RetrogeneDB ID: retro_pabe_2960

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:63771356..63772153(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: RPL7A
• Ensembl ID: ENSPPYG00000019730
• Aliases: None
• Description: ribosomal protein L7a [Source:HGNC Symbol;Acc:10364]

Sequence

>retro_pabe_2960
CTGCCGAAAGGAAAGAAGGCCAAGGGGAAGAAGGTGGCTCCAGCCCTGCTGTCGTGAAGAAGCAGGAGGTTAAGAAAGTG
GTGAATCCCCTGTTTGTGAAACGGCCTAAGAATTTTGACATTGGACAGGACATTCAGCCCAAAAGAGACCTAACCAGCTT
TGTGAAATGGCCCCACTATATCAGGTTGCAGTGGCAGAGAGCCATCCTCTGTAAGTGGCTGAAAGTGTCTCCTGAGATTA
ACCAGTTCACCCAGGCCCTGGACCGCCAAACAGCTGCTCTGCTACTTCAGCTGGCCCACAAGTACAGATCAGAGACTAAG
CAAGAGAAGAAACAGAGGCTGTTGGCCCTGGCCAAAAAGAAAGCTGCTGGCAAAGGGGACATCCCCACTAGGAGACCACC
TGTCCTTCGAGCAGGAGTTAACACCATCACCACCTTGCTAGAGAACAAGGAAGCTCAGCTGGTGGTGATTGCACACGACG
CAGATCCCATCGAGTTGGTTGTCTTCTTGCCTGCCCTGTGTCCTAAAATGCGGGTCCCTTACTGCATTATCACGGGGGAG
GCAAGACTGGGATGTCTAGTCCACAGGAAGACCTGCACCGCTGTCGCCTTCACACAAGTTAACTCGGAAGACCAAGGCAC
TTTGGCTAAGCTAGTGGGAGCTATGAGGACTGATTACAACGACAGATACGATGAGATCCACCGTCACTGGGGAGGCAATG
TCCTGGGTCCCAAGTCTGTGGCTTGCATTGGCAAGCTCGAAAAGGCAAAGGCTCAAGAACTTGCAACTAAGCTGGGT

Alignment

ORF - retro_pabe_2960 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.02 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPKGKKAKGKKVAPA-PAVVKKQEAKKVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQRAI
          .PKGKKAKGKKVAPA.PAVVKKQE.KKVVNPLF.KRPKNF.IGQDIQPKRDLT.FVKWP.YIRLQ.QRAI
Retrocopy LPKGKKAKGKKVAPA<PAVVKKQEVKKVVNPLFVKRPKNFDIGQDIQPKRDLTSFVKWPHYIRLQWQRAI

Parental  LYKRLKVPPAINQFTQALDRQTATQLLKLAHKYRPETKQEKKQRLLARAEKKAAGKGDVPTKRPPVLRAG
          L.K.LKV.P.INQFTQALDRQTA..LL.LAHKYR.ETKQEKKQRLLA.A.KKAAGKGD.PT.RPPVLRAG
Retrocopy LCKWLKVSPEINQFTQALDRQTAALLLQLAHKYRSETKQEKKQRLLALAKKKAAGKGDIPTRRPPVLRAG

Parental  VNTVTTLVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVPYCIIKGKARLGRLVHRKTCTTVAFTQVNS
          VNT.TTL.ENK.AQLVVIAHD.DPIELVVFLPALC.KM.VPYCII.G.ARLG.LVHRKTCT.VAFTQVNS
Retrocopy VNTITTLLENKEAQLVVIAHDADPIELVVFLPALCPKMRVPYCIITGEARLGCLVHRKTCTAVAFTQVNS

