RetrogeneDB ID: retro_hsap_951

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 12:6993220..6993762(+)
• Located in intron of: ENSG00000010626

Retrocopy information

• Ensembl ID: ENSG00000240370
• Aliases: RPL13P5, RPL13-2, RPL13L, RPL13_4_1199, RRPL13L
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL13
• Ensembl ID: ENSG00000167526
• Aliases: RPL13, BBC1, D16S444E, D16S44E, L13
• Description: ribosomal protein L13 [Source:HGNC Symbol;Acc:10303]

Sequence

>retro_hsap_951
GTGGCCATGTGGCTCAGCCAGCCCATGGGGCAGACCTGCAGAAGCAAGGTGGCCAGCAAAAGCAGGCTGCATGGCCCACT
GATATGGGCCCATCCACCCATAGTAAGGTGCCCCATGCTGAGGCATCACTACAAAGCACAAGCTGGCAGGGGCCTCAGCT
TGGAGGAGTTAAGGGTGGCTGGCATTTACAAGAAGGTGGCCCAGACCATTGGCATCTCTGAGGATGCAAGGAGGAGGAAC
CAGTCCACCCAGGCCCTGCAGGCCAAGGTGCAGAGGCTGAAGGAGGACCGCTCCTCACTCATCCTCTTCCCCAGGAAGCC
CTTGGCCCCCAAGAAGGGAGACAGTTCTGCTGAAGAACTCGAACTGGATACTCAGCTGACAGGACCAGAAATGCCCATCG
GCAATGTCTACAAGGAGAAAGCCAGAGTCATCGCTGACTAGGAGGAAAACTTCCAGGCCTTGTTAGTCTCTGTATGGCCC
ATGCAAATGCCCAGCTCTTCGGCATATAGGCACAAAGAGCCAAGGAAGCTGTAGAAGAGGAC

Alignment

ORF - retro_hsap_951 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.13 %
• Parental protein coverage: 87.68 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VATWFNQPARKIRRRKARQAKARRIAPRPASGPIRPIVRCPTVRYHTKVRAGRGFSLEELRVAGIHKKVA
          VA.W..QP.....R.K....K.R...P.....P..PIVRCP..R.H.K..AGRG.SLEELRVAGI.KKVA
Retrocopy VAMWLSQPMGQTCRSKVA-SKSRLHGPLIWAHP--PIVRCPMLRHHYKAQAGRGLSLEELRVAGIYKKVA

Parental  RTIGISVDPRRRNKSTESLQANVQRLKEYRSKLILFPRKPSAPKKGDSSAEELKLATQLTGPVMPVRNVY
          .TIGIS.D.RRRN.ST..LQA.VQRLKE.RS.LILFPRKP.APKKGDSSAEEL.L.TQLTGP.MP..NVY
Retrocopy QTIGISEDARRRNQSTQALQAKVQRLKEDRSSLILFPRKPLAPKKGDSSAEELELDTQLTGPEMPIGNVY

Parental  KKEKARVITEEEKNFKA-FASLRMARANARLFGIRAKRAKEAAEQD
          .KEKARVI...E.NF.A...SL.MA.ANA.LFGI.A.RAKEA.E.D
Retrocopy -KEKARVIAD*EENFQA<LVSLCMAHANAQLFGI*AQRAKEAVEED

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	476.99 RPM
bodymap2_adrenal	0.74 RPM	586.53 RPM
bodymap2_brain	0.73 RPM	110.54 RPM
bodymap2_breast	0.58 RPM	300.39 RPM
bodymap2_colon	0.60 RPM	626.85 RPM
bodymap2_heart	0.15 RPM	135.26 RPM
bodymap2_kidney	2.61 RPM	213.55 RPM
bodymap2_liver	0.19 RPM	204.96 RPM
bodymap2_lung	0.86 RPM	687.47 RPM
bodymap2_lymph_node	0.93 RPM	880.08 RPM
bodymap2_ovary	1.70 RPM	665.98 RPM
bodymap2_prostate	1.11 RPM	974.39 RPM
bodymap2_skeletal_muscle	0.40 RPM	562.00 RPM
bodymap2_testis	0.98 RPM	347.76 RPM
bodymap2_thyroid	0.83 RPM	276.73 RPM
bodymap2_white_blood_cells	1.65 RPM	863.96 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_951 was not detected

EST

No EST(s) were mapped for retro_hsap_951 retrocopy.

TSS

No TSS is located nearby retro_hsap_951 retrocopy 5' end.

Lab

retro_hsap_951 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_951 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_658
Macaca mulatta	retro_mmul_781

