RetrogeneDB ID: retro_hsap_534

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:241468910..241469189(-)
• Located in intron of: ENSG00000182901

Retrocopy information

• Ensembl ID: ENSG00000224348
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL36
• Ensembl ID: ENSG00000130255
• Aliases: RPL36, L36
• Description: ribosomal protein L36 [Source:HGNC Symbol;Acc:13631]

Sequence

>retro_hsap_534
ATGGTCCTGCACTACCCCATGGCCGTGGGCCTCAACAAAGGCCACAAGGTGACCAAGAACGTGAGGAAACCAAGGCACAG
CCAAGCGGGCGCCTCAGCAAACACCAAAATCGCGCAAGACATGCCCCGAGAGGTGTGTGGCTTTGTCCCATAGAGCGGTG
TGCTGTGGAGTTGCTCAAGCTCTCCCAGGACAAACAGGCCCTCAAGTTCATCAGGAAAAGGGTGGGGGGCACACTTCCCC
CCCAAGAGAAAGTGAGAGAGCCTGTGCAATGTCCCGGCC

Alignment

ORF - retro_hsap_534 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.95 %
• Parental protein coverage: 90.48 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MALRYPMAVGLNKGHKVTKNVSKPRHSRRRGRLTKHTKFVRDMIREVCGF-APYERRAMELLKVSKDKRA
          M.L.YPMAVGLNKGHKVTKNV.KPRHS.........TK...DM.REVCGF..P.ER.A.ELLK.S.DK.A
Retrocopy MVLHYPMAVGLNKGHKVTKNVRKPRHS--QAGASANTKIAQDMPREVCGF<CPIERCAVELLKLSQDKQA

Parental  LKFIKKRV-GTHIRAKRKREELSNVLA
          LKFI.KRV.G.H...KRK.E.L.NV.A
Retrocopy LKFIRKRV>GAHFPPKRK*ESLCNVPA

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	87.64 RPM
bodymap2_adrenal	0.00 RPM	135.08 RPM
bodymap2_brain	0.05 RPM	23.58 RPM
bodymap2_breast	0.00 RPM	63.97 RPM
bodymap2_colon	0.00 RPM	125.47 RPM
bodymap2_heart	0.00 RPM	31.81 RPM
bodymap2_kidney	0.00 RPM	62.37 RPM
bodymap2_liver	0.00 RPM	51.52 RPM
bodymap2_lung	0.00 RPM	172.15 RPM
bodymap2_lymph_node	0.00 RPM	192.06 RPM
bodymap2_ovary	0.00 RPM	141.07 RPM
bodymap2_prostate	0.00 RPM	175.83 RPM
bodymap2_skeletal_muscle	0.00 RPM	119.46 RPM
bodymap2_testis	0.00 RPM	53.73 RPM
bodymap2_thyroid	0.00 RPM	45.29 RPM
bodymap2_white_blood_cells	0.00 RPM	177.56 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_534 was not detected

EST

No EST(s) were mapped for retro_hsap_534 retrocopy.

TSS

No TSS is located nearby retro_hsap_534 retrocopy 5' end.

Lab

retro_hsap_534 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_534 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_399
Gorilla gorilla	retro_ggor_487
Pongo abelii	retro_pabe_216

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 111 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012349	6 retrocopies	retro_amel_1222, retro_amel_1581, retro_amel_1935, retro_amel_748, retro_amel_799, retro_amel_835,
Bos taurus	ENSBTAG00000001794	3 retrocopies	retro_btau_139, retro_btau_238, retro_btau_81,
Callithrix jacchus	ENSCJAG00000017072	2 retrocopies	retro_cjac_280, retro_cjac_52,
Dasypus novemcinctus	ENSDNOG00000005163	8 retrocopies	retro_dnov_19, retro_dnov_2160, retro_dnov_311, retro_dnov_313, retro_dnov_457, retro_dnov_578, retro_dnov_595, retro_dnov_631,
Felis catus	ENSFCAG00000011838	5 retrocopies	retro_fcat_1152, retro_fcat_1168, retro_fcat_1216, retro_fcat_406, retro_fcat_94,
Homo sapiens	ENSG00000130255	13 retrocopies	retro_hsap_1059, retro_hsap_1440, retro_hsap_2000, retro_hsap_2434, retro_hsap_2577, retro_hsap_3051, retro_hsap_3248, retro_hsap_3769, retro_hsap_3892, retro_hsap_396, retro_hsap_4211, retro_hsap_4742, retro_hsap_534 ,
Gorilla gorilla	ENSGGOG00000015365	11 retrocopies	retro_ggor_1514, retro_ggor_1613, retro_ggor_180, retro_ggor_2211, retro_ggor_2535, retro_ggor_2620, retro_ggor_34, retro_ggor_487, retro_ggor_60, retro_ggor_82, retro_ggor_885,
Latimeria chalumnae	ENSLACG00000015161	1 retrocopy	retro_lcha_47,
Macropus eugenii	ENSMEUG00000002743	4 retrocopies	retro_meug_1318, retro_meug_176, retro_meug_261, retro_meug_283,
Monodelphis domestica	ENSMODG00000001275	2 retrocopies	retro_mdom_1353, retro_mdom_148,
Mustela putorius furo	ENSMPUG00000006166	6 retrocopies	retro_mputfur_1423, retro_mputfur_150, retro_mputfur_1562, retro_mputfur_747, retro_mputfur_749, retro_mputfur_773,
Mus musculus	ENSMUSG00000057863	9 retrocopies	retro_mmus_151, retro_mmus_1601, retro_mmus_1900, retro_mmus_1912, retro_mmus_193, retro_mmus_2864, retro_mmus_3379, retro_mmus_38, retro_mmus_652,
Otolemur garnettii	ENSOGAG00000027049	12 retrocopies	retro_ogar_1348, retro_ogar_18, retro_ogar_184, retro_ogar_2256, retro_ogar_2278, retro_ogar_2332, retro_ogar_2537, retro_ogar_2592, retro_ogar_3278, retro_ogar_358, retro_ogar_795, retro_ogar_888,
Pongo abelii	ENSPPYG00000009431	12 retrocopies	retro_pabe_1194, retro_pabe_137, retro_pabe_1639, retro_pabe_1792, retro_pabe_1834, retro_pabe_1898, retro_pabe_216, retro_pabe_3081, retro_pabe_3173, retro_pabe_318, retro_pabe_3443, retro_pabe_3688,
Rattus norvegicus	ENSRNOG00000033473	5 retrocopies	retro_rnor_11, retro_rnor_17, retro_rnor_170, retro_rnor_369, retro_rnor_687,
Sarcophilus harrisii	ENSSHAG00000013492	8 retrocopies	retro_shar_185, retro_shar_347, retro_shar_543, retro_shar_557, retro_shar_592, retro_shar_615, retro_shar_716, retro_shar_819,
Sus scrofa	ENSSSCG00000030010	2 retrocopies	retro_sscr_849, retro_sscr_960,
Ictidomys tridecemlineatus	ENSSTOG00000020518	2 retrocopies	retro_itri_43, retro_itri_593,