RetrogeneDB ID: retro_hsap_3287

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 5:13250387..13250740(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000242608
• Aliases: RPS23P5, RPS23_2_542
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS23
• Ensembl ID: ENSG00000186468
• Aliases: RPS23, S23
• Description: ribosomal protein S23 [Source:HGNC Symbol;Acc:10410]

Sequence

>retro_hsap_3287
AAGAATCTCCCTGTTCACTGACAGGAACATAAGTGGAATGACAAACAGTACAAGAAAGCCCATTTAGGCACAGCCTGAAG
GCCAACGCTTTTGGAAATGTTTCCCATACAAAGAGAACTGTGTTGGAAAAATAGGAGTTGAAGCCGAATGGCCAAATTCT
AATATCAGGAAGTGTACTATAGTTCAGCTGATTGAGAATGGCAAGAAAATCATAGTCTTTGTACCCAACGATGGTTGCTT
GAACTTTATTGAGGAAAAGATGAATTTCTGGTTGCTGAATTTGTCAAAAAGGTCATACTGTTGTTGACATTCCTGTAGTC
CGCTTTAATGTTGTCAGAGTAGCCAATGTCTCT

Alignment

ORF - retro_hsap_3287 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.11 %
• Parental protein coverage: 83.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RKLRSHRRDQKWHDKQYKKAHLGTA-LKANPFGGASHAKGIVLEK-VGVEAKQPNSAIRKCVRVQLIKNG
          ..L..H....KW.DKQYKKAHLGTA.LKAN.FG..SH.K..VLEK..GVEA..PNS.IRKC..VQLI.NG
Retrocopy KNLPVH*QEHKWNDKQYKKAHLGTA<LKANAFGNVSHTKRTVLEK<IGVEAEWPNSNIRKCTIVQLIENG

Parental  KKITAFVPNDGCLNFIEE-NDEVLVAGFGR-KGHAVGDIPGVRFKVVKVANVS
          KKI..FVPNDGCLNFIEE..DE.LVA.F...KGH.V.DIP.VRF.VV.VANVS
Retrocopy KKIIVFVPNDGCLNFIEE<KDEFLVAEFVK<KGHTVVDIPVVRFNVVRVANVS

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	396.60 RPM
bodymap2_adrenal	0.00 RPM	544.61 RPM
bodymap2_brain	0.00 RPM	271.39 RPM
bodymap2_breast	0.00 RPM	247.51 RPM
bodymap2_colon	0.00 RPM	746.94 RPM
bodymap2_heart	0.00 RPM	208.28 RPM
bodymap2_kidney	0.00 RPM	274.29 RPM
bodymap2_liver	0.00 RPM	163.71 RPM
bodymap2_lung	0.00 RPM	426.58 RPM
bodymap2_lymph_node	0.00 RPM	610.76 RPM
bodymap2_ovary	0.00 RPM	840.78 RPM
bodymap2_prostate	0.00 RPM	793.02 RPM
bodymap2_skeletal_muscle	0.00 RPM	545.76 RPM
bodymap2_testis	0.08 RPM	384.04 RPM
bodymap2_thyroid	0.00 RPM	329.68 RPM
bodymap2_white_blood_cells	0.00 RPM	777.71 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3287 was not detected

EST

No EST(s) were mapped for retro_hsap_3287 retrocopy.

TSS

No TSS is located nearby retro_hsap_3287 retrocopy 5' end.

Lab

retro_hsap_3287 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3287 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2223
Gorilla gorilla	retro_ggor_1316
Pongo abelii	retro_pabe_2716

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013358	3 retrocopies	retro_btau_173, retro_btau_205, retro_btau_80,
Callithrix jacchus	ENSCJAG00000011247	2 retrocopies	retro_cjac_126, retro_cjac_256,
Homo sapiens	ENSG00000186468	6 retrocopies	retro_hsap_1778, retro_hsap_2940, retro_hsap_3107, retro_hsap_3287 , retro_hsap_3989, retro_hsap_4697,
Gorilla gorilla	ENSGGOG00000025014	6 retrocopies	retro_ggor_1316, retro_ggor_2038, retro_ggor_2131, retro_ggor_2237, retro_ggor_2677, retro_ggor_286,
Macaca mulatta	ENSMMUG00000003578	4 retrocopies	retro_mmul_1239, retro_mmul_1974, retro_mmul_2305, retro_mmul_852,
Monodelphis domestica	ENSMODG00000020255	3 retrocopies	retro_mdom_1518, retro_mdom_1612, retro_mdom_395,
Mustela putorius furo	ENSMPUG00000008114	1 retrocopy	retro_mputfur_1298,
Nomascus leucogenys	ENSNLEG00000013203	3 retrocopies	retro_nleu_1353, retro_nleu_1909, retro_nleu_764,
Oryctolagus cuniculus	ENSOCUG00000010363	2 retrocopies	retro_ocun_195, retro_ocun_95,
Rattus norvegicus	ENSRNOG00000016580	12 retrocopies	retro_rnor_100, retro_rnor_1394, retro_rnor_149, retro_rnor_1691, retro_rnor_1941, retro_rnor_1959, retro_rnor_1982, retro_rnor_2119, retro_rnor_2182, retro_rnor_2492, retro_rnor_525, retro_rnor_559,
Sarcophilus harrisii	ENSSHAG00000008347	2 retrocopies	retro_shar_257, retro_shar_348,
Sus scrofa	ENSSSCG00000014133	1 retrocopy	retro_sscr_92,

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).