RetrogeneDB ID: retro_hsap_1398

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 14:31932003..31932577(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000239323
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL9
• Ensembl ID: ENSG00000163682
• Aliases: RPL9, L9, NPC-A-16
• Description: ribosomal protein L9 [Source:HGNC Symbol;Acc:10369]

Sequence

>retro_hsap_1398
ATGAAGACCATTCTCAGCAATCAGACAGTCAACATTCCAGAAAATGTTGATATCACTCTGAAGAAACACAGTTACTGTGA
AGGGCCCCAAAAGAACCCTGCAGAAGGACTTCAATCACACCAATGTAGAACTCAGTCTCCTTGGAAAGAAAAGGAAGAGG
CTCCAGGTTGACAACTTGTGGGGAAAGAGAAAGGAACTGGCTACCCTTCACACTATTTGTAGTCATGTACAGAACATGAT
CAAGGGTGCTACTGTGGGCTTCCATTACAAGATGAAGTCTCTGTAAGCTCACTTCCTCATCAATATCGTATTCTGGGAGA
ACAGGTCTCTTGTTGAAATCCACAATTTCTTGGGTAAAAAATACATCCGCAGGGTTCGAATGAGGATAAATGTTGTTTGT
TCAGTATCTCAAGCCCAGAAAGATGAATTAATCCTTGAAGGAAATGACATTGAGCTTGTTTCAAATTCAGTTGCCTTGAT
TCAGCAAGCCACAACAGTTAAAATCAAAGACATCAGAAAATTTTTGGATGGCATCTATGTCTCTGAAAAAGGAACTGTTC
AGCCGGCTGATGAA

Alignment

ORF - retro_hsap_1398 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.27 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKTILSNQTVDIPENVDITLKGRTVIVKGP-RGTLRRDFNHINVELSLLGKKKKRLRVDKWWGNRKELAT
          MKTILSNQTV.IPENVDITLK.......GP...TL..DFNH.NVELSLLGKK.KRL.VD..WG.RKELAT
Retrocopy MKTILSNQTVNIPENVDITLKKHS-YCEGP>KRTLQKDFNHTNVELSLLGKKRKRLQVDNLWGKRKELAT

Parental  VRTICSHVQNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGEKYIRRVRMRPGVACSVSQA
          ..TICSHVQNMIKG.T.GF.YKM.S..AHF.IN.V..EN.SLVEI.NFLG.KYIRRVRMR..V.CSVSQA
Retrocopy LHTICSHVQNMIKGATVGFHYKMKSL*AHFLINIVFWENRSLVEIHNFLGKKYIRRVRMRINVVCSVSQA

Parental  QKDELILEGNDIELVSNSAALIQQATTVKNKDIRKFLDGIYVSEKGTVQQADE
          QKDELILEGNDIELVSNS.ALIQQATTVK.KDIRKFLDGIYVSEKGTVQ.ADE
Retrocopy QKDELILEGNDIELVSNSVALIQQATTVKIKDIRKFLDGIYVSEKGTVQPADE

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	147.91 RPM
bodymap2_adrenal	0.00 RPM	379.40 RPM
bodymap2_brain	0.00 RPM	178.12 RPM
bodymap2_breast	0.00 RPM	155.94 RPM
bodymap2_colon	0.00 RPM	448.32 RPM
bodymap2_heart	0.00 RPM	107.31 RPM
bodymap2_kidney	0.04 RPM	291.26 RPM
bodymap2_liver	0.00 RPM	191.82 RPM
bodymap2_lung	0.00 RPM	719.74 RPM
bodymap2_lymph_node	0.02 RPM	640.38 RPM
bodymap2_ovary	0.02 RPM	597.16 RPM
bodymap2_prostate	0.02 RPM	889.35 RPM
bodymap2_skeletal_muscle	0.00 RPM	166.16 RPM
bodymap2_testis	0.00 RPM	275.37 RPM
bodymap2_thyroid	0.00 RPM	243.32 RPM
bodymap2_white_blood_cells	0.00 RPM	962.75 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1398 was not detected

EST

No EST(s) were mapped for retro_hsap_1398 retrocopy.

TSS

No TSS is located nearby retro_hsap_1398 retrocopy 5' end.

