RetrogeneDB ID: retro_hsap_3324

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 5:55800464..55800899(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000226221
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL26
• Ensembl ID: ENSG00000161970
• Aliases: RPL26, DBA11, L26
• Description: ribosomal protein L26 [Source:HGNC Symbol;Acc:10327]

Sequence

>retro_hsap_3324
ATGAAGTTTAATCCCTTTGTGACTTCCGACCGAAGCAAGAATCGCAAAAGGCATTTCAATGCACCTTCCCACATTCGAAG
GAAGACTATGTCTTCCCCTCTTTCCAAAGAGCTGAGACAGAAGTACAACGTGTGATCCATGCCCATCCGAAAGGATGATG
AAGTTCAGGTTGTACGTGGACACTATAAAGGTCAGCAAATTGGCAAAGTAGTCCAGGTTTACAGGAAGAAATATGTTATC
TACATTGAACGGGTGCAGCGGGAAAAGGCTAATGGCACAACTGTCCACGTAGGCATTCACCCCAGCAAGGTGGTTATCAC
TAGGCTAAAACTGGACAAAGACTGTGAAAAGATCCTTGAACGGAAAGCCAAATCTTGCCAAGTAGGAAAGGAAAAGGGCA
AATACAAGGAAGAAACAATTGAGAAGATGCAGGAA

Alignment

ORF - retro_hsap_3324 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.55 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKFNPFVTSDRSKNRKRHFNAPSHIRRKIMSSPLSKELRQKYNVRSMPIRKDDEVQVVRGHYKGQQIGKV
          MKFNPFVTSDRSKNRKRHFNAPSHIRRK.MSSPLSKELRQKYNV.SMPIRKDDEVQVVRGHYKGQQIGKV
Retrocopy MKFNPFVTSDRSKNRKRHFNAPSHIRRKTMSSPLSKELRQKYNV*SMPIRKDDEVQVVRGHYKGQQIGKV

Parental  VQVYRKKYVIYIERVQREKANGTTVHVGIHPSKVVITRLKLDKDRKKILERKAKSRQVGKEKGKYKEETI
          VQVYRKKYVIYIERVQREKANGTTVHVGIHPSKVVITRLKLDKD..KILERKAKS.QVGKEKGKYKEETI
Retrocopy VQVYRKKYVIYIERVQREKANGTTVHVGIHPSKVVITRLKLDKDCEKILERKAKSCQVGKEKGKYKEETI

Parental  EKMQE
          EKMQE
Retrocopy EKMQE

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	0.87 RPM	230.25 RPM
bodymap2_adrenal	0.72 RPM	312.12 RPM
bodymap2_brain	0.35 RPM	131.90 RPM
bodymap2_breast	0.37 RPM	213.50 RPM
bodymap2_colon	1.12 RPM	447.49 RPM
bodymap2_heart	0.30 RPM	108.92 RPM
bodymap2_kidney	0.33 RPM	180.52 RPM
bodymap2_liver	0.13 RPM	109.88 RPM
bodymap2_lung	0.77 RPM	352.18 RPM
bodymap2_lymph_node	0.95 RPM	392.35 RPM
bodymap2_ovary	1.04 RPM	384.53 RPM
bodymap2_prostate	1.21 RPM	473.22 RPM
bodymap2_skeletal_muscle	1.18 RPM	246.63 RPM
bodymap2_testis	0.77 RPM	253.88 RPM
bodymap2_thyroid	0.58 RPM	176.26 RPM
bodymap2_white_blood_cells	1.28 RPM	432.25 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3324 was not detected

EST

No EST(s) were mapped for retro_hsap_3324 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_154690	140 libraries	58 libraries	815 libraries	530 libraries	286 libraries

