RetrogeneDB ID: retro_cjac_1962

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:133657083..133657404(-)
• Located in intron of: ENSCJAG00000016802

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBX1
• Ensembl ID: ENSCJAG00000004763
• Aliases: None
• Description: ring-box 1, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:9928]

Sequence

>retro_cjac_1962
ATGGCGGCAGCAATGGATGTGGATACCCCGAGTGGCACCACCAGCGATGCGGGAAAGTGCTTTGAAGTGAAAAAGGGGAA
TGCAATAGCCCTCTGGGCCTGGGATATTGTGGTTGATAACTGTGCCATCTGCAGGAACCACATTATGGACCTTTGCATAG
AATGTCAAGCTAACTAGGCATCTGCTACTTCAGAAGAGTGTACCGTTGCATGGGGAGTCTGTAACCATGCTTTTCACTTC
CACTGCATCGCTCCCTGGCTCAAAACATGATAGGTGTGTCCACTGGACAACAGAGAGTGGGAATTCCAGAAGTATGGACA
C

Alignment

ORF - retro_cjac_1962 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.81 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTV
          MAAAMDVDTPSGT.S.AGK..FEVKK.NA.ALWAWDIVVDNCAICRNHIMDLCIECQAN.ASATSEECTV
Retrocopy MAAAMDVDTPSGTTSDAGKC-FEVKKGNAIALWAWDIVVDNCAICRNHIMDLCIECQAN*ASATSEECTV

Parental  AWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH
          AWGVCNHAFHFHCI..WLKT..VCPLDNREWEFQKYGH
Retrocopy AWGVCNHAFHFHCIAPWLKT**VCPLDNREWEFQKYGH

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	0.91 RPM	7.61 RPM
SRP051959_heart	0.65 RPM	11.51 RPM
SRP051959_kidney	1.00 RPM	12.22 RPM
SRP051959_liver	0.35 RPM	8.47 RPM
SRP051959_lung	1.02 RPM	10.09 RPM
SRP051959_lymph_node	1.44 RPM	11.03 RPM
SRP051959_skeletal_muscle	0.44 RPM	10.37 RPM
SRP051959_spleen	0.95 RPM	13.17 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1962 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1962 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1962 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000030225	2 retrocopies	retro_btau_1415, retro_btau_61,
Callithrix jacchus	ENSCJAG00000001991	2 retrocopies	retro_cjac_1391, retro_cjac_3943,
Callithrix jacchus	ENSCJAG00000004763	3 retrocopies	retro_cjac_1267, retro_cjac_1955, retro_cjac_1962 ,
Dasypus novemcinctus	ENSDNOG00000007595	1 retrocopy	retro_dnov_433,
Homo sapiens	ENSG00000100387	1 retrocopy	retro_hsap_2118,
Loxodonta africana	ENSLAFG00000008795	1 retrocopy	retro_lafr_943,
Microcebus murinus	ENSMICG00000008019	1 retrocopy	retro_mmur_750,
Myotis lucifugus	ENSMLUG00000007815	4 retrocopies	retro_mluc_1259, retro_mluc_1712, retro_mluc_20, retro_mluc_244,
Macaca mulatta	ENSMMUG00000012642	3 retrocopies	retro_mmul_702, retro_mmul_974, retro_mmul_996,
Monodelphis domestica	ENSMODG00000013054	1 retrocopy	retro_mdom_626,
Mus musculus	ENSMUSG00000022400	1 retrocopy	retro_mmus_1633,
Nomascus leucogenys	ENSNLEG00000015436	1 retrocopy	retro_nleu_1956,
Ochotona princeps	ENSOPRG00000006728	2 retrocopies	retro_opri_410, retro_opri_649,
Pongo abelii	ENSPPYG00000011861	2 retrocopies	retro_pabe_1986, retro_pabe_1987,
Pan troglodytes	ENSPTRG00000014417	1 retrocopy	retro_ptro_1550,
Rattus norvegicus	ENSRNOG00000019214	2 retrocopies	retro_rnor_1890, retro_rnor_2724,
Ictidomys tridecemlineatus	ENSSTOG00000015580	1 retrocopy	retro_itri_888,
Tupaia belangeri	ENSTBEG00000009043	4 retrocopies	retro_tbel_1175, retro_tbel_3306, retro_tbel_3756, retro_tbel_3805,
Tursiops truncatus	ENSTTRG00000012018	2 retrocopies	retro_ttru_1419, retro_ttru_583,
Vicugna pacos	ENSVPAG00000004894	2 retrocopies	retro_vpac_207, retro_vpac_502,
Drosophila melanogaster	FBgn0025638	1 retrocopy	retro_dmel_55,