RetrogeneDB ID: retro_cjac_3913

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286232.1:66138..66548(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1R35
• Ensembl ID: ENSCJAG00000015345
• Aliases: None
• Description: protein phosphatase 1, regulatory subunit 35 [Source:HGNC Symbol;Acc:28320]

Sequence

>retro_cjac_3913
CTTGGGTCTGGAGCTGAGAGCCGCAGCCGTGCGGCGAAAGCCGTGGAGGAACAGCTGAAAAAGTCGTTCCAGATCCGCTG
CTGCCTGGAGGAGAGCGTGTCCGAGGGGCCGAACATGCCGCGCTCCAAGAGGCTCTTCCGAGACCTGGTGAGCCTGCAGG
TGCTGGAGGAACCGGTTCTGAATGCCTCGCGGGGAGAAATTGGCTCTCCTGCCGCCGCAGTCTCAACCCCGCCCCAAAGG
AGCCACCTCGGCCAGGGCCAGACATGACCATCTTGTGTGACCCAGAAACACTATTTTATGAATCTCCACACCTGACCCTG
GACGATCTGACCCCTCTCCGGCTTCAGCTCCGGCCCCGCCCTTCAGAGGACACCTTCCTCATGCACGGGACACTGAGGCG
TTGGGAAGCG

Alignment

ORF - retro_cjac_3913 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.26 %
• Parental protein coverage: 54.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LRAAAGSHFDAAKAVEEQLRKSFQIRCGLEESVSEGLNVPRSRRLFRDLVSLQVPEEQVLNAALREKLAL
          L...A.S...AAKAVEEQL.KSFQIRC.LEESVSEG.N.PRS.RLFRDLVSLQV.EE.VLNA..R.....
Retrocopy LGSGAESRSRAAKAVEEQLKKSFQIRCCLEESVSEGPNMPRSKRLFRDLVSLQVLEEPVLNAS-RGEIGS

Parental  LPPQARAPP-PKEPPGPGPDMTILCDPETLFYESPHLTLDGLPPLRLQLRPRPSEDTFLMHRTLRRWEA
          .......PP.PKEPP.PGPDMTILCDPETLFYESPHLTLD.L.PLRLQLRPRPSEDTFLMH.TLRRWEA
Retrocopy PAAAVSTPP<PKEPPRPGPDMTILCDPETLFYESPHLTLDDLTPLRLQLRPRPSEDTFLMHGTLRRWEA

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	2.51 RPM
SRP051959_heart	0.00 RPM	1.81 RPM
SRP051959_kidney	0.00 RPM	2.82 RPM
SRP051959_liver	0.00 RPM	2.84 RPM
SRP051959_lung	0.00 RPM	2.96 RPM
SRP051959_lymph_node	0.00 RPM	2.79 RPM
SRP051959_skeletal_muscle	0.00 RPM	1.70 RPM
SRP051959_spleen	0.00 RPM	2.16 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3913 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3913 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3913 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015345	5 retrocopies	retro_cjac_3472, retro_cjac_3631, retro_cjac_3808, retro_cjac_3913 , retro_cjac_549,