RetrogeneDB ID: retro_hsap_2419

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 20:21482228..21482620(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000227693
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GSTM3
• Ensembl ID: ENSG00000134202
• Aliases: GSTM3, GST5, GSTB, GSTM3-3, GTM3
• Description: glutathione S-transferase mu 3 (brain) [Source:HGNC Symbol;Acc:4635]

Sequence

>retro_hsap_2419
GAGACTGAAGAAGGAAAGGTGCCAGGAGACATCAGGGAGGACCAAATGGTGGAATACCACCTGCAGCTGAAACAGCTCCA
CCATGACCCTGACATGAAACATGGAAGCCTCCATACTCGGAACTGCAACCTGGGCAGCTGAAACATTTCTCCTTGTTTCT
GAGGAAGTCATGGTTTCCAGGGGGAAAGCTCACCTTTTTGGATATTCTTACCTGTGATGTCTTAGATCAGAACTGTATGT
TTGAGCTCAAGTGCCTGTATGAGTTCCCAAATCTGAGGACTTCATGCACCACATTGCAGCTTTGGAGGAAAGAGCTGCCC
CTGTGCAATCTGCCTGTTCTTCGGGATGCCAGTCAGCAGCGAGATGGCCCAGTGGGGACCAAGAGCGTATGC

Alignment

ORF - retro_hsap_2419 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.01 %
• Parental protein coverage: 59.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ETEEEKIRVDIIENQVMDFRTQLIRLCYSSD-HEKLKPQYLEELPGQLKQFSMFLGKFSWFAGEKLTFVD
          ETEE.K...DI.E.Q......QL..L....D.HE..KP.Y.E..PGQLK.FS.FL.K.SWF.G.KLTF.D
Retrocopy ETEEGKVPGDIREDQMVEYHLQLKQLHHDPD<HETWKPPYSELQPGQLKHFSLFLRK-SWFPGGKLTFLD

Parental  FLTYDILDQNRIFDPKCLDEFPNLKA-FMCRFEALEKIAAYLQSD-QFCKMPINNKMAQW-GNKPVC
          .LT.D.LDQN..F..KCL.EFPNL...FM....ALE..AA..QS...F..MP....MAQW.G.K.VC
Retrocopy ILTCDVLDQNCMFELKCLYEFPNLRT<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
bodymap2_adipose	0.00 RPM	34.07 RPM
bodymap2_adrenal	0.00 RPM	34.39 RPM
bodymap2_brain	0.56 RPM	92.31 RPM
bodymap2_breast	0.00 RPM	65.74 RPM
bodymap2_colon	0.00 RPM	61.45 RPM
bodymap2_heart	0.00 RPM	42.53 RPM
bodymap2_kidney	0.12 RPM	107.52 RPM
bodymap2_liver	0.00 RPM	5.81 RPM
bodymap2_lung	0.00 RPM	73.63 RPM
bodymap2_lymph_node	0.00 RPM	36.27 RPM
bodymap2_ovary	0.00 RPM	212.30 RPM
bodymap2_prostate	0.00 RPM	162.34 RPM
bodymap2_skeletal_muscle	0.00 RPM	27.28 RPM
bodymap2_testis	0.08 RPM	362.21 RPM
bodymap2_thyroid	0.04 RPM	111.44 RPM
bodymap2_white_blood_cells	0.00 RPM	6.87 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_2419 was not detected

EST

No EST(s) were mapped for retro_hsap_2419 retrocopy.

TSS

No TSS is located nearby retro_hsap_2419 retrocopy 5' end.

Lab

retro_hsap_2419 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2419 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 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	ENSG00000134201	1 retrocopy	retro_hsap_2751,
Homo sapiens	ENSG00000134202	1 retrocopy	retro_hsap_2419 ,
Homo sapiens	ENSG00000213366	1 retrocopy	retro_hsap_3643,
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	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,