RetrogeneDB ID: retro_cjac_2160

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:94804838..94805085(+)
• Located in intron of: ENSCJAG00000007151

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000019848
• Aliases: None
• Description: None

Sequence

>retro_cjac_2160
CTGATGTATGAAAAAGAAGGAAAACAACAAGAAGAAAAGAAAAAAAGAGAGCTGAAGATGATGAAAACGATGCCATTAAA
AAGCAGGCAGAAATCCTGCAAGAATCCCAGGCGATAAGCTTGATTGACAGCACAGGTTGGAAGCTACATATACCATTCTT
AGGCAGTTGTTAGAAAGTGAAAAAGACTTGGAAGAAGCTGAGGAATATAAAGAATACTTAGTACTGGATTCAGTGAAGTT
AGAAGCC

Alignment

ORF - retro_cjac_2160 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 78.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VMYEKEAKQQEE-KIEKMRAEDGENYDIKKQVEILQESRMMIP-DCQRRLEAAYLDLQQILENEKDLEEA
          .MYEKE.K.Q.E...EK.RAED.EN..IKKQ.EILQES......D.Q.RLEA.Y..L.Q.LE.EKDLEEA
Retrocopy LMYEKEGK-QQE<RKEKKRAEDDENDAIKKQAEILQESQAISL<D*QHRLEATYTILRQLLESEKDLEEA

Parental  EEYKEARLVLDSMKLEA
          EEYKE..LVLDS.KLEA
Retrocopy EEYKE-YLVLDSVKLEA

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	0.58 RPM	6.35 RPM
SRP051959_heart	0.14 RPM	9.05 RPM
SRP051959_kidney	0.33 RPM	10.32 RPM
SRP051959_liver	0.30 RPM	8.12 RPM
SRP051959_lung	0.33 RPM	8.02 RPM
SRP051959_lymph_node	0.55 RPM	7.15 RPM
SRP051959_skeletal_muscle	0.20 RPM	7.34 RPM
SRP051959_spleen	0.65 RPM	7.65 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2160 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2160 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2160 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014223	4 retrocopies	retro_acar_11, retro_acar_130, retro_acar_142, retro_acar_195,
Choloepus hoffmanni	ENSCHOG00000002112	2 retrocopies	retro_chof_1592, retro_chof_304,
Callithrix jacchus	ENSCJAG00000019848	4 retrocopies	retro_cjac_114, retro_cjac_2160 , retro_cjac_2173, retro_cjac_2974,
Cavia porcellus	ENSCPOG00000012187	1 retrocopy	retro_cpor_930,
Echinops telfairi	ENSETEG00000016572	1 retrocopy	retro_etel_93,
Homo sapiens	ENSG00000171530	3 retrocopies	retro_hsap_3065, retro_hsap_346, retro_hsap_4667,
Loxodonta africana	ENSLAFG00000005316	1 retrocopy	retro_lafr_1212,
Macaca mulatta	ENSMMUG00000011853	1 retrocopy	retro_mmul_229,
Mus musculus	ENSMUSG00000042043	3 retrocopies	retro_mmus_1486, retro_mmus_2839, retro_mmus_2970,
Otolemur garnettii	ENSOGAG00000010198	1 retrocopy	retro_ogar_3193,
Ochotona princeps	ENSOPRG00000002460	4 retrocopies	retro_opri_550, retro_opri_727, retro_opri_879, retro_opri_91,
Procavia capensis	ENSPCAG00000011849	1 retrocopy	retro_pcap_394,
Pongo abelii	ENSPPYG00000015579	2 retrocopies	retro_pabe_2540, retro_pabe_350,
Pan troglodytes	ENSPTRG00000017013	2 retrocopies	retro_ptro_2067, retro_ptro_274,
Rattus norvegicus	ENSRNOG00000048342	1 retrocopy	retro_rnor_140,
Sorex araneus	ENSSARG00000009943	1 retrocopy	retro_sara_699,
Ictidomys tridecemlineatus	ENSSTOG00000009840	1 retrocopy	retro_itri_246,
Tupaia belangeri	ENSTBEG00000006034	6 retrocopies	retro_tbel_1073, retro_tbel_113, retro_tbel_1286, retro_tbel_2336, retro_tbel_2905, retro_tbel_756,
Tarsius syrichta	ENSTSYG00000000514	1 retrocopy	retro_tsyr_1038,
Vicugna pacos	ENSVPAG00000001561	1 retrocopy	retro_vpac_277,