RetrogeneDB ID: retro_hsap_526

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:230747754..230748158(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000235817
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS24
• Ensembl ID: ENSG00000138326
• Aliases: RPS24, DBA3, S24
• Description: ribosomal protein S24 [Source:HGNC Symbol;Acc:10411]

Sequence

>retro_hsap_526
ATGAATGACACAGTAACTATCTGGACCAGGGAACTCATGACCAACCAACTACTTCAAAGGAAACAAATGGTCATAGATAT
CCTTAACACTGGGAAGGCAACAGTACCAAAGACAGAAATTCTGGAAAAATTAGTCAAAATATACAAGACCACACTGGATG
TCATCTTTGTATTTGGATTCAGAACTTATTTTGGTGGTGGCAAGATAGCTGACTTTGGTGTGATTTATGATTTTTTTGGA
TTATGTAAAAAACCATGAACCCAAACATAGACTTGCAAGACATGGCCTGCCTCCATGAGAAGAAAAAGACCTCAAGAAAG
CAGTGAGACGAATGCAAGAATAGAATGAAAAAGCTCAGGGGGTTGGCAAAGGCCAATGTTGGTGCTGGCAAAAAGCCAAA
GGAG

Alignment

ORF - retro_hsap_526 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.21 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MNDTVTIRTRKFMTNRLLQRKQMVIDVLHPGKATVPKTEIREKLAKMYKTTPDVIFVFGFRTHFGGGKTT
          MNDTVTI.TR..MTN.LLQRKQMVID.L..GKATVPKTEI.EKL.K.YKTT.DVIFVFGFRT.FGGGK..
Retrocopy MNDTVTIWTRELMTNQLLQRKQMVIDILNTGKATVPKTEILEKLVKIYKTTLDVIFVFGFRTYFGGGKIA

Parental  GFGMIYD-SLDYAKKNEPKHRLARHGL-YEKKK-TSRKQRKERKNRMKKVRGTAKANVGAGKKPKE
          .FG.IYD..LDY.K..EPKHRLARHGL....KK.TSRKQ..E.KNRMKK.RG.AKANVGAGKKPKE
Retrocopy DFGVIYD>FLDYVKNHEPKHRLARHGL>LHEKKKTSRKQ*DECKNRMKKLRGLAKANVGAGKKPKE

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	571.79 RPM
bodymap2_adrenal	0.00 RPM	666.79 RPM
bodymap2_brain	0.00 RPM	239.02 RPM
bodymap2_breast	0.00 RPM	481.62 RPM
bodymap2_colon	0.00 RPM	877.27 RPM
bodymap2_heart	0.00 RPM	228.55 RPM
bodymap2_kidney	0.00 RPM	328.74 RPM
bodymap2_liver	0.00 RPM	280.08 RPM
bodymap2_lung	0.00 RPM	700.63 RPM
bodymap2_lymph_node	0.00 RPM	723.82 RPM
bodymap2_ovary	0.00 RPM	1199.50 RPM
bodymap2_prostate	0.00 RPM	1059.24 RPM
bodymap2_skeletal_muscle	0.00 RPM	755.85 RPM
bodymap2_testis	0.00 RPM	575.66 RPM
bodymap2_thyroid	0.00 RPM	557.71 RPM
bodymap2_white_blood_cells	0.00 RPM	796.10 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_526 was not detected

EST

No EST(s) were mapped for retro_hsap_526 retrocopy.

TSS

No TSS is located nearby retro_hsap_526 retrocopy 5' end.

Lab

retro_hsap_526 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_526 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_393

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013264	9 retrocopies	retro_btau_1137, retro_btau_1311, retro_btau_1562, retro_btau_285, retro_btau_467, retro_btau_577, retro_btau_586, retro_btau_788, retro_btau_980,
Felis catus	ENSFCAG00000000849	3 retrocopies	retro_fcat_19, retro_fcat_772, retro_fcat_85,
Homo sapiens	ENSG00000138326	3 retrocopies	retro_hsap_1511, retro_hsap_526 , retro_hsap_658,
Gadus morhua	ENSGMOG00000012595	1 retrocopy	retro_gmor_15,
Loxodonta africana	ENSLAFG00000027878	10 retrocopies	retro_lafr_1017, retro_lafr_190, retro_lafr_303, retro_lafr_340, retro_lafr_439, retro_lafr_558, retro_lafr_596, retro_lafr_669, retro_lafr_854, retro_lafr_995,
Myotis lucifugus	ENSMLUG00000024102	1 retrocopy	retro_mluc_260,
Mustela putorius furo	ENSMPUG00000003778	1 retrocopy	retro_mputfur_10,
Oryctolagus cuniculus	ENSOCUG00000012472	1 retrocopy	retro_ocun_16,
Otolemur garnettii	ENSOGAG00000011005	3 retrocopies	retro_ogar_1000, retro_ogar_2, retro_ogar_2130,
Pan troglodytes	ENSPTRG00000002666	10 retrocopies	retro_ptro_1023, retro_ptro_1114, retro_ptro_1257, retro_ptro_1555, retro_ptro_1885, retro_ptro_2376, retro_ptro_362, retro_ptro_393, retro_ptro_478, retro_ptro_983,
Ictidomys tridecemlineatus	ENSSTOG00000013000	4 retrocopies	retro_itri_167, retro_itri_376, retro_itri_528, retro_itri_728,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

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Indel association:

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