RetrogeneDB ID: retro_cjac_2687

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:154508835..154509182(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAC3
• Ensembl ID: ENSCJAG00000018194
• Aliases: None
• Description: ras-related C3 botulinum toxin substrate 3 (rho family, small GTP binding protein Rac3) [Source:HGNC Symbol;Acc:9803]

Sequence

>retro_cjac_2687
CCATTCTATCTGTAAACAGACAGAGTTTTAGTATGCTTCTCCTTGGTAAGTACTGCATCATTTGAAAATGTCTGTGCAGA
GTGGCACCCCGAAATGCAGCACCGTTTCCCAACACTCCCATCGTCCTTGGAGGAAGTAAACTTGATCTTAGTGTTGTTAG
AGACGCAACTGAGAAACCGAAGAGGTTGACTCCCATCACCTATCTGCAGTTTTTAACCAGCGGTAAGGAGATTGGTGTGG
TAAATTACCTAACTGCTTGGCTGTCACACAGAGAGGCTTCGAAACTGTTTGACGAAGCCATCCTAGCGGTTCTCTGCCCA
CCTCCTGTGAAGAAGAGGTAGAGAAAA

Alignment

ORF - retro_cjac_2687 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.17 %
• Parental protein coverage: 56.4 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PHLLPKDVFLICFSLVSPASFENVRAKWYPEVRHHCP-HTPILLVGTKLDLRDDKDTIERLRDKKLAPIT
          P..L..D..L.CFSLVS.ASFENV.A.W.PE..H..P..TPI.L.G.KLDL....D..E....K.L.PIT
Retrocopy PFYL*TDRVLVCFSLVSTASFENVCAEWHPEMQHRFP<NTPIVLGGSKLDLSVVRDATEK--PKRLTPIT

Parental  YPQGLAMAREIGSVKYLECSALTQRGLKTVFDEAIRAVLCPPPVKKPGKK
          Y.Q.L....EIG.V.YL....L..R.....FDEAI.AVLCPPPVKK...K
Retrocopy YLQFLTSGKEIGVVNYLT-AWLSHREASKLFDEAILAVLCPPPVKKR*RK

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	0.20 RPM
SRP051959_heart	0.00 RPM	0.25 RPM
SRP051959_kidney	0.00 RPM	2.82 RPM
SRP051959_liver	0.02 RPM	11.61 RPM
SRP051959_lung	0.00 RPM	0.55 RPM
SRP051959_lymph_node	0.00 RPM	0.73 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.11 RPM
SRP051959_spleen	0.02 RPM	0.25 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2687 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2687 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2687 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017364	1 retrocopy	retro_amel_1104,
Callithrix jacchus	ENSCJAG00000000685	1 retrocopy	retro_cjac_2403,
Callithrix jacchus	ENSCJAG00000002144	4 retrocopies	retro_cjac_1158, retro_cjac_1954, retro_cjac_2917, retro_cjac_847,
Callithrix jacchus	ENSCJAG00000005912	6 retrocopies	retro_cjac_1275, retro_cjac_1808, retro_cjac_1826, retro_cjac_2251, retro_cjac_751, retro_cjac_911,
Callithrix jacchus	ENSCJAG00000018194	1 retrocopy	retro_cjac_2687 ,
Cavia porcellus	ENSCPOG00000013861	1 retrocopy	retro_cpor_18,
Echinops telfairi	ENSETEG00000012902	3 retrocopies	retro_etel_1565, retro_etel_1645, retro_etel_42,
Macropus eugenii	ENSMEUG00000006196	1 retrocopy	retro_meug_201,
Otolemur garnettii	ENSOGAG00000012467	1 retrocopy	retro_ogar_2140,
Procavia capensis	ENSPCAG00000009949	1 retrocopy	retro_pcap_16,
Pongo abelii	ENSPPYG00000008763	2 retrocopies	retro_pabe_1047, retro_pabe_2546,
Tupaia belangeri	ENSTBEG00000007272	4 retrocopies	retro_tbel_1796, retro_tbel_2564, retro_tbel_4296, retro_tbel_9,
Takifugu rubripes	ENSTRUG00000016201	1 retrocopy	retro_trub_15,