RetrogeneDB ID: retro_cjac_468

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:137810461..137811268(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RSRC2
• Ensembl ID: ENSCJAG00000020419
• Aliases: None
• Description: arginine/serine-rich coiled-coil 2 [Source:HGNC Symbol;Acc:30559]

Sequence

>retro_cjac_468
TCAAGATTCAGAAACAGGAAAAGAAAACAGTGGATCAGGTCTCATTCCTGCTCAAGATTGAGACATAGGCATAGGACTAG
AAGCAGGAGTAGAACAAGGAGTAGGAGTTAAGAGACAAAGAAGAGAATTGAAAAGCCCAGAAGATTTAGCAGAAGTTTAA
GCCAGACTCTGAGTCCACCTCCCTTCAGTGGCAGAAACGCAGCAATGGATGCACAAGAAGGCTTAGCTAGGAGATTAGAA
AGGATGAAGAAATTACAAGAACAGCGAGAAAAGGAAAATGTTGAAAAACAAAAATAAGAAATAGCTGCAGCAGCTACAAC
TACTGAGGGTTCTCTTCCCAATGAAGCCACCCTGTTGGCATTAGGAACACAGGTAACACCTCAGATAGCCACGGCAACGC
AGATGGCAACCTGGCAAGCTAAAGCTGTGGCAGAGACAGGAACAGCTATACCTAGCTACTGTAACCCAGCAGCTAAATCC
AGTGAAATTTTCTGAACAAGAGAAAAAAGGAAAATGCTTTGACAGGGCAAGAAAGAAGGGGACAAATCCCAGTCTGCTGA
AATATGGGAAAAATTGCATTTTGGAAACAAGGACCAAAATGTCAAATTTAGGAAATTGATGGGTATGAAGAGTGAAACTG
AAGCTGGATGTAGCTCAGTTGATGAAGAAAATTCCAAGCCTCTGAAGCAACAGGAAGAAGTATTTAGAAGTTTAGATGCT
CAGTATGAAATGGCAAGATCACAAACCCACACATAAAGAGGAATGGGTTTGGTTTTCACATCTTCAATGTGAGAAATGGA
TGCAGTT

Alignment

ORF - retro_cjac_468 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.97 %
• Parental protein coverage: 62.3 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SRSRSRERKRRIRSRSRSRSRHRHRTRSRSRTRSRSRDRKKRIEKPRRFSRSLSRTPSPPPFRGRNTAMD
          SR.R.R.RK..IRS.S.SR.RHRHRTRSRSRTRSRS...KKRIEKPRRFSRSLS.T.SPPPF.GRN.AMD
Retrocopy SRFRNRKRKQWIRSHSCSRLRHRHRTRSRSRTRSRS*ETKKRIEKPRRFSRSLSQTLSPPPFSGRNAAMD

Parental  AQEALARRLERAKKLQEQREKEMVEKQKQQEIAAAAAATGGSVLNVAALLASGTQVTPQIAMAAQMAALQ
          AQE.LARRLER.KKLQEQREKE.VEKQK..EIAAAA..T.GS..N.A.LLA.GTQVTPQIA.A.QMA..Q
Retrocopy AQEGLARRLERMKKLQEQREKENVEKQK*-EIAAAATTTEGSLPNEATLLALGTQVTPQIATATQMATWQ

Parental  AKALAETGIAVPSYYNPAAVNPMKFAEQEKKRKMLWQGKKEGDKSQSAEIWEKLNFGNKDQNVKFRKLMG
          AKA.AETG.A.PSY.NPAA.....F...E.KRKML.QGKKEGDKSQSAEIWEKL.FGNKDQNVKFRKLMG
Retrocopy AKAVAETGTAIPSYCNPAAKSSEIF*TRE-KRKML*QGKKEGDKSQSAEIWEKLHFGNKDQNVKFRKLMG

Parental  IKSEDEAGCSSVDEESYKTLKQQEEVFRNLDAQYEMARSQTHTQRGMGLGFTSSMRGMDAV
          .KSE.EAGCSSVDEE..K.LKQQEEVFR.LDAQYEMARSQTHT.RGMGL.FTSSM..MDAV
Retrocopy MKSETEAGCSSVDEENSKPLKQQEEVFRSLDAQYEMARSQTHT*RGMGLVFTSSM*EMDAV

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	25.01 RPM
SRP051959_heart	0.05 RPM	31.33 RPM
SRP051959_kidney	0.00 RPM	34.06 RPM
SRP051959_liver	0.00 RPM	23.11 RPM
SRP051959_lung	0.07 RPM	46.75 RPM
SRP051959_lymph_node	0.02 RPM	52.17 RPM
SRP051959_skeletal_muscle	0.04 RPM	29.39 RPM
SRP051959_spleen	0.00 RPM	49.66 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_468 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_468 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_468 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020419	1 retrocopy	retro_cjac_468 ,
Dasypus novemcinctus	ENSDNOG00000008912	1 retrocopy	retro_dnov_303,
Macaca mulatta	ENSMMUG00000004412	1 retrocopy	retro_mmul_1179,
Mus musculus	ENSMUSG00000029422	1 retrocopy	retro_mmus_2465,
Rattus norvegicus	ENSRNOG00000001238	1 retrocopy	retro_rnor_1536,