Parental  EDKGALAKLVEAIRTNYNDRYDEIRRHWGGNILGPKSVARIAKLEKAKAKELATKLG
          ED.G.LAKLV.A.RT.YNDRYDEI.RHWGGN.LGPKSVA.I.KLEKAKA.ELATKLG
Retrocopy EDQGTLAKLVGAMRTDYNDRYDEIHRHWGGNVLGPKSVACIGKLEKAKAQELATKLG

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	169.30 RPM
SRP007412_cerebellum	0.00 RPM	97.28 RPM
SRP007412_heart	0.00 RPM	150.31 RPM
SRP007412_kidney	0.10 RPM	335.58 RPM
SRP007412_liver	0.95 RPM	292.34 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2960 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2960 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2960 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 378 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011708	29 retrocopies	retro_amel_1000, retro_amel_1058, retro_amel_1149, retro_amel_1159, retro_amel_1207, retro_amel_1220, retro_amel_1269, retro_amel_1314, retro_amel_1417, retro_amel_142, retro_amel_1429, retro_amel_1471, retro_amel_1499, retro_amel_1506, retro_amel_1641, retro_amel_1644, retro_amel_169, retro_amel_170, retro_amel_1812, retro_amel_1873, retro_amel_357, retro_amel_463, retro_amel_525, retro_amel_529, retro_amel_544, retro_amel_671, retro_amel_726, retro_amel_758, retro_amel_801,
Canis familiaris	ENSCAFG00000017680	36 retrocopies	retro_cfam_1121, retro_cfam_1123, retro_cfam_1165, retro_cfam_1187, retro_cfam_1242, retro_cfam_1365, retro_cfam_1429, retro_cfam_1471, retro_cfam_1497, retro_cfam_1532, retro_cfam_1553, retro_cfam_1563, retro_cfam_1683, retro_cfam_1711, retro_cfam_1721, retro_cfam_1750, retro_cfam_1865, retro_cfam_1898, retro_cfam_2032, retro_cfam_2103, retro_cfam_2111, retro_cfam_2120, retro_cfam_2144, retro_cfam_311, retro_cfam_340, retro_cfam_380, retro_cfam_423, retro_cfam_476, retro_cfam_518, retro_cfam_605, retro_cfam_694, retro_cfam_723, retro_cfam_827, retro_cfam_853, retro_cfam_927, retro_cfam_935,
Callithrix jacchus	ENSCJAG00000014827	3 retrocopies	retro_cjac_199, retro_cjac_343, retro_cjac_49,
Cavia porcellus	ENSCPOG00000001324	4 retrocopies	retro_cpor_1296, retro_cpor_423, retro_cpor_828, retro_cpor_850,
Dasypus novemcinctus	ENSDNOG00000024424	8 retrocopies	retro_dnov_1245, retro_dnov_1509, retro_dnov_169, retro_dnov_1861, retro_dnov_2538, retro_dnov_2591, retro_dnov_302, retro_dnov_825,
Dipodomys ordii	ENSDORG00000006471	3 retrocopies	retro_dord_198, retro_dord_218, retro_dord_516,
Equus caballus	ENSECAG00000008548	2 retrocopies	retro_ecab_4, retro_ecab_402,
Erinaceus europaeus	ENSEEUG00000000203	2 retrocopies	retro_eeur_114, retro_eeur_490,
Felis catus	ENSFCAG00000005825	20 retrocopies	retro_fcat_1123, retro_fcat_1137, retro_fcat_1170, retro_fcat_1277, retro_fcat_1315, retro_fcat_1318, retro_fcat_1344, retro_fcat_1528, retro_fcat_1583, retro_fcat_1771, retro_fcat_1980, retro_fcat_214, retro_fcat_252, retro_fcat_385, retro_fcat_389, retro_fcat_468, retro_fcat_542, retro_fcat_628, retro_fcat_694, retro_fcat_943,