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 121 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017072	1 retrocopy	retro_acar_70,
Canis familiaris	ENSCAFG00000019840	5 retrocopies	retro_cfam_1135, retro_cfam_1919, retro_cfam_2122, retro_cfam_565, retro_cfam_897,
Callithrix jacchus	ENSCJAG00000009672	5 retrocopies	retro_cjac_2607, retro_cjac_2961, retro_cjac_4054, retro_cjac_663, retro_cjac_747,
Cavia porcellus	ENSCPOG00000027348	4 retrocopies	retro_cpor_1014, retro_cpor_1192, retro_cpor_1242, retro_cpor_491,
Echinops telfairi	ENSETEG00000015057	4 retrocopies	retro_etel_1240, retro_etel_1382, retro_etel_1606, retro_etel_703,
Felis catus	ENSFCAG00000003338	4 retrocopies	retro_fcat_1946, retro_fcat_706, retro_fcat_852, retro_fcat_866,
Homo sapiens	ENSG00000167526	12 retrocopies	retro_hsap_1377, retro_hsap_1810, retro_hsap_2070, retro_hsap_2430, retro_hsap_2485, retro_hsap_2824, retro_hsap_3207, retro_hsap_3281, retro_hsap_3443, retro_hsap_4074, retro_hsap_478, retro_hsap_951 ,
Microcebus murinus	ENSMICG00000008191	4 retrocopies	retro_mmur_249, retro_mmur_288, retro_mmur_779, retro_mmur_908,
Myotis lucifugus	ENSMLUG00000010950	6 retrocopies	retro_mluc_1431, retro_mluc_1436, retro_mluc_1549, retro_mluc_2022, retro_mluc_891, retro_mluc_991,
Monodelphis domestica	ENSMODG00000003663	4 retrocopies	retro_mdom_1001, retro_mdom_416, retro_mdom_439, retro_mdom_674,
Mus musculus	ENSMUSG00000000740	23 retrocopies	retro_mmus_1091, retro_mmus_1522, retro_mmus_1533, retro_mmus_1854, retro_mmus_2074, retro_mmus_2163, retro_mmus_2186, retro_mmus_2321, retro_mmus_2333, retro_mmus_2351, retro_mmus_25, retro_mmus_2668, retro_mmus_2718, retro_mmus_3097, retro_mmus_3274, retro_mmus_3453, retro_mmus_3489, retro_mmus_3500, retro_mmus_355, retro_mmus_3711, retro_mmus_692, retro_mmus_732, retro_mmus_863,
Nomascus leucogenys	ENSNLEG00000015774	13 retrocopies	retro_nleu_1156, retro_nleu_1202, retro_nleu_2299, retro_nleu_238, retro_nleu_2457, retro_nleu_2530, retro_nleu_2657, retro_nleu_273, retro_nleu_2732, retro_nleu_2885, retro_nleu_3016, retro_nleu_789, retro_nleu_892,
Ornithorhynchus anatinus	ENSOANG00000006729	1 retrocopy	retro_oana_78,
Otolemur garnettii	ENSOGAG00000026444	3 retrocopies	retro_ogar_1165, retro_ogar_1831, retro_ogar_1853,
Pan troglodytes	ENSPTRG00000008480	12 retrocopies	retro_ptro_1175, retro_ptro_1382, retro_ptro_1402, retro_ptro_1438, retro_ptro_1914, retro_ptro_2219, retro_ptro_2242, retro_ptro_2336, retro_ptro_2761, retro_ptro_359, retro_ptro_658, retro_ptro_946,
Pteropus vampyrus	ENSPVAG00000015130	6 retrocopies	retro_pvam_1174, retro_pvam_1289, retro_pvam_1344, retro_pvam_228, retro_pvam_58, retro_pvam_616,
Rattus norvegicus	ENSRNOG00000015335	14 retrocopies	retro_rnor_1054, retro_rnor_1260, retro_rnor_158, retro_rnor_160, retro_rnor_1719, retro_rnor_1720, retro_rnor_1834, retro_rnor_1848, retro_rnor_2471, retro_rnor_2574, retro_rnor_2608, retro_rnor_2787, retro_rnor_2854, retro_rnor_682,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	1.33 RPM
CEU_NA11843	1.19 RPM
CEU_NA11930	1.14 RPM
CEU_NA12004	1.03 RPM
CEU_NA12400	0.77 RPM
CEU_NA12751	1.43 RPM
CEU_NA12760	1.57 RPM
CEU_NA12827	1.56 RPM
CEU_NA12872	1.50 RPM
CEU_NA12873	0.93 RPM
FIN_HG00183	0.99 RPM
FIN_HG00277	1.48 RPM
FIN_HG00315	1.10 RPM
FIN_HG00321	1.72 RPM
FIN_HG00328	1.94 RPM
FIN_HG00338	1.11 RPM
FIN_HG00349	1.20 RPM
FIN_HG00375	2.03 RPM
FIN_HG00377	1.31 RPM
FIN_HG00378	1.68 RPM
GBR_HG00099	1.16 RPM
GBR_HG00111	1.27 RPM
GBR_HG00114	1.68 RPM
GBR_HG00119	1.46 RPM
GBR_HG00131	1.26 RPM
GBR_HG00133	1.42 RPM
GBR_HG00134	1.55 RPM
GBR_HG00137	1.62 RPM
GBR_HG00142	1.83 RPM
GBR_HG00143	1.53 RPM
TSI_NA20512	1.16 RPM
TSI_NA20513	1.74 RPM
TSI_NA20518	1.50 RPM
TSI_NA20532	1.50 RPM
TSI_NA20538	1.70 RPM
TSI_NA20756	1.28 RPM
TSI_NA20765	1.89 RPM
TSI_NA20771	1.59 RPM
TSI_NA20786	1.99 RPM
TSI_NA20798	1.68 RPM
YRI_NA18870	1.90 RPM
YRI_NA18907	1.46 RPM
YRI_NA18916	1.05 RPM
YRI_NA19093	1.69 RPM
YRI_NA19099	1.38 RPM
YRI_NA19114	1.00 RPM
YRI_NA19118	1.41 RPM
YRI_NA19213	1.65 RPM
YRI_NA19214	1.72 RPM
YRI_NA19223	1.67 RPM

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Indel association:

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