The graphical summary, for retro_hsap_3324 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_3324 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3324 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 234 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002453	7 retrocopies	retro_amel_1175, retro_amel_1535, retro_amel_1885, retro_amel_1934, retro_amel_360, retro_amel_499, retro_amel_900,
Bos taurus	ENSBTAG00000012344	2 retrocopies	retro_btau_1090, retro_btau_230,
Choloepus hoffmanni	ENSCHOG00000004703	10 retrocopies	retro_chof_149, retro_chof_1893, retro_chof_2147, retro_chof_2276, retro_chof_2333, retro_chof_2383, retro_chof_244, retro_chof_312, retro_chof_816, retro_chof_942,
Callithrix jacchus	ENSCJAG00000014372	8 retrocopies	retro_cjac_110, retro_cjac_119, retro_cjac_240, retro_cjac_250, retro_cjac_270, retro_cjac_297, retro_cjac_321, retro_cjac_362,
Cavia porcellus	ENSCPOG00000001315	10 retrocopies	retro_cpor_1009, retro_cpor_1161, retro_cpor_1346, retro_cpor_1421, retro_cpor_1503, retro_cpor_1526, retro_cpor_167, retro_cpor_522, retro_cpor_585, retro_cpor_858,
Dasypus novemcinctus	ENSDNOG00000002470	3 retrocopies	retro_dnov_2054, retro_dnov_2174, retro_dnov_378,
Equus caballus	ENSECAG00000015757	4 retrocopies	retro_ecab_429, retro_ecab_473, retro_ecab_515, retro_ecab_609,
Homo sapiens	ENSG00000037241	2 retrocopies	retro_hsap_586, retro_hsap_837,
Homo sapiens	ENSG00000161970	27 retrocopies	retro_hsap_1137, retro_hsap_1309, retro_hsap_1376, retro_hsap_1394, retro_hsap_191, retro_hsap_2108, retro_hsap_2165, retro_hsap_2253, retro_hsap_253, retro_hsap_267, retro_hsap_2946, retro_hsap_3118, retro_hsap_3260, retro_hsap_3324 , retro_hsap_3490, retro_hsap_3700, retro_hsap_3803, retro_hsap_3813, retro_hsap_3914, retro_hsap_4043, retro_hsap_4061, retro_hsap_4874, retro_hsap_4932, retro_hsap_642, retro_hsap_691, retro_hsap_915, retro_hsap_998,
Gorilla gorilla	ENSGGOG00000023944	4 retrocopies	retro_ggor_2565, retro_ggor_270, retro_ggor_51, retro_ggor_974,
Macropus eugenii	ENSMEUG00000009891	7 retrocopies	retro_meug_1239, retro_meug_1538, retro_meug_1607, retro_meug_1827, retro_meug_262, retro_meug_322, retro_meug_534,
Myotis lucifugus	ENSMLUG00000002176	1 retrocopy	retro_mluc_232,
Macaca mulatta	ENSMMUG00000003448	22 retrocopies	retro_mmul_1117, retro_mmul_1361, retro_mmul_1398, retro_mmul_1497, retro_mmul_1710, retro_mmul_1773, retro_mmul_1899, retro_mmul_1986, retro_mmul_2052, retro_mmul_2163, retro_mmul_2332, retro_mmul_2344, retro_mmul_325, retro_mmul_360, retro_mmul_398, retro_mmul_405, retro_mmul_448, retro_mmul_548, retro_mmul_805, retro_mmul_903, retro_mmul_920, retro_mmul_992,
Monodelphis domestica	ENSMODG00000006201	2 retrocopies	retro_mdom_36, retro_mdom_64,
Mustela putorius furo	ENSMPUG00000007988	12 retrocopies	retro_mputfur_1003, retro_mputfur_1146, retro_mputfur_1385, retro_mputfur_1428, retro_mputfur_1595, retro_mputfur_251, retro_mputfur_365, retro_mputfur_395, retro_mputfur_488, retro_mputfur_522, retro_mputfur_643, retro_mputfur_685,
Nomascus leucogenys	ENSNLEG00000009981	1 retrocopy	retro_nleu_76,
Otolemur garnettii	ENSOGAG00000017070	3 retrocopies	retro_ogar_118, retro_ogar_255, retro_ogar_66,
Pan troglodytes	ENSPTRG00000008742	3 retrocopies	retro_ptro_1546, retro_ptro_2510, retro_ptro_73,
