RetrogeneDB ID: retro_pabe_2944

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:30700590..30701051(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL23A
• Ensembl ID: ENSPPYG00000008108
• Aliases: None
• Description: ribosomal protein L23a [Source:HGNC Symbol;Acc:10317]

Sequence

>retro_pabe_2944
AAAAATGAGAAGGAAGCTTCTGCCCCTCCTAAAGCCAAAGCCAAAGTGAAGGCTTTGCAAGGCCGAGAAGGCAGTGTTGA
AAGATGTCCACAGCCACAATAAAACAGAAGATCCACACATCACCCACCTTCCAGCGGCCCAAGATGATGTGACTCCGGAG
GCAGCCCAAATATCATTGGAAGAGCACCTGCAGGAGAAATAAGCTTGATCACTGTGCTATCATCAAGTTTCCGCTGACCA
CTGAGTCCACCACGAAGAAGACAGAAGACAACAAAACACTTATATTCATGGTGGATGTTAAAGCCAACAAGCACCAGATC
AAACAGGCTGTGAAGAAGCTCTGTGACATTGATGTGGCCAAGGTCAACACCCTGATTCAGTCTGATGGAGAGAAGAAGGC
ATATGTTCGACTGTCTCCTGACTATGATGCTTTGATTGTTGCCAACAAAATTGGGATCATT

Alignment

ORF - retro_pabe_2944 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.35 %
• Parental protein coverage: 98.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KAKKEAPAPPKAEAKAKAL-KAKKAVLKGVHSHKK-KKIRTSPTFRRPKTLRLRRQPKYPRKSAPRRNKL
          K..KEA.APPKA.AK.KAL.KA.KAVLK.VHSH.K..KI.TSPTF.RPK...LRRQPKY..KS..RRNKL
Retrocopy KNEKEASAPPKAKAKVKAL>KAEKAVLKDVHSHNK>QKIHTSPTFQRPKMM*LRRQPKYHWKSTCRRNKL

Parental  DHYAIIKFPLTTESAMKKIEDNNTLVFIVDVKANKHQIKQAVKKLYDIDVAKVNTLIRPDGEKKAYVRLA
          DH.AIIKFPLTTES..KK.EDN.TL.F.VDVKANKHQIKQAVKKL.DIDVAKVNTLI..DGEKKAYVRL.
Retrocopy DHCAIIKFPLTTESTTKKTEDNKTLIFMVDVKANKHQIKQAVKKLCDIDVAKVNTLIQSDGEKKAYVRLS

Parental  PDYDALDVANKIGII
          PDYDAL.VANKIGII
Retrocopy PDYDALIVANKIGII

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	0.06 RPM	84.59 RPM
SRP007412_cerebellum	0.49 RPM	123.67 RPM
SRP007412_heart	0.06 RPM	136.34 RPM
SRP007412_kidney	0.03 RPM	189.50 RPM
SRP007412_liver	0.00 RPM	164.09 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2944 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2944 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2944 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3571

---

Parental genes homology:

