RetrogeneDB ID: retro_hsap_2220

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 2:232120809..232121016(+)
• Located in intron of: ENSG00000135931

Retrocopy information

• Ensembl ID: ENSG00000237039
• 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_2220
ATGGACACCAGCCGTGTGCAGCCTATCAAGCTGGCCAGGGTCACCAAGGTCCTGGGCAGGACCGGCTCTCAGGGACAGTG
CACGCAGGTGCGCGTGGAATTCATGGACGACACGAGCCGATCCATCATCCGCAATGTAAAAGGCCCCGTGCGCGAGGGCG
ACGTGCTCACCCTTTTGGAGTCAGAGCGAGAAGCCCGGAGGTTGCGC

Alignment

ORF - retro_hsap_2220 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	0.70 RPM	59.97 RPM
bodymap2_adrenal	1.58 RPM	157.29 RPM
bodymap2_brain	0.77 RPM	21.10 RPM
bodymap2_breast	0.84 RPM	44.71 RPM
bodymap2_colon	2.88 RPM	136.61 RPM
bodymap2_heart	0.50 RPM	24.70 RPM
bodymap2_kidney	0.91 RPM	27.38 RPM
bodymap2_liver	1.37 RPM	40.01 RPM
bodymap2_lung	1.65 RPM	87.59 RPM
bodymap2_lymph_node	4.31 RPM	144.33 RPM
bodymap2_ovary	0.85 RPM	60.16 RPM
bodymap2_prostate	2.51 RPM	99.05 RPM
bodymap2_skeletal_muscle	0.89 RPM	61.27 RPM
bodymap2_testis	0.98 RPM	41.76 RPM
bodymap2_thyroid	0.24 RPM	40.73 RPM
bodymap2_white_blood_cells	5.71 RPM	193.16 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2220 was not detected

EST

No EST(s) were mapped for retro_hsap_2220 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_120036	963 libraries	723 libraries	137 libraries	5 libraries	1 library

The graphical summary, for retro_hsap_2220 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_2220 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2220 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	6.25 RPM
CEU_NA11843	8.22 RPM
CEU_NA11930	1.53 RPM
CEU_NA12004	1.94 RPM
CEU_NA12400	3.89 RPM
CEU_NA12751	3.52 RPM
CEU_NA12760	8.26 RPM
CEU_NA12827	3.91 RPM
CEU_NA12872	7.16 RPM
CEU_NA12873	6.13 RPM
FIN_HG00183	6.42 RPM
FIN_HG00277	0.74 RPM
FIN_HG00315	6.29 RPM
FIN_HG00321	2.54 RPM
FIN_HG00328	5.18 RPM
FIN_HG00338	2.90 RPM
FIN_HG00349	1.79 RPM
FIN_HG00375	5.33 RPM
FIN_HG00377	3.68 RPM
FIN_HG00378	1.38 RPM
GBR_HG00099	3.23 RPM
GBR_HG00111	2.00 RPM
GBR_HG00114	3.79 RPM
GBR_HG00119	1.20 RPM
GBR_HG00131	2.82 RPM
GBR_HG00133	2.17 RPM
GBR_HG00134	2.21 RPM
GBR_HG00137	4.81 RPM
GBR_HG00142	4.22 RPM
GBR_HG00143	2.39 RPM
TSI_NA20512	9.41 RPM
TSI_NA20513	3.14 RPM
TSI_NA20518	1.75 RPM
TSI_NA20532	4.18 RPM
TSI_NA20538	4.79 RPM
TSI_NA20756	2.88 RPM
TSI_NA20765	3.90 RPM
TSI_NA20771	6.07 RPM
TSI_NA20786	3.53 RPM
TSI_NA20798	4.21 RPM
YRI_NA18870	4.10 RPM
YRI_NA18907	1.91 RPM
YRI_NA18916	1.58 RPM
YRI_NA19093	3.15 RPM
YRI_NA19099	1.12 RPM
YRI_NA19114	1.47 RPM
YRI_NA19118	6.96 RPM
YRI_NA19213	1.15 RPM
YRI_NA19214	2.31 RPM
YRI_NA19223	1.83 RPM

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Indel association:

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