RetrogeneDB ID: retro_cjac_428

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:79672793..79673042(+)
• Located in intron of: ENSCJAG00000012556

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1R14B
• Ensembl ID: ENSCJAG00000018111
• Aliases: None
• Description: protein phosphatase 1, regulatory (inhibitor) subunit 14B [Source:HGNC Symbol;Acc:9057]

Sequence

>retro_cjac_428
CTCCAGAAGCGCCTCAACCTACAGGAGTAGATCTTGGAGCAGCTCACGTGCCTCTACAACTGCCAGGAAGAGGAGATCCC
AGAACTGAAGATTGACGTGGATGAGCTCCTGGACATGGAGAGTGAGGATGCCCAGGCTGCCAGGGTCAAGGAGCTGCTGG
TTGACTGTTAGAAACCCACAGAGGCCTTCATCTCTAGCCTGCTGGACAAGATCGGGGGCATGCAGAAGCTGAGCACACCC
CAGAAGAAA

Alignment

ORF - retro_cjac_428 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.75 %
• Parental protein coverage: 56.46 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LRKRLNLEEWILEQLTRLYDCQEEEIPELEIDVDELLDMESDDARAARVKELLVDCYKPTEAFISGLLDK
          L.KRLNL.E.ILEQLT.LY.CQEEEIPEL.IDVDELLDMES.DA.AARVKELLVDC.KPTEAFIS.LLDK
Retrocopy LQKRLNLQE*ILEQLTCLYNCQEEEIPELKIDVDELLDMESEDAQAARVKELLVDC*KPTEAFISSLLDK

Parental  IRGMQKLSTPQKK
          I.GMQKLSTPQKK
Retrocopy IGGMQKLSTPQKK

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	9.76 RPM
SRP051959_heart	0.18 RPM	9.82 RPM
SRP051959_kidney	0.07 RPM	9.61 RPM
SRP051959_liver	0.17 RPM	6.87 RPM
SRP051959_lung	0.28 RPM	6.67 RPM
SRP051959_lymph_node	0.41 RPM	8.17 RPM
SRP051959_skeletal_muscle	0.04 RPM	9.61 RPM
SRP051959_spleen	0.17 RPM	9.29 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_428 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_428 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_428 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018111	3 retrocopies	retro_cjac_3591, retro_cjac_428 , retro_cjac_532,
Homo sapiens	ENSG00000173457	4 retrocopies	retro_hsap_2205, retro_hsap_3101, retro_hsap_3655, retro_hsap_3838,
Mustela putorius furo	ENSMPUG00000013208	2 retrocopies	retro_mputfur_235, retro_mputfur_798,
Nomascus leucogenys	ENSNLEG00000004890	2 retrocopies	retro_nleu_324, retro_nleu_335,
Pan troglodytes	ENSPTRG00000041138	6 retrocopies	retro_ptro_1674, retro_ptro_2097, retro_ptro_2480, retro_ptro_2614, retro_ptro_3089, retro_ptro_935,
Sus scrofa	ENSSSCG00000013035	2 retrocopies	retro_sscr_1087, retro_sscr_892,
Ictidomys tridecemlineatus	ENSSTOG00000021959	1 retrocopy	retro_itri_1110,