RetrogeneDB ID: retro_hsap_2513

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 21:17116322..17116629(-)
• Located in intron of: ENSG00000155313

Retrocopy information

• Ensembl ID: ENSG00000234159
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RBPMS2
• Ensembl ID: ENSG00000166831
• Aliases: None
• Description: RNA binding protein with multiple splicing 2 [Source:HGNC Symbol;Acc:19098]

Sequence

>retro_hsap_2513
CTAAGGTTTGCCTAAGCCAACACCAAGATGGACAAAAATAAAGTAATGGCAAACCCCACCAATGTTCACACAGCCCTAGG
ACCACACCTCCTAGCACAGGACCCCATGACCTGAGGGAGTGGCTCTGATCTCTGTAACCCCAAAGGCCTGAAACCCCTAC
CCACTTTACACCATAGAAACCACAGAGCTGACCAGGGTCATCTTATATGCTGCTTTCAGCTACTCTGCTACAGTTCGACA
TGCTCAGGTACACTGGTGCTCTCCTCCTGGCGCCACCCAGCAAGAATGGAAACACTGTCAGTTCTGT

Alignment

ORF - retro_hsap_2513 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.57 %
• Parental protein coverage: 51.2 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LEFAKANTKMAKSKLMATPNPSNVHPALGAHFIARDP-YDLM-GAALIPASPEAWAPYPLYT---TELTP
          L.FA.ANTKM.K.K.MA..NP.NVH.ALG.H..A.DP..DL..G.ALI...P.A..PYPLYT...TELT.
Retrocopy LRFA*ANTKMDKNKVMA--NPTNVHTALGPHLLAQDP<HDLR<GVALISVTPKA*NPYPLYTIETTELTR

Parental  AISHAAFTYPTATAAAAALHAQVRWYPSSDTTQQGWKYRQFC
          .I..AAF.Y..AT...A..H....W......TQQ.WK..QFC
Retrocopy VILYAAFSY-SATVRHAQVH----WCSPPGATQQEWKHCQFC

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	14.35 RPM
bodymap2_adrenal	0.10 RPM	8.56 RPM
bodymap2_brain	0.00 RPM	1.38 RPM
bodymap2_breast	0.16 RPM	23.11 RPM
bodymap2_colon	0.00 RPM	85.21 RPM
bodymap2_heart	0.00 RPM	132.88 RPM
bodymap2_kidney	0.00 RPM	13.86 RPM
bodymap2_liver	0.04 RPM	8.11 RPM
bodymap2_lung	0.00 RPM	8.19 RPM
bodymap2_lymph_node	0.00 RPM	8.06 RPM
bodymap2_ovary	0.00 RPM	16.79 RPM
bodymap2_prostate	0.00 RPM	147.86 RPM
bodymap2_skeletal_muscle	0.00 RPM	3.73 RPM
bodymap2_testis	0.00 RPM	15.63 RPM
bodymap2_thyroid	0.00 RPM	9.85 RPM
bodymap2_white_blood_cells	0.00 RPM	1.10 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2513 was not detected

EST

No EST(s) were mapped for retro_hsap_2513 retrocopy.

TSS

No TSS is located nearby retro_hsap_2513 retrocopy 5' end.

Lab

retro_hsap_2513 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2513 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1458

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011037	1 retrocopy	retro_btau_1674,
Callithrix jacchus	ENSCJAG00000005200	2 retrocopies	retro_cjac_1775, retro_cjac_298,
Dipodomys ordii	ENSDORG00000004025	1 retrocopy	retro_dord_438,
Homo sapiens	ENSG00000166831	2 retrocopies	retro_hsap_2513 , retro_hsap_3613,
Gorilla gorilla	ENSGGOG00000008984	1 retrocopy	retro_ggor_2438,
Loxodonta africana	ENSLAFG00000018725	6 retrocopies	retro_lafr_344, retro_lafr_393, retro_lafr_445, retro_lafr_481, retro_lafr_550, retro_lafr_859,
Macaca mulatta	ENSMMUG00000013270	1 retrocopy	retro_mmul_1837,
Monodelphis domestica	ENSMODG00000010487	1 retrocopy	retro_mdom_571,
Mus musculus	ENSMUSG00000032387	9 retrocopies	retro_mmus_2671, retro_mmus_3408, retro_mmus_3410, retro_mmus_3429, retro_mmus_3431, retro_mmus_3437, retro_mmus_3562, retro_mmus_3588, retro_mmus_3596,
Nomascus leucogenys	ENSNLEG00000012505	1 retrocopy	retro_nleu_2209,
Otolemur garnettii	ENSOGAG00000026017	1 retrocopy	retro_ogar_3254,
Pongo abelii	ENSPPYG00000006553	1 retrocopy	retro_pabe_2963,
Pan troglodytes	ENSPTRG00000007165	2 retrocopies	retro_ptro_1458, retro_ptro_2441,
Sus scrofa	ENSSSCG00000004549	1 retrocopy	retro_sscr_851,
Ictidomys tridecemlineatus	ENSSTOG00000010055	2 retrocopies	retro_itri_1512, retro_itri_556,
Tarsius syrichta	ENSTSYG00000008996	3 retrocopies	retro_tsyr_1433, retro_tsyr_171, retro_tsyr_445,
Tursiops truncatus	ENSTTRG00000011840	3 retrocopies	retro_ttru_1046, retro_ttru_1212, retro_ttru_1790,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.04 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	0.02 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	0.02 RPM
GBR_HG00131	0.03 RPM
GBR_HG00133	0.05 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.03 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.03 RPM
TSI_NA20538	0.05 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.03 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.03 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.03 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.02 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.02 RPM

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Indel association:

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