RetrogeneDB ID: retro_cjac_1751

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 19:33501572..33502018(-)
• Located in intron of: ENSCJAG00000016730

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM96A
• Ensembl ID: ENSCJAG00000004834
• Aliases: None
• Description: family with sequence similarity 96, member A [Source:HGNC Symbol;Acc:26235]

Sequence

>retro_cjac_1751
ATGGAGGGGGCATCTGGGCTGCTCTCCTGGACACAAGCAGAGTCCTGTGGCTCTCAGACCTCTCTGAGCAGGGAGCTGCC
TGGCAGCCCTGGATCATGGAAGAGAAAGTGCTAGAGGTTTATGATTTGATTCAAACTATCCCAGACCCAGAAAAGCCTAA
TATTTTAGAAGAACTGGAATTGGCAATGGAAAGTTGTGTGGAAGTTCAGAAGATAAACGAACAAGACTATGTGGTTATTA
TCAAGGTGACACCACAGTACCGCATTGATATTTGGTGACTCCTATGGAGCTGTGCTTAAAACTTAAGCCATGTTTACCAT
TTAAACATAAGTCGGAAATCTACATTTCTGAAGGAAGCCACTCAACAGAAGAAGACATCAATAAGGGAGATAAATGACAA
AGAAAGAGTGGTGGCTGCAATTGAAAACCCCAACTTAGGGGAAGTG

Alignment

ORF - retro_cjac_1751 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 94.38 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MQRVSGLLSWT-LNRVLWLSGLSEPGAARQLRIMEEKALEVYDLIRTIRDPEKPSTLEELEVVSESCVEV
          M...SGLLSWT...RVLWLS.LSE.GAA.Q..IMEEK.LEVYDLI.TI.DPEKP..LEELE...ESCVEV
Retrocopy MEGASGLLSWT<TSRVLWLSDLSEQGAAWQPWIMEEKVLEVYDLIQTIPDPEKPNILEELELAMESCVEV

Parental  QEINEEEYLVIIRFTP-TVPHCSLATLIGLCLRVKLQRCLPFKHKLEIYISEGTHSTEEDINK-QINDKE
          Q.INE..Y.VII..TP.TVPH..L.T...LCL..KL..CLPFKHK.EIYISEG.HSTEEDINK..INDKE
Retrocopy QKINEQDYVVIIKVTP<TVPH*YLVTPMELCL--KLKPCLPFKHKSEIYISEGSHSTEEDINK>EINDKE

Parental  RVAAAMENPNLREI
          RV.AA.ENPNL.E.
Retrocopy RVVAAIENPNLGEV

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	0.11 RPM	7.61 RPM
SRP051959_heart	0.09 RPM	6.75 RPM
SRP051959_kidney	0.13 RPM	8.30 RPM
SRP051959_liver	0.02 RPM	30.09 RPM
SRP051959_lung	0.05 RPM	6.80 RPM
SRP051959_lymph_node	0.02 RPM	10.32 RPM
SRP051959_skeletal_muscle	0.09 RPM	3.87 RPM
SRP051959_spleen	0.02 RPM	14.52 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1751 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1751 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1751 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002448	1 retrocopy	retro_amel_1707,
Bos taurus	ENSBTAG00000002012	2 retrocopies	retro_btau_509, retro_btau_984,
Canis familiaris	ENSCAFG00000017035	2 retrocopies	retro_cfam_1450, retro_cfam_439,
Callithrix jacchus	ENSCJAG00000004834	1 retrocopy	retro_cjac_1751 ,
Equus caballus	ENSECAG00000010303	1 retrocopy	retro_ecab_364,
Erinaceus europaeus	ENSEEUG00000000854	1 retrocopy	retro_eeur_323,
Felis catus	ENSFCAG00000004178	1 retrocopy	retro_fcat_1379,
Homo sapiens	ENSG00000166797	2 retrocopies	retro_hsap_2763, retro_hsap_522,
Gorilla gorilla	ENSGGOG00000016550	2 retrocopies	retro_ggor_1921, retro_ggor_481,
Loxodonta africana	ENSLAFG00000011114	1 retrocopy	retro_lafr_758,
Macropus eugenii	ENSMEUG00000005979	2 retrocopies	retro_meug_471, retro_meug_85,
Microcebus murinus	ENSMICG00000011072	1 retrocopy	retro_mmur_233,
Myotis lucifugus	ENSMLUG00000028233	2 retrocopies	retro_mluc_578, retro_mluc_893,
Mustela putorius furo	ENSMPUG00000000605	1 retrocopy	retro_mputfur_722,
Mus musculus	ENSMUSG00000032381	1 retrocopy	retro_mmus_1919,
Nomascus leucogenys	ENSNLEG00000026932	3 retrocopies	retro_nleu_156, retro_nleu_2577, retro_nleu_667,
Ochotona princeps	ENSOPRG00000015229	5 retrocopies	retro_opri_476, retro_opri_522, retro_opri_828, retro_opri_84, retro_opri_999,
Pongo abelii	ENSPPYG00000006544	1 retrocopy	retro_pabe_224,
Pan troglodytes	ENSPTRG00000007153	2 retrocopies	retro_ptro_1870, retro_ptro_390,
Sorex araneus	ENSSARG00000002068	3 retrocopies	retro_sara_54, retro_sara_597, retro_sara_742,
Tarsius syrichta	ENSTSYG00000004186	2 retrocopies	retro_tsyr_195, retro_tsyr_62,