Lab

retro_hsap_1398 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1398 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_1157

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 471 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000007317	1 retrocopy	retro_acar_163,
Ailuropoda melanoleuca	ENSAMEG00000003187	31 retrocopies	retro_amel_1018, retro_amel_1078, retro_amel_1080, retro_amel_1081, retro_amel_1108, retro_amel_1132, retro_amel_1137, retro_amel_1226, retro_amel_1246, retro_amel_1315, retro_amel_1374, retro_amel_1413, retro_amel_1498, retro_amel_1507, retro_amel_1539, retro_amel_1645, retro_amel_1690, retro_amel_1779, retro_amel_1848, retro_amel_247, retro_amel_256, retro_amel_380, retro_amel_457, retro_amel_652, retro_amel_665, retro_amel_702, retro_amel_727, retro_amel_872, retro_amel_881, retro_amel_951, retro_amel_963,
Bos taurus	ENSBTAG00000014518	3 retrocopies	retro_btau_200, retro_btau_231, retro_btau_51,
Canis familiaris	ENSCAFG00000016008	28 retrocopies	retro_cfam_1044, retro_cfam_1334, retro_cfam_1401, retro_cfam_1455, retro_cfam_1565, retro_cfam_1571, retro_cfam_1610, retro_cfam_1693, retro_cfam_1737, retro_cfam_1809, retro_cfam_1922, retro_cfam_1938, retro_cfam_207, retro_cfam_245, retro_cfam_288, retro_cfam_416, retro_cfam_434, retro_cfam_460, retro_cfam_636, retro_cfam_642, retro_cfam_644, retro_cfam_722, retro_cfam_769, retro_cfam_793, retro_cfam_86, retro_cfam_890, retro_cfam_952, retro_cfam_982,
Callithrix jacchus	ENSCJAG00000000723	29 retrocopies	retro_cjac_1075, retro_cjac_1115, retro_cjac_1335, retro_cjac_1589, retro_cjac_1735, retro_cjac_1780, retro_cjac_1872, retro_cjac_2166, retro_cjac_2549, retro_cjac_2554, retro_cjac_2621, retro_cjac_2637, retro_cjac_2741, retro_cjac_2826, retro_cjac_2847, retro_cjac_3069, retro_cjac_3070, retro_cjac_3103, retro_cjac_3134, retro_cjac_3245, retro_cjac_392, retro_cjac_593, retro_cjac_627, retro_cjac_650, retro_cjac_684, retro_cjac_690, retro_cjac_709, retro_cjac_784, retro_cjac_825,
Danio rerio	ENSDARG00000037350	1 retrocopy	retro_drer_18,
Dasypus novemcinctus	ENSDNOG00000007411	18 retrocopies	retro_dnov_1298, retro_dnov_1560, retro_dnov_1684, retro_dnov_1845, retro_dnov_1877, retro_dnov_1936, retro_dnov_2148, retro_dnov_2277, retro_dnov_2624, retro_dnov_2659, retro_dnov_282, retro_dnov_407, retro_dnov_437, retro_dnov_450, retro_dnov_615, retro_dnov_787, retro_dnov_82, retro_dnov_975,
Equus caballus	ENSECAG00000016489	7 retrocopies	retro_ecab_183, retro_ecab_368, retro_ecab_405, retro_ecab_630, retro_ecab_638, retro_ecab_818, retro_ecab_867,
Erinaceus europaeus	ENSEEUG00000004394	39 retrocopies	retro_eeur_11, retro_eeur_136, retro_eeur_153, retro_eeur_162, retro_eeur_184, retro_eeur_191, retro_eeur_229, retro_eeur_246, retro_eeur_27, retro_eeur_279, retro_eeur_280, retro_eeur_282, retro_eeur_296, retro_eeur_307, retro_eeur_352, retro_eeur_383, retro_eeur_399, retro_eeur_410, retro_eeur_429, retro_eeur_433, retro_eeur_449, retro_eeur_453, retro_eeur_461, retro_eeur_471, retro_eeur_486, retro_eeur_493, retro_eeur_51, retro_eeur_540, retro_eeur_572, retro_eeur_590, retro_eeur_599, retro_eeur_600, retro_eeur_619, retro_eeur_624, retro_eeur_65, retro_eeur_670, retro_eeur_678, retro_eeur_68, retro_eeur_98,
