RetrogeneDB ID: retro_cjac_1387

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:24999853..25000206(-)
• Located in intron of: ENSCJAG00000003788

Retrocopy information

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

Parental gene information

• Parental gene symbol: SSNA1
• Ensembl ID: ENSCJAG00000013053
• Aliases: None
• Description: Sjogren syndrome nuclear autoantigen 1 [Source:HGNC Symbol;Acc:11321]

Sequence

>retro_cjac_1387
TTGACCCAGCAGGGTATGATACTGCAGAACTACAACAACGAGCTGGTCGAGTGCATAAAGGAGCTGTGCCAGAAGCAGGA
GGAGCTGTGCCAGCAGATCCAGCAGGAGGAAGATAAGAAGCAGCGCAGAATGAGTTGAGGCAGCTAACAGAGAAGCTGGC
TCTCGTCAACGAGAACCTAGCACACAGGATTGCTGTTCGCAACAAGTTCTACCGGACCACTGCAGAGATGGAGGACACCT
TCCTCCAGATCCTGGAGAGCTCCCAGACTTTACTTAGTGTCCTGAAGAGGGAAGCTGGGAACCTGACCAAGGTTACAGCC
TTAGACTAGAAAAGTAGCGGTGGCAGGGGCAGC

Alignment

ORF - retro_cjac_1387 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.17 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTQQGAALQNYNNELVKCIEELCQKREDLCRQIQQEEDEKQR-LQNEVRQLTEKLARVNENLARKIASRN
          .TQQG..LQNYNNELV.CI.ELCQK.E.LC.QIQQEE..K....QNE.RQLTEKLA.VNENLA..IA.RN
Retrocopy LTQQGMILQNYNNELVECIKELCQKQEELCQQIQQEE-DKKQ<AQNELRQLTEKLALVNENLAHRIAVRN

Parental  EFDRTIAETEAAYLKILESSQTLLSVLKREAGNLTKATASDQKSSGGRDS
          .F.RT.AE.E...L.ILESSQTLLSVLKREAGNLTK.TA.D.KSSGGR.S
Retrocopy KFYRTTAEMEDTFLQILESSQTLLSVLKREAGNLTKVTALD*KSSGGRGS

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	1.18 RPM	3.57 RPM
SRP051959_heart	0.70 RPM	4.58 RPM
SRP051959_kidney	0.75 RPM	4.19 RPM
SRP051959_liver	0.50 RPM	3.29 RPM
SRP051959_lung	1.24 RPM	4.15 RPM
SRP051959_lymph_node	1.39 RPM	4.57 RPM
SRP051959_skeletal_muscle	0.72 RPM	4.35 RPM
SRP051959_spleen	0.82 RPM	3.99 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1387 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1387 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1387 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013053	1 retrocopy	retro_cjac_1387 ,