RetrogeneDB ID: retro_hsap_799

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 11:82400600..82400807(+)
• Located in intron of: ENSG00000245832

Retrocopy information

• Ensembl ID: ENSG00000227097
• 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_799
ATGGACACCAGCCGTGTGCAGCCTATCAAGCTGGCCAGGGTCACCAAGGTCCTGGGCAGGACCGGTTCTCAGGGACAGTG
CACGCAGGTGCGCGTGGAATTCATGGACGACACGAGCCGATCCATCATCCGCAATGTAAAAGGCCCCGTGCGCGAGGGCG
ACGTGCTCACCCTTTTGGAGTCAGAGCGAGAAGCCCGGAGGTTGCGC

Alignment

ORF - retro_hsap_799 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MDTSRVQPIKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLESEREARRLR
          MDTSRVQPIKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLESEREARRLR
Retrocopy MDTSRVQPIKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLESEREARRLR

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	142.03 RPM	59.97 RPM
bodymap2_adrenal	89.94 RPM	157.29 RPM
bodymap2_brain	11.02 RPM	21.10 RPM
bodymap2_breast	119.67 RPM	44.71 RPM
bodymap2_colon	75.49 RPM	136.61 RPM
bodymap2_heart	12.18 RPM	24.70 RPM
bodymap2_kidney	43.10 RPM	27.38 RPM
bodymap2_liver	19.33 RPM	40.01 RPM
bodymap2_lung	40.17 RPM	87.59 RPM
bodymap2_lymph_node	0.42 RPM	144.33 RPM
bodymap2_ovary	148.66 RPM	60.16 RPM
bodymap2_prostate	43.51 RPM	99.05 RPM
bodymap2_skeletal_muscle	67.82 RPM	61.27 RPM
bodymap2_testis	100.47 RPM	41.76 RPM
bodymap2_thyroid	93.76 RPM	40.73 RPM
bodymap2_white_blood_cells	0.73 RPM	193.16 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_799 was not detected

EST

No EST(s) were mapped for retro_hsap_799 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_18985	537 libraries	830 libraries	442 libraries	17 libraries	3 libraries

The graphical summary, for retro_hsap_799 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_799 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_799 has 0 orthologous retrocopies within eutheria group .

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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	23.71 RPM
CEU_NA11843	38.30 RPM
CEU_NA11930	22.88 RPM
CEU_NA12004	51.58 RPM
CEU_NA12400	62.71 RPM
CEU_NA12751	18.38 RPM
CEU_NA12760	2.56 RPM
CEU_NA12827	23.02 RPM
CEU_NA12872	1.06 RPM
CEU_NA12873	22.94 RPM
FIN_HG00183	1.24 RPM
FIN_HG00277	24.96 RPM
FIN_HG00315	1.27 RPM
FIN_HG00321	14.21 RPM
FIN_HG00328	0.69 RPM
FIN_HG00338	14.94 RPM
FIN_HG00349	49.37 RPM
FIN_HG00375	23.62 RPM
FIN_HG00377	18.73 RPM
FIN_HG00378	31.02 RPM
GBR_HG00099	17.44 RPM
GBR_HG00111	51.46 RPM
GBR_HG00114	22.19 RPM
GBR_HG00119	27.44 RPM
GBR_HG00131	14.34 RPM
GBR_HG00133	48.09 RPM
GBR_HG00134	19.72 RPM
GBR_HG00137	29.58 RPM
GBR_HG00142	23.95 RPM
GBR_HG00143	43.84 RPM
TSI_NA20512	1.22 RPM
TSI_NA20513	13.90 RPM
TSI_NA20518	41.38 RPM
TSI_NA20532	15.47 RPM
TSI_NA20538	0.92 RPM
TSI_NA20756	13.76 RPM
TSI_NA20765	0.56 RPM
TSI_NA20771	24.42 RPM
TSI_NA20786	19.85 RPM
TSI_NA20798	20.05 RPM
YRI_NA18870	23.46 RPM
YRI_NA18907	39.79 RPM
YRI_NA18916	35.05 RPM
YRI_NA19093	36.75 RPM
YRI_NA19099	20.96 RPM
YRI_NA19114	30.88 RPM
YRI_NA19118	25.19 RPM
YRI_NA19213	18.56 RPM
YRI_NA19214	15.74 RPM
YRI_NA19223	31.20 RPM

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Indel association:

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