RetrogeneDB ID: retro_hsap_1069

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 12:133610063..133610556(+)
• Located in intron of: ENSG00000246394

Retrocopy information

• Ensembl ID: ENSG00000255807
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PTP4A2
• Ensembl ID: ENSG00000184007
• Aliases: PTP4A2, HH13, HH7-2, HU-PP-1, OV-1, PRL-2, PRL2, PTP4A, PTPCAAX2, ptp-IV1a, ptp-IV1b
• Description: protein tyrosine phosphatase type IVA, member 2 [Source:HGNC Symbol;Acc:9635]

Sequence

>retro_hsap_1069
ATGGACTGTTCAGCCCCTGTGGAGATTTACAGGAACATGCATTTTCTCATAACCCACAAGTCTACCAGTGCCACTGCAAC
AAGTTCACAGAGGAATGTGAGACGTGTGGAGTGACACCTTTGGTTTGAGTTTGTGATGCTACATTTGGTAAAGTTCCAGT
TGAAAAAGAAGGAATCCATATTTTAGATTGGTCTTTTGACGATGAAGCTCCACCACCTAATCAGATAGCAGATGACTGGC
TAAACCTGTTAATCACTAAAGGGCGTGAAAAGCCAGGTTGCTGCCTTGCAGTGCATTGTGCTGTGGGATTGGGAAGGGCA
CCTGTGCTGGCAGCGCTTGCTTTGAATATGGAATTAAGTATGAAGATGCAGTTCAGTTTATAAGACAAAAAAGAAGGGGA
GCATTCAATTCCAAACAGCTGCTTTACTTGGAGAAATGCCGACCTAAGGTGCAATTACACTTCAGAGATACCAGTGGGCA
TTGCTGTGTTCAG

Alignment

ORF - retro_hsap_1069 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.01 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MNRPAPVEISYENMRFLITHNPTNATL-NKFTEELKKYGVTTLVRVCDATYDKAPVEKEGIHVLDWPFDD
          M...APVEI.Y.NM.FLITH..T.AT..NKFTEE....GVT.LV.VCDAT..K.PVEKEGIH.LDW.FDD
Retrocopy MDCSAPVEI-YRNMHFLITHKSTSATA<NKFTEECETCGVTPLV*VCDATFGKVPVEKEGIHILDWSFDD

Parental  GAPPPNQIVDDWLNLLKTKFREEPGCCVAVHCVA-GLGRAPVLVALALIECGMKYEDAVQFIRQKRRGAF
          .APPPNQI.DDWLNLL.TK.RE.PGCC.AVHC...G.G........A..E.G.KYEDAVQFIRQKRRGAF
Retrocopy EAPPPNQIADDWLNLLITKGREKPGCCLAVHCAV<GIGKG-TCAGSACFEYGIKYEDAVQFIRQKRRGAF

Parental  NSKQLLYLEKYRPKMRLRFRDTNGHCCVQ
          NSKQLLYLEK.RPK..L.FRDT.GHCCVQ
Retrocopy NSKQLLYLEKCRPKVQLHFRDTSGHCCVQ

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	574.21 RPM
bodymap2_adrenal	0.00 RPM	318.20 RPM
bodymap2_brain	0.00 RPM	334.61 RPM
bodymap2_breast	0.00 RPM	434.95 RPM
bodymap2_colon	0.00 RPM	272.98 RPM
bodymap2_heart	0.00 RPM	189.34 RPM
bodymap2_kidney	0.00 RPM	186.85 RPM
bodymap2_liver	0.00 RPM	104.10 RPM
bodymap2_lung	0.00 RPM	295.96 RPM
bodymap2_lymph_node	0.00 RPM	311.00 RPM
bodymap2_ovary	0.00 RPM	426.92 RPM
bodymap2_prostate	0.00 RPM	332.86 RPM
bodymap2_skeletal_muscle	0.00 RPM	538.11 RPM
bodymap2_testis	0.00 RPM	264.30 RPM
bodymap2_thyroid	0.00 RPM	390.94 RPM
bodymap2_white_blood_cells	0.00 RPM	654.97 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1069 was not detected

EST

No EST(s) were mapped for retro_hsap_1069 retrocopy.

TSS

No TSS is located nearby retro_hsap_1069 retrocopy 5' end.

Lab

retro_hsap_1069 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1069 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_727
Gorilla gorilla	retro_ggor_843
Pongo abelii	retro_pabe_890

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000039121	1 retrocopy	retro_btau_638,
Callithrix jacchus	ENSCJAG00000006539	2 retrocopies	retro_cjac_3257, retro_cjac_566,
Homo sapiens	ENSG00000112245	5 retrocopies	retro_hsap_2171, retro_hsap_3212, retro_hsap_479, retro_hsap_4798, retro_hsap_807,
Homo sapiens	ENSG00000184007	4 retrocopies	retro_hsap_1069 , retro_hsap_1754, retro_hsap_4331, retro_hsap_944,
Mus musculus	ENSMUSG00000028788	2 retrocopies	retro_mmus_1894, retro_mmus_2432,
Nomascus leucogenys	ENSNLEG00000002137	3 retrocopies	retro_nleu_2880, retro_nleu_2956, retro_nleu_3015,