RetrogeneDB ID: retro_cjac_1272

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:36800187..36800771(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000033350
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PTGES2
• Ensembl ID: ENSCJAG00000019932
• Aliases: None
• Description: prostaglandin E synthase 2 [Source:HGNC Symbol;Acc:17822]

Sequence

>retro_cjac_1272
ATGGCCCCAGCTGCTCAGGTGGTGTGGGCGCTGTGGCCTGGCAGGTGCACCTTGGCCTGGAGGCTGGGCGGCCGCCCCCA
GCTGCTGCTCCCCACACAGAACCAGGCTGGCTTCACGGGGGTGGCGGGCGGCTCGGGTCCTGTGGCTGCCACCCATAAGG
GGAGCCCACGGCTGCTAGGGGCAGTGGCACTTGCCCTGGGGGGAACCCTGGGGCTGTACCACACAGCTCGGTGGCACCTG
CACACCCAGGACCTCCATGCAGAGCACTCAGCCACGCAGCTCTCCCTGTCCAGCCACCTGCAGCTGACCCTGTACCAATA
CAAGACGTGTCCCTTCTGCAGCAAGGTCCGAGCCTTCCTCGACTTCCATGCCCTGCCCTACCAGGTGGTGGAAGTCAATC
CTGTGCACAGGGCTGAGATCAAGTTCTCCTCCTACAGAAAGGTGCCCATCCTGGTGGCCCAGGTTGGAAAAAACAACAAC
TGAACAACTCCTCTGTCATCATCAGTGCCCTCAAGACGTACCTGGTTTCAGGGCAGCCCCTGGAAGAGATCATCACCTAC
TATCCAGCCATGAAGGCTGTGAAC

Alignment

ORF - retro_cjac_1272 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.7 %
• Parental protein coverage: 51.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAPAARVARALWPGGCALAWRLSGRPQLLLPTQNRAGFAGSAGGPGPVAAALKGSPRLLGAAALALGGAL
          MAPAA.V..ALWPG.C.LAWRL.GRPQLLLPTQN.AGF.G.AGG.GPVAA..KGSPRLLGA.ALALGG.L
Retrocopy MAPAAQVVWALWPGRCTLAWRLGGRPQLLLPTQNQAGFTGVAGGSGPVAATHKGSPRLLGAVALALGGTL

Parental  GLYHTARWHLRAQDLHAEHSAAQLSLSSHLQLTLYQYKTCPFCSKVRAFLDFHALPYQVVEVNPVRRAEI
          GLYHTARWHL..QDLHAEH................QYKTCPFCSKVRAFLDFHALPYQVVEVNPV.RAEI
Retrocopy GLYHTARWHLHTQDLHAEHXXXXXXXXXXXXXXXXQYKTCPFCSKVRAFLDFHALPYQVVEVNPVHRAEI

Parental  KFSSYRKVPILVAQVGENS-QQLNDSSVIISALKTYLVSGQPLEEIITYYPAMKAVN
          KFSSYRKVPILVAQVG.N..Q..N.S.VIISALKTYLVSGQPLEEIITYYPAMKAVN
Retrocopy KFSSYRKVPILVAQVGKNN<QLNNSS-VIISALKTYLVSGQPLEEIITYYPAMKAVN

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	0.62 RPM	14.75 RPM
SRP051959_heart	0.23 RPM	15.35 RPM
SRP051959_kidney	0.42 RPM	14.64 RPM
SRP051959_liver	0.69 RPM	11.11 RPM
SRP051959_lung	0.81 RPM	4.52 RPM
SRP051959_lymph_node	1.51 RPM	4.82 RPM
SRP051959_skeletal_muscle	0.46 RPM	31.77 RPM
SRP051959_spleen	0.84 RPM	5.04 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1272 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1272 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1272 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	ENSCJAG00000019932	1 retrocopy	retro_cjac_1272 ,