Felis catus	ENSFCAG00000012284	34 retrocopies	retro_fcat_1010, retro_fcat_1076, retro_fcat_1093, retro_fcat_1121, retro_fcat_1183, retro_fcat_1304, retro_fcat_1329, retro_fcat_1531, retro_fcat_1541, retro_fcat_1560, retro_fcat_1597, retro_fcat_160, retro_fcat_1623, retro_fcat_167, retro_fcat_1675, retro_fcat_169, retro_fcat_1700, retro_fcat_1786, retro_fcat_1828, retro_fcat_272, retro_fcat_330, retro_fcat_341, retro_fcat_356, retro_fcat_403, retro_fcat_491, retro_fcat_651, retro_fcat_744, retro_fcat_747, retro_fcat_748, retro_fcat_788, retro_fcat_871, retro_fcat_874, retro_fcat_880, retro_fcat_914,
Homo sapiens	ENSG00000163682	28 retrocopies	retro_hsap_115, retro_hsap_1318, retro_hsap_1344, retro_hsap_1398 , retro_hsap_1554, retro_hsap_1585, retro_hsap_1605, retro_hsap_1606, retro_hsap_1717, retro_hsap_1739, retro_hsap_1840, retro_hsap_1864, retro_hsap_1888, retro_hsap_2048, retro_hsap_2326, retro_hsap_2380, retro_hsap_2867, retro_hsap_3008, retro_hsap_321, retro_hsap_3251, retro_hsap_3303, retro_hsap_3604, retro_hsap_3696, retro_hsap_4023, retro_hsap_4793, retro_hsap_666, retro_hsap_773, retro_hsap_802,
Gorilla gorilla	ENSGGOG00000022799	26 retrocopies	retro_ggor_1029, retro_ggor_1084, retro_ggor_1114, retro_ggor_1180, retro_ggor_1204, retro_ggor_1286, retro_ggor_1311, retro_ggor_1328, retro_ggor_1383, retro_ggor_1476, retro_ggor_1805, retro_ggor_1854, retro_ggor_1985, retro_ggor_2148, retro_ggor_219, retro_ggor_2212, retro_ggor_2260, retro_ggor_2431, retro_ggor_2498, retro_ggor_2499, retro_ggor_2700, retro_ggor_347, retro_ggor_392, retro_ggor_577, retro_ggor_641, retro_ggor_660,
Gadus morhua	ENSGMOG00000001002	1 retrocopy	retro_gmor_28,
Loxodonta africana	ENSLAFG00000012021	38 retrocopies	retro_lafr_1009, retro_lafr_1020, retro_lafr_1047, retro_lafr_1095, retro_lafr_1106, retro_lafr_1126, retro_lafr_1145, retro_lafr_1147, retro_lafr_1151, retro_lafr_1174, retro_lafr_1205, retro_lafr_1224, retro_lafr_1225, retro_lafr_1254, retro_lafr_139, retro_lafr_216, retro_lafr_229, retro_lafr_232, retro_lafr_246, retro_lafr_29, retro_lafr_310, retro_lafr_317, retro_lafr_373, retro_lafr_423, retro_lafr_451, retro_lafr_470, retro_lafr_495, retro_lafr_561, retro_lafr_569, retro_lafr_590, retro_lafr_644, retro_lafr_657, retro_lafr_735, retro_lafr_744, retro_lafr_857, retro_lafr_889, retro_lafr_934, retro_lafr_95,
Macropus eugenii	ENSMEUG00000016722	8 retrocopies	retro_meug_1087, retro_meug_1411, retro_meug_1961, retro_meug_22, retro_meug_440, retro_meug_490, retro_meug_650, retro_meug_763,
Microcebus murinus	ENSMICG00000016778	18 retrocopies	retro_mmur_105, retro_mmur_1141, retro_mmur_1183, retro_mmur_1201, retro_mmur_121, retro_mmur_1292, retro_mmur_1418, retro_mmur_1472, retro_mmur_16, retro_mmur_277, retro_mmur_307, retro_mmur_465, retro_mmur_531, retro_mmur_574, retro_mmur_599, retro_mmur_668, retro_mmur_704, retro_mmur_768,