Parental genes homology involve 20 parental genes, and 463 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005311	2 retrocopies	retro_acar_152, retro_acar_173,
Bos taurus	ENSBTAG00000046394	6 retrocopies	retro_btau_132, retro_btau_159, retro_btau_169, retro_btau_178, retro_btau_237, retro_btau_8,
Callithrix jacchus	ENSCJAG00000013126	7 retrocopies	retro_cjac_118, retro_cjac_154, retro_cjac_20, retro_cjac_258, retro_cjac_30, retro_cjac_315, retro_cjac_46,
Dasypus novemcinctus	ENSDNOG00000019487	65 retrocopies	retro_dnov_1018, retro_dnov_1065, retro_dnov_1069, retro_dnov_1082, retro_dnov_1169, retro_dnov_120, retro_dnov_123, retro_dnov_1238, retro_dnov_127, retro_dnov_1283, retro_dnov_1365, retro_dnov_1460, retro_dnov_1514, retro_dnov_1538, retro_dnov_1541, retro_dnov_1597, retro_dnov_171, retro_dnov_1781, retro_dnov_1793, retro_dnov_1816, retro_dnov_183, retro_dnov_1835, retro_dnov_1837, retro_dnov_1873, retro_dnov_1926, retro_dnov_203, retro_dnov_2046, retro_dnov_2051, retro_dnov_2089, retro_dnov_2178, retro_dnov_2256, retro_dnov_2278, retro_dnov_2284, retro_dnov_2343, retro_dnov_2368, retro_dnov_246, retro_dnov_2493, retro_dnov_2563, retro_dnov_2573, retro_dnov_267, retro_dnov_372, retro_dnov_401, retro_dnov_429, retro_dnov_470, retro_dnov_499, retro_dnov_556, retro_dnov_581, retro_dnov_591, retro_dnov_611, retro_dnov_625, retro_dnov_636, retro_dnov_64, retro_dnov_67, retro_dnov_683, retro_dnov_704, retro_dnov_718, retro_dnov_731, retro_dnov_736, retro_dnov_749, retro_dnov_769, retro_dnov_813, retro_dnov_832, retro_dnov_903, retro_dnov_929, retro_dnov_972,
Felis catus	ENSFCAG00000004021	35 retrocopies	retro_fcat_1003, retro_fcat_1011, retro_fcat_1030, retro_fcat_1039, retro_fcat_1054, retro_fcat_1071, retro_fcat_1073, retro_fcat_11, retro_fcat_1124, retro_fcat_1161, retro_fcat_1202, retro_fcat_1205, retro_fcat_1275, retro_fcat_1389, retro_fcat_1659, retro_fcat_1670, retro_fcat_1748, retro_fcat_1787, retro_fcat_1796, retro_fcat_1810, retro_fcat_182, retro_fcat_185, retro_fcat_1856, retro_fcat_1905, retro_fcat_1909, retro_fcat_1944, retro_fcat_2022, retro_fcat_289, retro_fcat_364, retro_fcat_476, retro_fcat_603, retro_fcat_657, retro_fcat_765, retro_fcat_898, retro_fcat_950,
Homo sapiens	ENSG00000198242	57 retrocopies	retro_hsap_110, retro_hsap_1139, retro_hsap_1177, retro_hsap_1315, retro_hsap_1316, retro_hsap_1460, retro_hsap_1616, retro_hsap_1660, retro_hsap_1714, retro_hsap_1775, retro_hsap_1791, retro_hsap_1807, retro_hsap_1833, retro_hsap_1924, retro_hsap_1970, retro_hsap_2021, retro_hsap_2024, retro_hsap_2134, retro_hsap_2169, retro_hsap_2210, retro_hsap_2222, retro_hsap_2271, retro_hsap_2310, retro_hsap_2356, retro_hsap_2359, retro_hsap_2390, retro_hsap_2404, retro_hsap_2446, retro_hsap_2509, retro_hsap_2511, retro_hsap_2528, retro_hsap_2567, retro_hsap_2602, retro_hsap_2629, retro_hsap_2748, retro_hsap_2804, retro_hsap_2874, retro_hsap_3282, retro_hsap_334, retro_hsap_3377, retro_hsap_341, retro_hsap_342, retro_hsap_345, retro_hsap_3545, retro_hsap_3571, retro_hsap_3815, retro_hsap_4118, retro_hsap_4127, retro_hsap_4329, retro_hsap_490, retro_hsap_504, retro_hsap_641, retro_hsap_672, retro_hsap_725, retro_hsap_751, retro_hsap_775, retro_hsap_945,
