RetrogeneDB ID: retro_hsap_4090

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 8:92921963..92922419(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000271202
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PRR13
• Ensembl ID: ENSG00000205352
• Aliases: PRR13, TXR1
• Description: proline rich 13 [Source:HGNC Symbol;Acc:24528]

Sequence

>retro_hsap_4090
GGCTGGAGGACACATCTAAACACGTGGAATCCCAATGCCGGGCAGCCAGGGCCAAATCTATATTCTCCCAACATTGGGTA
CCCTGGAGGCCCAATCCTGCCCACCCACCACCTATCAATCCACCCTTTCCCCAGGCCCCTTTCCTCCTCCCTGAGGAGCT
CTGCAGGGCAATCCAACTTTTCCCCCAAGTGGAGCCCCTCATCCTGTGCCACAGCCACAGTATCCAGGATGCCAACCCTT
GGTTCCCCACCCTCTTTCACACCCCCTCCTGCCCCTGGAATGCCTCCTGTGAATCCCTTGGCTCCTGACATGGTTGGACC
AGGAGTGATAGTGGACAAGAAGATTCAGAAGAAAATGAAGAAATTTCCTAAAAAGGTACACAAGCACTACAAGCACCACA
AGCATGCCAAGCATTCCTCCTCCCCTTCCTCCTCCTCTTCCAGCAGTGACTCTGAC

Alignment

ORF - retro_hsap_4090 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.44 %
• Parental protein coverage: 94.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GWRTHLNMWNPNAGQPGPNPYPPNIGCPGGS-NPAHPPPINPPFP-PGPCPPPPGAPHGNPAFPPGGPPH
          GWRTHLN.WNPNAGQPGPN.Y.PNIG.PGG..NPAHPPPINPPFP.PGP.PPP.GA..GNP.FPP.G.PH
Retrocopy GWRTHLNTWNPNAGQPGPNLYSPNIGYPGGP<NPAHPPPINPPFP<PGPFPPP*GALQGNPTFPPSGAPH

Parental  PVPQPGYPGCQPLGPYPPPYP-PPAPGIPPVNPLAPGMVGPAVIVDKKMQKKMKKAHKKMHKHQKHHKYH
          PVPQP.YPGCQPL.P.P...P.PPAPG.PPVNPLAP.MVGP.VIVDKK.QKKMKK..KK...........
Retrocopy PVPQPQYPGCQPLVPHPLSHP<PPAPGMPPVNPLAPDMVGPGVIVDKKIQKKMKKFPKKVXXXXXXXXXA

Parental  KHGKHSSSSSSSSSSD
          KH....SSSSSSS.SD
Retrocopy KHSSSPSSSSSSSDSD

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	56.27 RPM
bodymap2_adrenal	0.00 RPM	51.62 RPM
bodymap2_brain	0.00 RPM	19.24 RPM
bodymap2_breast	0.00 RPM	38.23 RPM
bodymap2_colon	0.00 RPM	25.72 RPM
bodymap2_heart	0.00 RPM	16.19 RPM
bodymap2_kidney	0.00 RPM	114.34 RPM
bodymap2_liver	0.00 RPM	31.52 RPM
bodymap2_lung	0.00 RPM	55.92 RPM
bodymap2_lymph_node	0.00 RPM	46.07 RPM
bodymap2_ovary	0.00 RPM	38.11 RPM
bodymap2_prostate	0.00 RPM	54.23 RPM
bodymap2_skeletal_muscle	0.00 RPM	19.35 RPM
bodymap2_testis	0.00 RPM	23.34 RPM
bodymap2_thyroid	0.00 RPM	48.19 RPM
bodymap2_white_blood_cells	0.00 RPM	159.39 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_4090 was not detected

EST

No EST(s) were mapped for retro_hsap_4090 retrocopy.

TSS

No TSS is located nearby retro_hsap_4090 retrocopy 5' end.

Lab

retro_hsap_4090 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4090 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000205352	3 retrocopies	retro_hsap_2058, retro_hsap_4090 , retro_hsap_931,