RetrogeneDB ID: retro_cjac_1865

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:160325417..160326101(+)
• Located in intron of: ENSCJAG00000001269

Retrocopy information

• Ensembl ID: ENSCJAG00000001275
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PGRMC2
• Ensembl ID: ENSCJAG00000003328
• Aliases: None
• Description: progesterone receptor membrane component 2 [Source:HGNC Symbol;Acc:16089]

Sequence

>retro_cjac_1865
TGGCGGGCAATGATGGCGGCGGGTGATGGGGACGTGAAGCTAGGCACCCTGGGGAGTGGCAGCGAGAGCAGTAGCAACGC
CAGCCACCAGAGCCCCGGTGGCGTGGGAGTGTCAGCGGAAGGGGGAGGCTGGGCGGCGGCCGCGGCATTGGCTATTCTGA
CCGGCGGGGGCGGGGACATGCTGCTGAATGTGGCGCTGGTGCTGATGGGGGCCTACTGGGTGTGGGTGCGATGGGGGGGC
GGGGTATGGGGTCTGGGTCCGGGGCGGGGCGGGCGAGGAGACACCCGCCGCCTCTCTGCCTCACATTGGGAAGTGGGACT
TCAGCTTGGAGCAGCTGGGCCTGTATGACGGGTCCCGCAACCCGCTCATCCTGCTCTCGATCAGTGGGAAAAGTCTTCCA
TGTGACCAAAGGAAACAAGTTCTAAGGCCGGGCGGGTCCGTATGGAATATTTGCTGGGAGGGATGCCTCTAGAGGACTGG
CAACATTTTTGCCTAGATAAACATGCACTTAGAGAGGAATATGATGATCTCTCAGATTTGAATGCAGTACAAATGGAGAG
TGCTCGAGAATGGGAAATGCAGTTTAAAGAAAAATATGATGATGTAGGCAGACTCCTAAAACCAGGGGAAGAGTCATCAG
AATATACAGATGAGGACGATACCAAGGATCACAATAAACAGGAT

Alignment

ORF - retro_cjac_1865 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.72 %
• Parental protein coverage: 91.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  WRAVMAAGDGDLKLGTLGSGSESSSDGSSESPGGAGAAAEGGGWAAAA-LALLTGGG-EMLLNVALVALV
          WRA.MAAGDGD.KLGTLGSGSESSS..S..SPGG.G..AEGGGWAAAA.LA.LTGGG..MLLN...VALV
Retrocopy WRAMMAAGDGDVKLGTLGSGSESSSNASHQSPGGVGVSAEGGGWAAAAALAILTGGGGDMLLN---VALV

Parental  LLGAYRLWVRW-GRRGLGA--GAG-AGEESPAASLPRMKKRDFSLEQLRQYDGSRNPRILLAVNGK-VFD
          L.GAY..WVRW.G.RG.G...GAG.AGEE.PAASLP...K.DFSLEQL..YDGSRNP.ILL...GK.VF.
Retrocopy LMGAYWVWVRW<GGRGMGSGSGAG<AGEETPAASLPHIGKWDFSLEQLGLYDGSRNPLILLSISGK>VFH

Parental  VTKGSKFYGPAGPYGIFAGRDASRGLATF-CLDKDALRDEYDDLSELNAVQMESVREWEMQFKEKYDYVG
          VTKG.KF.G.AGPYGIFAGRDASRGLATF.CLDK.ALR.EYDDLS.LNAVQMES.REWEMQFKEKYD.VG
Retrocopy VTKGNKF*GRAGPYGIFAGRDASRGLATF>CLDKHALREEYDDLSDLNAVQMESAREWEMQFKEKYDDVG

Parental  RLLKPGEEPSEYTDEEDTKDHNKQD
          RLLKPGEE.SEYTDE.DTKDHNKQD
Retrocopy RLLKPGEESSEYTDEDDTKDHNKQD

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	0.07 RPM	7.01 RPM
SRP051959_heart	0.05 RPM	23.56 RPM
SRP051959_kidney	0.09 RPM	20.06 RPM
SRP051959_liver	0.06 RPM	18.09 RPM
SRP051959_lung	0.34 RPM	10.22 RPM
SRP051959_lymph_node	0.27 RPM	8.58 RPM
SRP051959_skeletal_muscle	0.04 RPM	8.19 RPM
SRP051959_spleen	0.06 RPM	10.17 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1865 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1865 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1865 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003328	1 retrocopy	retro_cjac_1865 ,
Gorilla gorilla	ENSGGOG00000026492	1 retrocopy	retro_ggor_2170,
Procavia capensis	ENSPCAG00000002433	1 retrocopy	retro_pcap_239,