Gorilla gorilla	ENSGGOG00000016736	26 retrocopies	retro_ggor_1027, retro_ggor_1028, retro_ggor_1123, retro_ggor_120, retro_ggor_123, retro_ggor_1284, retro_ggor_140, retro_ggor_1431, retro_ggor_158, retro_ggor_1650, retro_ggor_1743, retro_ggor_1789, retro_ggor_1911, retro_ggor_1948, retro_ggor_2164, retro_ggor_2239, retro_ggor_2285, retro_ggor_229, retro_ggor_2409, retro_ggor_2475, retro_ggor_2568, retro_ggor_2764, retro_ggor_2773, retro_ggor_580, retro_ggor_611, retro_ggor_642,
Loxodonta africana	ENSLAFG00000013387	16 retrocopies	retro_lafr_1176, retro_lafr_153, retro_lafr_237, retro_lafr_33, retro_lafr_335, retro_lafr_442, retro_lafr_510, retro_lafr_525, retro_lafr_551, retro_lafr_557, retro_lafr_643, retro_lafr_78, retro_lafr_891, retro_lafr_908, retro_lafr_957, retro_lafr_96,
Myotis lucifugus	ENSMLUG00000012448	4 retrocopies	retro_mluc_175, retro_mluc_2375, retro_mluc_353, retro_mluc_91,
Monodelphis domestica	ENSMODG00000019297	3 retrocopies	retro_mdom_120, retro_mdom_870, retro_mdom_912,
Mustela putorius furo	ENSMPUG00000014179	12 retrocopies	retro_mputfur_102, retro_mputfur_106, retro_mputfur_123, retro_mputfur_159, retro_mputfur_168, retro_mputfur_179, retro_mputfur_3, retro_mputfur_333, retro_mputfur_42, retro_mputfur_52, retro_mputfur_599, retro_mputfur_91,
Mus musculus	ENSMUSG00000058546	8 retrocopies	retro_mmus_1, retro_mmus_126, retro_mmus_130, retro_mmus_184, retro_mmus_224, retro_mmus_64, retro_mmus_84, retro_mmus_95,
Nomascus leucogenys	ENSNLEG00000002872	60 retrocopies	retro_nleu_1004, retro_nleu_1216, retro_nleu_1273, retro_nleu_1290, retro_nleu_1398, retro_nleu_1448, retro_nleu_145, retro_nleu_1544, retro_nleu_158, retro_nleu_160, retro_nleu_161, retro_nleu_1775, retro_nleu_1782, retro_nleu_2004, retro_nleu_2010, retro_nleu_203, retro_nleu_211, retro_nleu_2115, retro_nleu_213, retro_nleu_2312, retro_nleu_2339, retro_nleu_2406, retro_nleu_2413, retro_nleu_2455, retro_nleu_2468, retro_nleu_2474, retro_nleu_2492, retro_nleu_2514, retro_nleu_2594, retro_nleu_2661, retro_nleu_2664, retro_nleu_2784, retro_nleu_2788, retro_nleu_2925, retro_nleu_2943, retro_nleu_2960, retro_nleu_2964, retro_nleu_3026, retro_nleu_3031, retro_nleu_3037, retro_nleu_3056, retro_nleu_3096, retro_nleu_3101, retro_nleu_3107, retro_nleu_3108, retro_nleu_3110, retro_nleu_3114, retro_nleu_3118, retro_nleu_3123, retro_nleu_3124, retro_nleu_328, retro_nleu_355, retro_nleu_356, retro_nleu_401, retro_nleu_473, retro_nleu_518, retro_nleu_641, retro_nleu_902, retro_nleu_938, retro_nleu_966,
