RetrogeneDB ID: retro_cjac_3313

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:68620130..68620490(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RALA
• Ensembl ID: ENSCJAG00000007630
• Aliases: None
• Description: v-ral simian leukemia viral oncogene homolog A (ras related) [Source:HGNC Symbol;Acc:9839]

Sequence

>retro_cjac_3313
ATGGCCGCAAAGAAGCCCAAGAATCAGAATAATTTGGCCTTGCACCAAGGCATCACGGTGGGCAGTGCCAGTATGGGCAA
GGCAGCTCTGACTCTACAGTTCACGGACGATGAATTTGTGGAGAGTTATAAGCTTACCAAAGAAAGCAGCTATCAGAAGA
AAATAGTACTGGATGGCGAGGAAGTATAGATTGATATCTTAGAAACAGCTGGGCAGGAGGACTACGCTGCAATTAGAGAC
AGCTAAAGCAGGGAGGGGTTCCTCTGTGTCTTCTCCATTACAGAAATAGAATCCTTTGCAGCTACAGCTGACTTCAGGGA
GGAGATTTTAAGAGCAAAAGCAGATGAGAATGTTCCATTT

Alignment

ORF - retro_cjac_3313 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.41 %
• Parental protein coverage: 59.22 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAANKPKGQNSLALHKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVVLDGEEVQIDILDTA
          MAA.KPK.QN.LALH..I.VGS...GK.ALTLQF..DEFVE.Y..TK..SY.KK.VLDGEEV.IDIL.TA
Retrocopy MAAKKPKNQNNLALHQGITVGSASMGKAALTLQFTDDEFVESYKLTKESSYQKKIVLDGEEV*IDILETA

Parental  GQEDYAAIRDNYFRSGEGFLCVFSITEMESFAATADFREQILRVKEDENVPF
          GQEDYAAIRD...R..EGFLCVFSITE.ESFAATADFRE.ILR.K.DENVPF
Retrocopy GQEDYAAIRDS*SR--EGFLCVFSITEIESFAATADFREEILRAKADENVPF

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	17.55 RPM
SRP051959_heart	0.00 RPM	14.15 RPM
SRP051959_kidney	0.00 RPM	13.31 RPM
SRP051959_liver	0.00 RPM	12.00 RPM
SRP051959_lung	0.00 RPM	28.97 RPM
SRP051959_lymph_node	0.00 RPM	18.61 RPM
SRP051959_skeletal_muscle	0.00 RPM	8.10 RPM
SRP051959_spleen	0.00 RPM	14.66 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3313 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3313 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3313 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
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	ENSDNOG00000017413	1 retrocopy	retro_dnov_573,
Homo sapiens	ENSG00000006451	2 retrocopies	retro_hsap_1136, retro_hsap_3707,
Macropus eugenii	ENSMEUG00000000259	1 retrocopy	retro_meug_1638,
Macaca mulatta	ENSMMUG00000016059	2 retrocopies	retro_mmul_1706, retro_mmul_882,
Nomascus leucogenys	ENSNLEG00000003055	1 retrocopy	retro_nleu_935,
Pongo abelii	ENSPPYG00000017619	3 retrocopies	retro_pabe_3148, retro_pabe_3208, retro_pabe_945,
Pan troglodytes	ENSPTRG00000019108	1 retrocopy	retro_ptro_2511,
Sus scrofa	ENSSSCG00000029741	1 retrocopy	retro_sscr_634,
Ictidomys tridecemlineatus	ENSSTOG00000020292	2 retrocopies	retro_itri_1314, retro_itri_1315,
Vicugna pacos	ENSVPAG00000002810	1 retrocopy	retro_vpac_211,