RetrogeneDB ID: retro_ptro_1393

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 20:21620479..21620874(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GSTM3
• Ensembl ID: ENSPTRG00000001063
• Aliases: None
• Description: Pan troglodytes glutathione S-transferase mu 3 (brain) (GSTM3), mRNA. [Source:RefSeq mRNA;Acc:NM_001246568]

Sequence

>retro_ptro_1393
GGTGAGACTGAAGAAGGAAAGGTGCCAGGAGACATCAGGGAGGACCAAATGGTGGAATACCACCTGCAGCTGAAACAGCT
CCACCATGACCCTGACATGAAACATGGAAGCCTCCATACTCGGAACTGCAACCTGGGCAGCTGAAACATTTCTCCTTGTT
TCTGAGGAAGTCATGGTTTCCAGGGGGAAAGCTCACCTTTTTGGATATTCTTACCTGTGATGTCTTAGATCAGAACTGTA
TGTTTGAGCTCAAGTGCCTGTATGAGTTCCCAAATCTGAGGACTTCATGCATCACATTGCAGCTTTGGAGGAAAGAGCTG
CCCCTGTGCAATCTGCCTGTTCTTCGGGATGCCAGTCAGCAGCGAGATGGCCCAGTGGGGACCAAGAGCGTATGC

Alignment

ORF - retro_ptro_1393 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.07 %
• Parental protein coverage: 59.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GETEEEKIRVDIIENQVMDFRTQLIRLCYSSD-HEKLKPQYLEELPGQLKQFSMFLGKFSWFAGEKLTFV
          GETEE.K...DI.E.Q......QL..L....D.HE..KP.Y.E..PGQLK.FS.FL.K.SWF.G.KLTF.
Retrocopy GETEEGKVPGDIREDQMVEYHLQLKQLHHDPD<HETWKPPYSELQPGQLKHFSLFLRK-SWFPGGKLTFL

Parental  DFLTYDILDQNRIFDPKCLDEFPNLKA-FMCRFEALEKIAAYLQSD-QFFKMPINNKMAQW-GNKPVC
          D.LT.D.LDQN..F..KCL.EFPNL...FM....ALE..AA..QS...FF.MP....MAQW.G.K.VC
Retrocopy DILTCDVLDQNCMFELKCLYEFPNLRT<FMHHIAALEERAAPVQSA<LFFGMPVSSEMAQW<GTKSVC

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
SRP007412_brain_prefrontal_cortex	1.57 RPM	16.50 RPM
SRP007412_cerebellum	0.43 RPM	7.21 RPM
SRP007412_heart	0.00 RPM	1.78 RPM
SRP007412_kidney	0.00 RPM	87.74 RPM
SRP007412_liver	0.00 RPM	0.69 RPM
SRP007412_testis	0.00 RPM	1080.92 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1393 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1393 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1393 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_610

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005380	2 retrocopies	retro_chof_1850, retro_chof_1989,
Callithrix jacchus	ENSCJAG00000003168	1 retrocopy	retro_cjac_4,
Erinaceus europaeus	ENSEEUG00000014211	1 retrocopy	retro_eeur_112,
Echinops telfairi	ENSETEG00000005817	2 retrocopies	retro_etel_1074, retro_etel_1910,
Homo sapiens	ENSG00000134202	1 retrocopy	retro_hsap_2419,
Microcebus murinus	ENSMICG00000005185	1 retrocopy	retro_mmur_1571,
Macaca mulatta	ENSMMUG00000008029	2 retrocopies	retro_mmul_610, retro_mmul_941,
Monodelphis domestica	ENSMODG00000001899	1 retrocopy	retro_mdom_331,
Mus musculus	ENSMUSG00000004032	2 retrocopies	retro_mmus_491, retro_mmus_547,
Nomascus leucogenys	ENSNLEG00000003302	1 retrocopy	retro_nleu_1895,
Pan troglodytes	ENSPTRG00000001061	2 retrocopies	retro_ptro_1859, retro_ptro_2468,
Pan troglodytes	ENSPTRG00000001063	2 retrocopies	retro_ptro_1393 , retro_ptro_1709,
Rattus norvegicus	ENSRNOG00000047034	1 retrocopy	retro_rnor_963,
Sus scrofa	ENSSSCG00000006821	2 retrocopies	retro_sscr_10, retro_sscr_855,
Tarsius syrichta	ENSTSYG00000006736	1 retrocopy	retro_tsyr_145,
Tursiops truncatus	ENSTTRG00000009682	1 retrocopy	retro_ttru_1828,