RetrogeneDB ID: retro_hsap_1725

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 17:18476065..18476272(+)
• Located in intron of: ENSG00000154874

Retrocopy information

• Ensembl ID: ENSG00000227077
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS28
• Ensembl ID: ENSG00000233927
• Aliases: None
• Description: ribosomal protein S28 [Source:HGNC Symbol;Acc:10418]

Sequence

>retro_hsap_1725
TTGGACACCAGCCGTGTGCAGCCTATCAAGCTGGCCAGGGTCACCAAGGTCCTGGGCAGGACCGGCTCTCAGGGACAGTG
CACGCAGGTGCGCGTGGAATTCATGGACGACACGAGCCGATCCATCATCCGCAATGTAAAAGGCCCCGTGCGCGAGGGCG
ACGTGCTCACCCTTTTGGAGTCAGAGCGAGAAGCCCGGAGGTTGCGC

Alignment

ORF - retro_hsap_1725 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.55 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDTSRVQPIKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLESEREARRLR
          .DTSRVQPIKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLESEREARRLR
Retrocopy LDTSRVQPIKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLESEREARRLR

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	0.06 RPM	59.97 RPM
bodymap2_adrenal	0.14 RPM	157.29 RPM
bodymap2_brain	0.02 RPM	21.10 RPM
bodymap2_breast	0.14 RPM	44.71 RPM
bodymap2_colon	0.02 RPM	136.61 RPM
bodymap2_heart	0.00 RPM	24.70 RPM
bodymap2_kidney	0.02 RPM	27.38 RPM
bodymap2_liver	0.00 RPM	40.01 RPM
bodymap2_lung	0.09 RPM	87.59 RPM
bodymap2_lymph_node	0.05 RPM	144.33 RPM
bodymap2_ovary	0.04 RPM	60.16 RPM
bodymap2_prostate	0.02 RPM	99.05 RPM
bodymap2_skeletal_muscle	0.02 RPM	61.27 RPM
bodymap2_testis	0.08 RPM	41.76 RPM
bodymap2_thyroid	0.02 RPM	40.73 RPM
bodymap2_white_blood_cells	0.02 RPM	193.16 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1725 was not detected

EST

No EST(s) were mapped for retro_hsap_1725 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_56087	143 libraries	218 libraries	1062 libraries	299 libraries	107 libraries

The graphical summary, for retro_hsap_1725 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_1725 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1725 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1228

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000233927	9 retrocopies	retro_hsap_1192, retro_hsap_1352, retro_hsap_1725 , retro_hsap_2220, retro_hsap_2279, retro_hsap_3748, retro_hsap_505, retro_hsap_523, retro_hsap_799,
Loxodonta africana	ENSLAFG00000029923	2 retrocopies	retro_lafr_168, retro_lafr_755,
Macaca mulatta	ENSMMUG00000028895	3 retrocopies	retro_mmul_122, retro_mmul_182, retro_mmul_807,
Monodelphis domestica	ENSMODG00000003890	1 retrocopy	retro_mdom_291,
Mus musculus	ENSMUSG00000067288	3 retrocopies	retro_mmus_2949, retro_mmus_3283, retro_mmus_91,
Pan troglodytes	ENSPTRG00000040141	6 retrocopies	retro_ptro_1228, retro_ptro_1613, retro_ptro_3037, retro_ptro_378, retro_ptro_391, retro_ptro_927,
Rattus norvegicus	ENSRNOG00000042886	2 retrocopies	retro_rnor_95, retro_rnor_96,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.62 RPM
CEU_NA11843	0.82 RPM
CEU_NA11930	0.07 RPM
CEU_NA12004	0.15 RPM
CEU_NA12400	0.39 RPM
CEU_NA12751	0.36 RPM
CEU_NA12760	1.21 RPM
CEU_NA12827	0.19 RPM
CEU_NA12872	0.44 RPM
CEU_NA12873	0.64 RPM
FIN_HG00183	0.49 RPM
FIN_HG00277	0.11 RPM
FIN_HG00315	0.39 RPM
FIN_HG00321	0.18 RPM
FIN_HG00328	0.43 RPM
FIN_HG00338	0.45 RPM
FIN_HG00349	0.17 RPM
FIN_HG00375	0.42 RPM
FIN_HG00377	0.25 RPM
FIN_HG00378	0.17 RPM
GBR_HG00099	0.26 RPM
GBR_HG00111	0.32 RPM
GBR_HG00114	0.39 RPM
GBR_HG00119	0.14 RPM
GBR_HG00131	0.32 RPM
GBR_HG00133	0.19 RPM
GBR_HG00134	0.35 RPM
GBR_HG00137	0.69 RPM
GBR_HG00142	0.31 RPM
GBR_HG00143	0.29 RPM
TSI_NA20512	0.79 RPM
TSI_NA20513	0.19 RPM
TSI_NA20518	0.22 RPM
TSI_NA20532	0.17 RPM
TSI_NA20538	0.60 RPM
TSI_NA20756	0.52 RPM
TSI_NA20765	0.39 RPM
TSI_NA20771	0.31 RPM
TSI_NA20786	0.47 RPM
TSI_NA20798	0.34 RPM
YRI_NA18870	0.30 RPM
YRI_NA18907	0.24 RPM
YRI_NA18916	0.17 RPM
YRI_NA19093	0.26 RPM
YRI_NA19099	0.11 RPM
YRI_NA19114	0.16 RPM
YRI_NA19118	0.62 RPM
YRI_NA19213	0.05 RPM
YRI_NA19214	0.20 RPM
YRI_NA19223	0.14 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).