Gorilla gorilla	ENSGGOG00000014442	48 retrocopies	retro_ggor_1034, retro_ggor_1042, retro_ggor_1087, retro_ggor_1107, retro_ggor_1190, retro_ggor_1249, retro_ggor_1408, retro_ggor_1409, retro_ggor_1460, retro_ggor_1541, retro_ggor_1591, retro_ggor_172, retro_ggor_1724, retro_ggor_1881, retro_ggor_194, retro_ggor_2004, retro_ggor_2033, retro_ggor_2087, retro_ggor_2117, retro_ggor_2147, retro_ggor_2313, retro_ggor_2410, retro_ggor_2430, retro_ggor_2480, retro_ggor_2522, retro_ggor_2578, retro_ggor_2611, retro_ggor_2617, retro_ggor_2618, retro_ggor_2779, retro_ggor_2781, retro_ggor_2871, retro_ggor_2872, retro_ggor_288, retro_ggor_2960, retro_ggor_310, retro_ggor_333, retro_ggor_386, retro_ggor_539, retro_ggor_626, retro_ggor_636, retro_ggor_640, retro_ggor_658, retro_ggor_663, retro_ggor_815, retro_ggor_865, retro_ggor_904, retro_ggor_963,
Loxodonta africana	ENSLAFG00000006436	2 retrocopies	retro_lafr_1059, retro_lafr_1132,
Macropus eugenii	ENSMEUG00000014550	16 retrocopies	retro_meug_1268, retro_meug_133, retro_meug_1362, retro_meug_1523, retro_meug_1581, retro_meug_1872, retro_meug_2011, retro_meug_2080, retro_meug_2101, retro_meug_2123, retro_meug_401, retro_meug_632, retro_meug_654, retro_meug_687, retro_meug_699, retro_meug_919,
Myotis lucifugus	ENSMLUG00000004666	10 retrocopies	retro_mluc_1033, retro_mluc_1087, retro_mluc_1359, retro_mluc_1365, retro_mluc_1745, retro_mluc_1877, retro_mluc_2074, retro_mluc_541, retro_mluc_558, retro_mluc_670,
Macaca mulatta	ENSMMUG00000022341	9 retrocopies	retro_mmul_113, retro_mmul_130, retro_mmul_204, retro_mmul_230, retro_mmul_252, retro_mmul_259, retro_mmul_309, retro_mmul_33, retro_mmul_4,
Monodelphis domestica	ENSMODG00000012754	3 retrocopies	retro_mdom_1347, retro_mdom_418, retro_mdom_586,
Mustela putorius furo	ENSMPUG00000012398	13 retrocopies	retro_mputfur_1081, retro_mputfur_1210, retro_mputfur_1281, retro_mputfur_1344, retro_mputfur_1380, retro_mputfur_1611, retro_mputfur_1612, retro_mputfur_325, retro_mputfur_459, retro_mputfur_656, retro_mputfur_698, retro_mputfur_792, retro_mputfur_900,
Mus musculus	ENSMUSG00000062647	10 retrocopies	retro_mmus_120, retro_mmus_141, retro_mmus_165, retro_mmus_166, retro_mmus_214, retro_mmus_226, retro_mmus_267, retro_mmus_34, retro_mmus_43, retro_mmus_93,
Nomascus leucogenys	ENSNLEG00000013068	22 retrocopies	retro_nleu_1051, retro_nleu_1056, retro_nleu_137, retro_nleu_1404, retro_nleu_1418, retro_nleu_1682, retro_nleu_1920, retro_nleu_2130, retro_nleu_2254, retro_nleu_2341, retro_nleu_2397, retro_nleu_2423, retro_nleu_2641, retro_nleu_267, retro_nleu_2822, retro_nleu_2853, retro_nleu_399, retro_nleu_432, retro_nleu_562, retro_nleu_780, retro_nleu_796, retro_nleu_82,
