RetrogeneDB ID: retro_cjac_1817

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:80089998..80090358(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C1orf146
• Ensembl ID: ENSCJAG00000017547
• Aliases: None
• Description: chromosome 1 open reading frame 146 [Source:HGNC Symbol;Acc:24032]

Sequence

>retro_cjac_1817
ATAGCTGAAAGTGGTGGAAAATAAAAAATAAAATGAACAAAAACAATTCATATTAGTTCATTTCTTTAGTGTTATGAAGT
TGTAGCTGCCCTAGAAAATTAAGGCCACAACTTTTGGTAATCAAATAAATGAAAAATAAATCAATTACAGTTTCTTTTTC
TGGAGTTGCATTTTAGTTGATGGGTGCTAAGGAATGCCTATGTTAGCTGAAGCAATACTCCTAGCAAAATATGAGAAGTT
TATAAATATTCACTGAAGTAACTTTTTGGATTTATCTACTGCCCTTTATGGACCCAAGAAATGGGAACTACTGAGTATTT
TTCAGAGATTCTGAGTAGTAATTTACAAATAGTTCCAGTA

Alignment

ORF - retro_cjac_1817 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.4 %
• Parental protein coverage: 67.22 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAESG-KEKIKWTTTIIVSSSLKSYEIATALENRSHKVRYSDS-VENGSIIFSLSGVAFLLMDTKECLT-
          .AESG.K.KIK.T.TI..SS.L..YE...ALEN..H....S.....N.SI..S.SGVAF.LM..KECL..
Retrocopy IAESGGK*KIK*TKTIHISSFL*CYEVVAALEN*GHNFW*SNK<MKNKSITVSFSGVAF*LMGAKECLC<

Parental  STEEIFLAKIEKFINIHQNSFLVLSAALHGPEERKLMFRIQQRF-LGCNLRILPV
          ..E.I.LAK.EKFINIH...FL.LS.AL.GP....L...I.QRF.L..NL.I.PV
Retrocopy LAEAILLAKYEKFINIH*SNFLDLSTALYGPKKWELL-SIFQRF<LSSNLQIVPV

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	0.00 RPM
SRP051959_heart	0.00 RPM	0.00 RPM
SRP051959_kidney	0.00 RPM	0.00 RPM
SRP051959_liver	0.00 RPM	0.00 RPM
SRP051959_lung	0.00 RPM	0.02 RPM
SRP051959_lymph_node	0.00 RPM	0.02 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.00 RPM
SRP051959_spleen	0.00 RPM	0.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1817 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1817 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1817 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3381
Pan troglodytes	retro_ptro_2298
Gorilla gorilla	retro_ggor_2289
Pongo abelii	retro_pabe_2780
Macaca mulatta	retro_mmul_2107

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000027936	1 retrocopy	retro_btau_490,
Choloepus hoffmanni	ENSCHOG00000004012	1 retrocopy	retro_chof_2167,
Callithrix jacchus	ENSCJAG00000017547	1 retrocopy	retro_cjac_1817 ,
Erinaceus europaeus	ENSEEUG00000003083	1 retrocopy	retro_eeur_601,
Homo sapiens	ENSG00000203910	1 retrocopy	retro_hsap_3381,
Gorilla gorilla	ENSGGOG00000006653	1 retrocopy	retro_ggor_2289,
Macropus eugenii	ENSMEUG00000013311	1 retrocopy	retro_meug_143,
Myotis lucifugus	ENSMLUG00000016984	1 retrocopy	retro_mluc_1260,
Macaca mulatta	ENSMMUG00000010094	1 retrocopy	retro_mmul_2107,
Nomascus leucogenys	ENSNLEG00000010426	1 retrocopy	retro_nleu_970,
Pongo abelii	ENSPPYG00000001156	1 retrocopy	retro_pabe_2780,
Pan troglodytes	ENSPTRG00000030530	1 retrocopy	retro_ptro_2298,
Ictidomys tridecemlineatus	ENSSTOG00000012506	1 retrocopy	retro_itri_404,
Tursiops truncatus	ENSTTRG00000014426	1 retrocopy	retro_ttru_1727,