus	ENSMUSG00000068798	2 retrocopies	retro_mmus_1963, retro_mmus_3027,
Nomascus leucogenys	ENSNLEG00000004018	1 retrocopy	retro_nleu_1069,
Ochotona princeps	ENSOPRG00000003999	3 retrocopies	retro_opri_321, retro_opri_460, retro_opri_875,
Pongo abelii	ENSPPYG00000001028	1 retrocopy	retro_pabe_1132,
Pan troglodytes	ENSPTRG00000001102	1 retrocopy	retro_ptro_937,
Rattus norvegicus	ENSRNOG00000032463	3 retrocopies	retro_rnor_1147, retro_rnor_1494, retro_rnor_1639,
Ictidomys tridecemlineatus	ENSSTOG00000027847	1 retrocopy	retro_itri_81,
Tarsius syrichta	ENSTSYG00000004521	3 retrocopies	retro_tsyr_1546, retro_tsyr_1829, retro_tsyr_2140,
Vicugna pacos	ENSVPAG00000010033	1 retrocopy	retro_vpac_491,