Otolemur garnettii	ENSOGAG00000014027	16 retrocopies	retro_ogar_1014, retro_ogar_1172, retro_ogar_1638, retro_ogar_1735, retro_ogar_1815, retro_ogar_2774, retro_ogar_3012, retro_ogar_3097, retro_ogar_319, retro_ogar_404, retro_ogar_57, retro_ogar_685, retro_ogar_758, retro_ogar_850, retro_ogar_926, retro_ogar_994,
Ochotona princeps	ENSOPRG00000005726	4 retrocopies	retro_opri_451, retro_opri_629, retro_opri_65, retro_opri_922,
Pongo abelii	ENSPPYG00000019730	52 retrocopies	retro_pabe_1022, retro_pabe_1104, retro_pabe_1112, retro_pabe_1160, retro_pabe_1189, retro_pabe_1305, retro_pabe_1368, retro_pabe_1652, retro_pabe_1662, retro_pabe_1871, retro_pabe_2059, retro_pabe_2264, retro_pabe_2286, retro_pabe_2305, retro_pabe_2394, retro_pabe_2501, retro_pabe_2522, retro_pabe_2534, retro_pabe_2553, retro_pabe_2588, retro_pabe_2654, retro_pabe_267, retro_pabe_271, retro_pabe_2896, retro_pabe_293, retro_pabe_2960 , retro_pabe_3009, retro_pabe_3033, retro_pabe_3079, retro_pabe_3118, retro_pabe_3171, retro_pabe_3231, retro_pabe_330, retro_pabe_3444, retro_pabe_3467, retro_pabe_3469, retro_pabe_3500, retro_pabe_3700, retro_pabe_379, retro_pabe_519, retro_pabe_540, retro_pabe_549, retro_pabe_581, retro_pabe_645, retro_pabe_664, retro_pabe_682, retro_pabe_715, retro_pabe_725, retro_pabe_755, retro_pabe_864, retro_pabe_914, retro_pabe_963,
Rattus norvegicus	ENSRNOG00000049097	10 retrocopies	retro_rnor_123, retro_rnor_15, retro_rnor_238, retro_rnor_303, retro_rnor_323, retro_rnor_346, retro_rnor_368, retro_rnor_398, retro_rnor_403, retro_rnor_86,
Sarcophilus harrisii	ENSSHAG00000004337	4 retrocopies	retro_shar_157, retro_shar_338, retro_shar_401, retro_shar_494,
Ictidomys tridecemlineatus	ENSSTOG00000003671	3 retrocopies	retro_itri_1034, retro_itri_53, retro_itri_920,
Tupaia belangeri	ENSTBEG00000008595	26 retrocopies	retro_tbel_1102, retro_tbel_112, retro_tbel_1314, retro_tbel_1420, retro_tbel_1484, retro_tbel_174, retro_tbel_1770, retro_tbel_1892, retro_tbel_1916, retro_tbel_2015, retro_tbel_2063, retro_tbel_2630, retro_tbel_2748, retro_tbel_2896, retro_tbel_3005, retro_tbel_3017, retro_tbel_3445, retro_tbel_4295, retro_tbel_4298, retro_tbel_4737, retro_tbel_542, retro_tbel_686, retro_tbel_861, retro_tbel_949, retro_tbel_950, retro_tbel_960,
Tarsius syrichta	ENSTSYG00000005467	20 retrocopies	retro_tsyr_1009, retro_tsyr_1012, retro_tsyr_1166, retro_tsyr_1168, retro_tsyr_1280, retro_tsyr_1346, retro_tsyr_158, retro_tsyr_1798, retro_tsyr_182, retro_tsyr_1824, retro_tsyr_1939, retro_tsyr_2039, retro_tsyr_214, retro_tsyr_251, retro_tsyr_484, retro_tsyr_63, retro_tsyr_696, retro_tsyr_880, retro_tsyr_907, retro_tsyr_911,
Tursiops truncatus	ENSTTRG00000007645	3 retrocopies	retro_ttru_1334, retro_ttru_1681, retro_ttru_1824,