Myotis lucifugus	ENSMLUG00000004597	34 retrocopies	retro_mluc_1028, retro_mluc_1029, retro_mluc_1261, retro_mluc_1269, retro_mluc_127, retro_mluc_1320, retro_mluc_1368, retro_mluc_1380, retro_mluc_1572, retro_mluc_1655, retro_mluc_1704, retro_mluc_1757, retro_mluc_1813, retro_mluc_1858, retro_mluc_1880, retro_mluc_1983, retro_mluc_2041, retro_mluc_2067, retro_mluc_2112, retro_mluc_2119, retro_mluc_220, retro_mluc_2229, retro_mluc_223, retro_mluc_2230, retro_mluc_2370, retro_mluc_2428, retro_mluc_2495, retro_mluc_2611, retro_mluc_293, retro_mluc_461, retro_mluc_533, retro_mluc_648, retro_mluc_75, retro_mluc_895,
Macaca mulatta	ENSMMUG00000008553	22 retrocopies	retro_mmul_1053, retro_mmul_1076, retro_mmul_1097, retro_mmul_1220, retro_mmul_1259, retro_mmul_1272, retro_mmul_1316, retro_mmul_1336, retro_mmul_1404, retro_mmul_1513, retro_mmul_1714, retro_mmul_180, retro_mmul_1924, retro_mmul_2044, retro_mmul_2070, retro_mmul_2167, retro_mmul_2177, retro_mmul_2185, retro_mmul_321, retro_mmul_345, retro_mmul_833, retro_mmul_961,
Monodelphis domestica	ENSMODG00000020553	7 retrocopies	retro_mdom_1026, retro_mdom_1078, retro_mdom_1261, retro_mdom_1352, retro_mdom_1414, retro_mdom_401, retro_mdom_637,
Nomascus leucogenys	ENSNLEG00000017100	26 retrocopies	retro_nleu_1308, retro_nleu_1400, retro_nleu_1417, retro_nleu_1469, retro_nleu_1700, retro_nleu_1723, retro_nleu_174, retro_nleu_1764, retro_nleu_1829, retro_nleu_2064, retro_nleu_2072, retro_nleu_2223, retro_nleu_2490, retro_nleu_2568, retro_nleu_2634, retro_nleu_2718, retro_nleu_2799, retro_nleu_2832, retro_nleu_367, retro_nleu_400, retro_nleu_410, retro_nleu_610, retro_nleu_660, retro_nleu_707, retro_nleu_755, retro_nleu_806,
Otolemur garnettii	ENSOGAG00000004935	20 retrocopies	retro_ogar_117, retro_ogar_1223, retro_ogar_1471, retro_ogar_1614, retro_ogar_1694, retro_ogar_1807, retro_ogar_1884, retro_ogar_1906, retro_ogar_1933, retro_ogar_2162, retro_ogar_2173, retro_ogar_2806, retro_ogar_3036, retro_ogar_3115, retro_ogar_3276, retro_ogar_329, retro_ogar_429, retro_ogar_864, retro_ogar_886, retro_ogar_963,
Pongo abelii	ENSPPYG00000014675	10 retrocopies	retro_pabe_1117, retro_pabe_1157, retro_pabe_1433, retro_pabe_1521, retro_pabe_1523, retro_pabe_162, retro_pabe_2148, retro_pabe_2372, retro_pabe_2695, retro_pabe_3155,
Sarcophilus harrisii	ENSSHAG00000004918	8 retrocopies	retro_shar_191, retro_shar_192, retro_shar_236, retro_shar_340, retro_shar_359, retro_shar_406, retro_shar_600, retro_shar_607,
Sus scrofa	ENSSSCG00000025192	15 retrocopies	retro_sscr_1018, retro_sscr_1021, retro_sscr_1065, retro_sscr_1091, retro_sscr_1160, retro_sscr_1196, retro_sscr_1199, retro_sscr_272, retro_sscr_316, retro_sscr_411, retro_sscr_826, retro_sscr_886, retro_sscr_920, retro_sscr_921, retro_sscr_972,
Tupaia belangeri	ENSTBEG00000006042	18 retrocopies	retro_tbel_1061, retro_tbel_142, retro_tbel_1761, retro_tbel_18, retro_tbel_1852, retro_tbel_2152, retro_tbel_28, retro_tbel_2902, retro_tbel_2937, retro_tbel_30, retro_tbel_325, retro_tbel_340, retro_tbel_3744, retro_tbel_4288, retro_tbel_44, retro_tbel_4430, retro_tbel_4492, retro_tbel_995,
Vicugna pacos	ENSVPAG00000002023	1 retrocopy	retro_vpac_11,

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	0.03 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	0.03 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).