RetrogeneDB ID: retro_cjac_1653

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 18:2155021..2155601(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTGR1
• Ensembl ID: ENSCJAG00000017571
• Aliases: None
• Description: prostaglandin reductase 1 [Source:HGNC Symbol;Acc:18429]

Sequence

>retro_cjac_1653
TACTTCAGCCTACTTGACCTCTGTGGTGCGCAGCGTGTAGAAACAGTGATGGTTAATGCAGCAGCTGGAGCTGTGGGCTC
TGTGCTGGGGCAACTTGCAAAGCTCAAGGGCTGCAAAGTTGTTGGAGAAGTAGGGTCCGACGAAAAGGTTGCCTACCTTA
AAAAGCTTGGATTTGATGTTAACTACAAGACAGGAGAGCCTTTGAAGAAACTCTGAAGAAAGCCTCCCCTGATGGATACG
ATTGTTATTTTGATAATGTAGGTGGAGAGTTTTCAAACACTGTTCTCTCTCAGATGAAGACATTTGGAAGAATTGCCATA
TGAGGAGTCACCTCTACACATAAGAGTACTGGACCACCTTCCCCAGGCCCACCACCAGAGATTTTTATCTGTCAGGAGCT
TCACATGAAAGGGTTCATCATCACCTGCCGGCAAGGAGATGCCTGCCAAAAAGCTCTGAAGGACTTGCTAAAATGGGTCT
CGGGTAAAATCCAGTTCAGGAATATATCACTGAAGGATCTGAAAACATGCCAGCTGCATTTATGGGACTGCTGAAAGGAG
CGAATGTGGGGAAAACAGTG

Alignment

ORF - retro_cjac_1653 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.87 %
• Parental protein coverage: 59.88 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YFGLLDICGVKGGETVMVNAASGAVGSVVGQIAKLKGCKVVGAVGSDEKVAYLQELGFDVVFNYKTVESL
          YF.LLD.CG....ETVMVNAA.GAVGSV.GQ.AKLKGCKVVG.VGSDEKVAYL..LGFDV..NYKT.E.L
Retrocopy YFSLLDLCGAQRVETVMVNAAAGAVGSVLGQLAKLKGCKVVGEVGSDEKVAYLKKLGFDV--NYKTGEPL

Parental  -EETLKKASPDGYDCYFDNVGGEFSNTVISQMKKYGRIALCGAISTYNRTGPLPPGPPPEIVIYQELRME
          .EETLKKASPDGYDCYFDNVGGEFSNTV.SQMK..GRIA..G..ST...TGP..PGPPPEI.I.QEL.M.
Retrocopy <EETLKKASPDGYDCYFDNVGGEFSNTVLSQMKTFGRIAI*GVTSTHKSTGPPSPGPPPEIFICQELHMK

Parental  GFTVLRWQGDVRQKALKDLLKWVSEGKIQ-CKEYIIEGFENMPAAFMGMLKGDNLGKTI
          GF.....QGD..QKALKDLLKWVS.GKIQ...EYI.EG.ENMPAAFMG.LKG.N.GKT.
Retrocopy GFIITCRQGDACQKALKDLLKWVS-GKIQ<VQEYITEGSENMPAAFMGLLKGANVGKTV

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	158.73 RPM
SRP051959_heart	0.00 RPM	3.02 RPM
SRP051959_kidney	0.00 RPM	25.45 RPM
SRP051959_liver	0.00 RPM	57.03 RPM
SRP051959_lung	0.00 RPM	5.03 RPM
SRP051959_lymph_node	0.00 RPM	1.23 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.68 RPM
SRP051959_spleen	0.00 RPM	6.18 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1653 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1653 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1653 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003000	2 retrocopies	retro_cfam_1290, retro_cfam_1876,
Callithrix jacchus	ENSCJAG00000017571	1 retrocopy	retro_cjac_1653 ,
Echinops telfairi	ENSETEG00000006136	1 retrocopy	retro_etel_358,
Felis catus	ENSFCAG00000004339	1 retrocopy	retro_fcat_1898,
Homo sapiens	ENSG00000106853	1 retrocopy	retro_hsap_219,
Nomascus leucogenys	ENSNLEG00000017487	1 retrocopy	retro_nleu_2424,
Otolemur garnettii	ENSOGAG00000011144	1 retrocopy	retro_ogar_2834,
Pongo abelii	ENSPPYG00000019499	1 retrocopy	retro_pabe_283,