RetrogeneDB ID: retro_hsap_505

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:213028516..213028708(-)
• Located in intron of: ENSG00000198468

Retrocopy information

• Ensembl ID: ENSG00000236317
• 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_505
GACACCAGCCATGTGCAGCCTATCTAGCTAGCCAGGGTCACCAAGGTCCTGGGCAGAACCAGCTCTCAGGGACAGTGCAT
GCGGGAATTTATGGAAGACACAAGCCACTCCATCATCCACAGTGTAAAAGACCCCATGCGCAAGGGCTATGTGCTCACCC
TGTTGGAGTCAGAGCGAGAGGCCTGGAGGTTG

Alignment

ORF - retro_hsap_505 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.63 %
• Parental protein coverage: 97.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DTSRVQPIKLARVTKVLGRTGSQGQCTQVRVEFMDDTSRSIIRNVKGPVREGDVLTLLESEREARRL
          DTS.VQPI.LARVTKVLGRT.SQGQC.....EFM.DTS.SII..VK.P.R.G.VLTLLESEREA.RL
Retrocopy DTSHVQPI*LARVTKVLGRTSSQGQCMR---EFMEDTSHSIIHSVKDPMRKGYVLTLLESEREAWRL

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

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_505 was not detected

EST

No EST(s) were mapped for retro_hsap_505 retrocopy.

TSS

No TSS is located nearby retro_hsap_505 retrocopy 5' end.

Lab

retro_hsap_505 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_505 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_378

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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	0.02 RPM
CEU_NA11843	0.06 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.11 RPM
CEU_NA12751	0.12 RPM
CEU_NA12760	0.09 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.14 RPM
CEU_NA12873	0.10 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.07 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.09 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.09 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.05 RPM
FIN_HG00378	0.06 RPM
GBR_HG00099	0.12 RPM
GBR_HG00111	0.02 RPM
GBR_HG00114	0.03 RPM
GBR_HG00119	0.05 RPM
GBR_HG00131	0.03 RPM
GBR_HG00133	0.02 RPM
GBR_HG00134	0.11 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.06 RPM
GBR_HG00143	0.03 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.10 RPM
TSI_NA20518	0.06 RPM
TSI_NA20532	0.07 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.03 RPM
TSI_NA20765	0.12 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.05 RPM
TSI_NA20798	0.03 RPM
YRI_NA18870	0.07 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.02 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.03 RPM
YRI_NA19114	0.03 RPM
YRI_NA19118	0.02 RPM
YRI_NA19213	0.10 RPM
YRI_NA19214	0.12 RPM
YRI_NA19223	0.06 RPM

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Indel association:

The presence of retro_hsap_505 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_505 presence in various populations. Based on Kabza et al. 2015 (PubMed).

#	Indel coordinates	AFR, African			AMR, Ad Mixed American			EUR, European					EAS, East Asian
		ASW	YRI	LWK	MXL	PUR	CLM	CEU	IBS	GBR	FIN	TSI	JPT	CHB	CHS
1.	1:213027399..213029000	98.36	99.43	95.36	100	100	100	100	100	100	100	100	100	100	100

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Indel #1, located at the genomic coordinates 1:213027399..213029000.