RetrogeneDB ID: retro_cjac_2853

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:133025174..133025557(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTS
• Ensembl ID: ENSCJAG00000012437
• Aliases: None
• Description: 6-pyruvoyltetrahydropterin synthase [Source:HGNC Symbol;Acc:9689]

Sequence

>retro_cjac_2853
ATCTCCTTCAGCGCGAGCCGCCGGCTGCACAGTGAATTTCTAAGTGATAAAGAAAACTTGAAACTGTTGAGGAAATGCAT
TAATCCAAATGGCTGTGGGCACAATTATAAAGCTGTGGTGACAACACGTAGAGAGGTTGACCCTGCTACGGGAATGGTTA
TGAATTTGGCTGCTCTCAAAAAATATATGGAGGAGGCGGTTATGCAGCCCTTTGATCATAAGAATCTGAATATGGATGTG
CCATACTTTGCGACGCGGTGAGCACGACTGAAAATGTAGCTGTTTATATCTGGGACACCCTCCAGAAAGTTCTTCCTGTA
GGAGTTCTTCATAAAGCAAAAGTATGTGAAACTGACAATAATGTTGCAGTTTATAAAGGAGAA

Alignment

ORF - retro_cjac_2853 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.52 %
• Parental protein coverage: 88.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ISFSASHRLHSKFLSEEENLKLFGKCSNPNGHGHNYKVVVTVHGQIDPATGMVMNLTDLKKHMEEAIMQP
          ISFSAS.RLHS.FLS..ENLKL..KC.NPNG.GHNYK.VVT.....DPATGMVMNL..LKK.MEEA.MQP
Retrocopy ISFSASRRLHSEFLSDKENLKLLRKCINPNGCGHNYKAVVTTRREVDPATGMVMNLAALKKYMEEAVMQP

Parental  LDHKNLDLDVPYFA-DVVSTTENVAVYIWDNLQKVLPVGVLYKVKVYETDNNIVVYKGE
          .DHKNL..DVPYFA.D.VSTTENVAVYIWD.LQKVLPVGVL.K.KV.ETDNN..VYKGE
Retrocopy FDHKNLNMDVPYFA<DAVSTTENVAVYIWDTLQKVLPVGVLHKAKVCETDNNVAVYKGE

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	1.46 RPM
SRP051959_heart	0.02 RPM	2.86 RPM
SRP051959_kidney	0.00 RPM	8.54 RPM
SRP051959_liver	0.00 RPM	11.42 RPM
SRP051959_lung	0.00 RPM	2.28 RPM
SRP051959_lymph_node	0.00 RPM	1.55 RPM
SRP051959_skeletal_muscle	0.00 RPM	1.75 RPM
SRP051959_spleen	0.00 RPM	2.35 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2853 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2853 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2853 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000013	2 retrocopies	retro_chof_1925, retro_chof_2556,
Callithrix jacchus	ENSCJAG00000012437	2 retrocopies	retro_cjac_2534, retro_cjac_2853 ,
Dasypus novemcinctus	ENSDNOG00000014823	1 retrocopy	retro_dnov_1747,
Echinops telfairi	ENSETEG00000008145	2 retrocopies	retro_etel_1924, retro_etel_2039,
Homo sapiens	ENSG00000150787	1 retrocopy	retro_hsap_3408,
Macaca mulatta	ENSMMUG00000015255	1 retrocopy	retro_mmul_995,
Nomascus leucogenys	ENSNLEG00000007299	1 retrocopy	retro_nleu_1856,
Otolemur garnettii	ENSOGAG00000017191	3 retrocopies	retro_ogar_1718, retro_ogar_2790, retro_ogar_609,
Pongo abelii	ENSPPYG00000003880	1 retrocopy	retro_pabe_432,
Pan troglodytes	ENSPTRG00000004288	3 retrocopies	retro_ptro_2315, retro_ptro_2979, retro_ptro_337,