Procavia capensis	ENSPCAG00000017002	30 retrocopies	retro_pcap_103, retro_pcap_122, retro_pcap_131, retro_pcap_187, retro_pcap_213, retro_pcap_215, retro_pcap_221, retro_pcap_233, retro_pcap_246, retro_pcap_279, retro_pcap_320, retro_pcap_321, retro_pcap_331, retro_pcap_336, retro_pcap_342, retro_pcap_347, retro_pcap_368, retro_pcap_372, retro_pcap_382, retro_pcap_390, retro_pcap_392, retro_pcap_396, retro_pcap_437, retro_pcap_450, retro_pcap_453, retro_pcap_460, retro_pcap_61, retro_pcap_70, retro_pcap_82, retro_pcap_96,
Pongo abelii	ENSPPYG00000008108	49 retrocopies	retro_pabe_1030, retro_pabe_1203, retro_pabe_1206, retro_pabe_1335, retro_pabe_1430, retro_pabe_1459, retro_pabe_1590, retro_pabe_1721, retro_pabe_1747, retro_pabe_1752, retro_pabe_1766, retro_pabe_1797, retro_pabe_1846, retro_pabe_1848, retro_pabe_1867, retro_pabe_1926, retro_pabe_1947, retro_pabe_1995, retro_pabe_2018, retro_pabe_2057, retro_pabe_2075, retro_pabe_2082, retro_pabe_2091, retro_pabe_2132, retro_pabe_2156, retro_pabe_2221, retro_pabe_2334, retro_pabe_234, retro_pabe_243, retro_pabe_2612, retro_pabe_2738, retro_pabe_2773, retro_pabe_2820, retro_pabe_2944 , retro_pabe_3006, retro_pabe_3036, retro_pabe_3200, retro_pabe_3371, retro_pabe_3477, retro_pabe_351, retro_pabe_3528, retro_pabe_354, retro_pabe_474, retro_pabe_627, retro_pabe_754, retro_pabe_765, retro_pabe_799, retro_pabe_946, retro_pabe_984,
Pteropus vampyrus	ENSPVAG00000002922	32 retrocopies	retro_pvam_1002, retro_pvam_1004, retro_pvam_1083, retro_pvam_1113, retro_pvam_113, retro_pvam_1211, retro_pvam_1226, retro_pvam_1268, retro_pvam_1300, retro_pvam_1329, retro_pvam_1350, retro_pvam_1363, retro_pvam_1456, retro_pvam_159, retro_pvam_249, retro_pvam_385, retro_pvam_425, retro_pvam_436, retro_pvam_445, retro_pvam_511, retro_pvam_526, retro_pvam_537, retro_pvam_564, retro_pvam_593, retro_pvam_72, retro_pvam_729, retro_pvam_752, retro_pvam_840, retro_pvam_897, retro_pvam_927, retro_pvam_947, retro_pvam_95,
Rattus norvegicus	ENSRNOG00000023344	6 retrocopies	retro_rnor_136, retro_rnor_145, retro_rnor_211, retro_rnor_40, retro_rnor_404, retro_rnor_62,
Sarcophilus harrisii	ENSSHAG00000014549	13 retrocopies	retro_shar_188, retro_shar_373, retro_shar_407, retro_shar_448, retro_shar_498, retro_shar_564, retro_shar_624, retro_shar_630, retro_shar_685, retro_shar_698, retro_shar_824, retro_shar_829, retro_shar_835,
Sus scrofa	ENSSSCG00000017768	9 retrocopies	retro_sscr_1025, retro_sscr_1047, retro_sscr_1133, retro_sscr_239, retro_sscr_356, retro_sscr_418, retro_sscr_598, retro_sscr_638, retro_sscr_952,
Ictidomys tridecemlineatus	ENSSTOG00000011328	23 retrocopies	retro_itri_1022, retro_itri_1035, retro_itri_1051, retro_itri_1059, retro_itri_1071, retro_itri_1150, retro_itri_1261, retro_itri_1327, retro_itri_1347, retro_itri_1460, retro_itri_1507, retro_itri_217, retro_itri_225, retro_itri_304, retro_itri_360, retro_itri_494, retro_itri_626, retro_itri_627, retro_itri_734, retro_itri_761, retro_itri_791, retro_itri_965, retro_itri_972,