Rattus norvegicus	ENSRNOG00000004214	3 retrocopies	retro_rnor_213, retro_rnor_260, retro_rnor_273,
Sorex araneus	ENSSARG00000005798	13 retrocopies	retro_sara_172, retro_sara_208, retro_sara_228, retro_sara_273, retro_sara_319, retro_sara_334, retro_sara_393, retro_sara_527, retro_sara_578, retro_sara_627, retro_sara_641, retro_sara_656, retro_sara_740,
Sarcophilus harrisii	ENSSHAG00000006890	1 retrocopy	retro_shar_458,
Sus scrofa	ENSSSCG00000028850	9 retrocopies	retro_sscr_261, retro_sscr_363, retro_sscr_426, retro_sscr_427, retro_sscr_471, retro_sscr_485, retro_sscr_508, retro_sscr_609, retro_sscr_736,
Ictidomys tridecemlineatus	ENSSTOG00000021923	6 retrocopies	retro_itri_1113, retro_itri_1145, retro_itri_1206, retro_itri_1262, retro_itri_1670, retro_itri_811,
Tupaia belangeri	ENSTBEG00000007749	53 retrocopies	retro_tbel_1053, retro_tbel_1088, retro_tbel_1103, retro_tbel_1140, retro_tbel_1366, retro_tbel_1389, retro_tbel_1390, retro_tbel_1391, retro_tbel_1433, retro_tbel_1497, retro_tbel_1512, retro_tbel_1767, retro_tbel_1793, retro_tbel_1928, retro_tbel_1930, retro_tbel_2005, retro_tbel_2033, retro_tbel_2053, retro_tbel_2057, retro_tbel_2099, retro_tbel_2105, retro_tbel_2332, retro_tbel_2416, retro_tbel_2465, retro_tbel_2500, retro_tbel_268, retro_tbel_2727, retro_tbel_2778, retro_tbel_2806, retro_tbel_2884, retro_tbel_3020, retro_tbel_3187, retro_tbel_3300, retro_tbel_3332, retro_tbel_3704, retro_tbel_3711, retro_tbel_3790, retro_tbel_3964, retro_tbel_404, retro_tbel_4162, retro_tbel_4200, retro_tbel_4381, retro_tbel_4416, retro_tbel_446, retro_tbel_4480, retro_tbel_470, retro_tbel_474, retro_tbel_495, retro_tbel_573, retro_tbel_863, retro_tbel_906, retro_tbel_964, retro_tbel_99,
Tarsius syrichta	ENSTSYG00000001483	17 retrocopies	retro_tsyr_1273, retro_tsyr_1274, retro_tsyr_1499, retro_tsyr_153, retro_tsyr_1705, retro_tsyr_1858, retro_tsyr_1869, retro_tsyr_2152, retro_tsyr_262, retro_tsyr_327, retro_tsyr_346, retro_tsyr_600, retro_tsyr_636, retro_tsyr_684, retro_tsyr_808, retro_tsyr_865, retro_tsyr_905,
Vicugna pacos	ENSVPAG00000000279	4 retrocopies	retro_vpac_214, retro_vpac_255, retro_vpac_26, retro_vpac_357,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	2.29 RPM
CEU_NA11843	3.41 RPM
CEU_NA11930	8.34 RPM
CEU_NA12004	0.76 RPM
CEU_NA12400	2.70 RPM
CEU_NA12751	1.38 RPM
CEU_NA12760	3.59 RPM
CEU_NA12827	2.50 RPM
CEU_NA12872	1.55 RPM
CEU_NA12873	1.95 RPM
FIN_HG00183	4.04 RPM
FIN_HG00277	2.03 RPM
FIN_HG00315	1.63 RPM
FIN_HG00321	2.45 RPM
FIN_HG00328	1.49 RPM
FIN_HG00338	1.70 RPM
FIN_HG00349	3.90 RPM
FIN_HG00375	1.93 RPM
FIN_HG00377	2.32 RPM
FIN_HG00378	2.00 RPM
GBR_HG00099	2.32 RPM
GBR_HG00111	1.68 RPM
GBR_HG00114	1.53 RPM
GBR_HG00119	2.51 RPM
GBR_HG00131	1.87 RPM
GBR_HG00133	1.71 RPM
GBR_HG00134	1.27 RPM
GBR_HG00137	1.46 RPM
GBR_HG00142	1.67 RPM
GBR_HG00143	1.50 RPM
TSI_NA20512	1.55 RPM
TSI_NA20513	1.26 RPM
TSI_NA20518	3.44 RPM
TSI_NA20532	2.01 RPM
TSI_NA20538	1.43 RPM
TSI_NA20756	3.52 RPM
TSI_NA20765	1.60 RPM
TSI_NA20771	3.91 RPM
TSI_NA20786	1.28 RPM
TSI_NA20798	1.40 RPM
YRI_NA18870	3.11 RPM
YRI_NA18907	0.97 RPM
YRI_NA18916	1.73 RPM
YRI_NA19093	1.07 RPM
YRI_NA19099	1.81 RPM
YRI_NA19114	1.26 RPM
YRI_NA19118	1.84 RPM
YRI_NA19213	1.75 RPM
YRI_NA19214	0.76 RPM
YRI_NA19223	1.09 RPM

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Indel association:

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