RetrogeneDB ID: retro_hsap_3532

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 6:149915219..149915676(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000220848
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS18
• Ensembl ID: ENSG00000235650
• Aliases: None
• Description: ribosomal protein S18 [Source:HGNC Symbol;Acc:10401]

Sequence

>retro_hsap_3532
ATGTCTCTAGTGATCCCTGAAAAGTCCCAGCATATTTTGCCGAGTAGTCAACACCAACATTGATGGGTGGCGGAAAATGG
CCTTTGCCATCACTGCCGTTAAGGGTGTGGGCCGAAGATATGCTCATGTGGTGTTGAGGAAAGCAGACACTGACCTCACC
AAGAGGGCGGGAGAACTCACTGAGGATGAGGTGGAACATGTGATCACCATTATGCAGAATCCACACTAGTACAAGATGCC
AGCCTGGTTCTTGAACAGACAGAAGGATGTAAAGGATGGAAAATATAGCCAGGTCCTAGCCAATGGTCTGGACAACAAGC
TCTGTGAAGACCTGGAGCGACTGAAAAAGATTCGGGCCCGTAGAGGGCTGCGTCACTTCTGGGGCCTTCGTGTCCGAGGC
CAGCACACCAAGACCACAGGCTGCCGTGGCCGCATCGTGGGTGTGTCTAAGAAGAAG

Alignment

ORF - retro_hsap_3532 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.54 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSLVIPEKFQHIL-RVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELTEDEVERVIT
          MSLVIPEK.QHIL.RV.NTNIDG.RK.AFAITA.KGVGRRYAHVVLRKAD.DLTKRAGELTEDEVE.VIT
Retrocopy MSLVIPEKSQHIL>RVVNTNIDGWRKMAFAITAVKGVGRRYAHVVLRKADTDLTKRAGELTEDEVEHVIT

Parental  IMQNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAHRGLRHFWGLRVRGQHTKTT
          IMQNP..YK.P.WFLNRQKDVKDGKYSQVLANGLDNKL.EDLERLKKIRA.RGLRHFWGLRVRGQHTKTT
Retrocopy IMQNPH*YKMPAWFLNRQKDVKDGKYSQVLANGLDNKLCEDLERLKKIRARRGLRHFWGLRVRGQHTKTT

Parental  GRRGRTVGVSKKK
          G.RGR.VGVSKKK
Retrocopy GCRGRIVGVSKKK

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	2.64 RPM	0.00 RPM
bodymap2_adrenal	1.70 RPM	0.00 RPM
bodymap2_brain	0.84 RPM	0.00 RPM
bodymap2_breast	1.95 RPM	0.00 RPM
bodymap2_colon	2.51 RPM	0.00 RPM
bodymap2_heart	0.79 RPM	0.00 RPM
bodymap2_kidney	1.28 RPM	0.00 RPM
bodymap2_liver	0.63 RPM	0.00 RPM
bodymap2_lung	2.09 RPM	0.00 RPM
bodymap2_lymph_node	1.50 RPM	0.00 RPM
bodymap2_ovary	2.91 RPM	0.00 RPM
bodymap2_prostate	1.07 RPM	0.00 RPM
bodymap2_skeletal_muscle	0.69 RPM	0.00 RPM
bodymap2_testis	1.68 RPM	0.00 RPM
bodymap2_thyroid	2.41 RPM	0.00 RPM
bodymap2_white_blood_cells	0.53 RPM	0.00 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3532 was not detected

EST

No EST(s) were mapped for retro_hsap_3532 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_160536	290 libraries	439 libraries	1004 libraries	87 libraries	9 libraries

The graphical summary, for retro_hsap_3532 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_3532 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3532 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	ENSG00000235650	3 retrocopies	retro_hsap_1371, retro_hsap_2408, retro_hsap_3532 ,