RetrogeneDB ID: retro_pabe_3325

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:49008206..49008809(-)
• Located in intron of: ENSPPYG00000018571

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS4X
• Ensembl ID: ENSPPYG00000020462
• Aliases: None
• Description: ribosomal protein S4, X-linked [Source:HGNC Symbol;Acc:10424]

Sequence

>retro_pabe_3325
GAGAAGATTTGCATGCAGTGGTTCATTAAGATCGATGGCAACGTTCGAACTGATATAACCCACCCCGCTGGATTCATAGA
TGTCATGGGCATTGACTAGATGGGAGAGAATTTTCGTCTCATCTATGACACCAAGGGTTGCTTTGCTGCACATCGTGTTA
CACCTGAGGAGCCCAAGTACAAGTTGTGCAAAGTGAGAAAAATCTTCATGGGCACAAAAGGAATCCCTCATCTGGTGACT
CATGATGCTCGCATCATCTGCTACCTTGATCCCCTCCATCGAGGTGAATGATCCCATTCAGACTGATTTGGAAACTGGCA
AGATCACTGATTTCATCAAGTTTGACACTGGTAACCTGTGGATGGTGACTGGAGGTGCTAACTGGGGAAGAATTGGTGTC
ATTACCCACAGAGAGAGGCACCCTTGATCTTTTGATGTGGTTCACGTGAAAGATGCCAATGGCAACAGCTTTGCCACCTG
GCTTTCCAACATTTTTGTTACTGGCAAGGGCAACAAACCATTAATTTCTCTTCCCTGAGGAAAGGTATATGCCTCACACT
GCTGAGAGAGAGACAGAGACTGGCAGCCAACACAGCAGTGGGT

Alignment

ORF - retro_pabe_3325 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.9 %
• Parental protein coverage: 76.81 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCKVRKIFV
          .KICMQ.FIKIDG.VRTDIT.PAGF.DV..ID..GENFRLIYDTKG.FA.HR.TPEE.KYKLCKVRKIF.
Retrocopy EKICMQWFIKIDGNVRTDITHPAGFIDVMGID*MGENFRLIYDTKGCFAAHRVTPEEPKYKLCKVRKIFM

Parental  GTKGIPHLVTHDARTIRYPDPL-IKVNDTIQIDLETGKITDFIKFDTGNLCMVTGGANLGRIGVITNRER
          GTKGIPHLVTHDAR.I.Y.DPL.I.VND.IQ.DLETGKITDFIKFDTGNL.MVTGGAN.GRIGVIT.RER
Retrocopy GTKGIPHLVTHDARIICYLDPL>IEVNDPIQTDLETGKITDFIKFDTGNLWMVTGGANWGRIGVITHRER

Parental  HPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKSWISLPRG-KGIRLTIAEERDKRLAAKQSSG
          HP.SFDVVHVKDANGNSFAT.LSNIFV.GKGNK..ISLP.G.KGI.LT...ER..RLAA....G
Retrocopy HP*SFDVVHVKDANGNSFATWLSNIFVTGKGNKPLISLP*G<KGICLTLLRER-QRLAANTAVG

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	58.39 RPM
SRP007412_cerebellum	0.00 RPM	73.08 RPM
SRP007412_heart	0.03 RPM	87.60 RPM
SRP007412_kidney	0.07 RPM	131.16 RPM
SRP007412_liver	0.03 RPM	137.65 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3325 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3325 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3325 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4051
Macaca mulatta	retro_mmul_2338

---

Parental genes homology:

Parental genes homology involve 26 parental genes, and 246 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014601	1 retrocopy	retro_acar_82,
Bos taurus	ENSBTAG00000018800	5 retrocopies	retro_btau_119, retro_btau_125, retro_btau_146, retro_btau_33, retro_btau_76,
Canis familiaris	ENSCAFG00000017151	2 retrocopies	retro_cfam_165, retro_cfam_194,
Callithrix jacchus	ENSCJAG00000004192	2 retrocopies	retro_cjac_19, retro_cjac_361,
Cavia porcellus	ENSCPOG00000006337	3 retrocopies	retro_cpor_1023, retro_cpor_1075, retro_cpor_31,
Equus caballus	ENSECAG00000010852	6 retrocopies	retro_ecab_34, retro_ecab_435, retro_ecab_443, retro_ecab_614, retro_ecab_757, retro_ecab_850,
Homo sapiens	ENSG00000129824	1 retrocopy	retro_hsap_1704,
Homo sapiens	ENSG00000198034	19 retrocopies	retro_hsap_1070, retro_hsap_1151, retro_hsap_120, retro_hsap_1204, retro_hsap_1792, retro_hsap_1868, retro_hsap_2026, retro_hsap_2051, retro_hsap_2052, retro_hsap_2270, retro_hsap_2437, retro_hsap_2443, retro_hsap_3162, retro_hsap_3423, retro_hsap_3519, retro_hsap_3986, retro_hsap_4051, retro_hsap_656, retro_hsap_875,
Loxodonta africana	ENSLAFG00000002654	4 retrocopies	retro_lafr_1007, retro_lafr_1081, retro_lafr_1238, retro_lafr_208,
Macropus eugenii	ENSMEUG00000007969	16 retrocopies	retro_meug_131, retro_meug_141, retro_meug_1644, retro_meug_1732, retro_meug_1814, retro_meug_194, retro_meug_2098, retro_meug_2121, retro_meug_228, retro_meug_562, retro_meug_628, retro_meug_673, retro_meug_843, retro_meug_872, retro_meug_972, retro_meug_999,
Meleagris gallopavo	ENSMGAG00000009671	1 retrocopy	retro_mgal_3,
Microcebus murinus	ENSMICG00000016606	58 retrocopies	retro_mmur_1107, retro_mmur_1108, retro_mmur_1123, retro_mmur_1136, retro_mmur_1168, retro_mmur_1208, retro_mmur_1209, retro_mmur_1229, retro_mmur_1231, retro_mmur_1257, retro_mmur_1268, retro_mmur_1334, retro_mmur_1411, retro_mmur_1416, retro_mmur_1430, retro_mmur_1442, retro_mmur_1454, retro_mmur_1467, retro_mmur_1471, retro_mmur_1519, retro_mmur_1578, retro_mmur_1584, retro_mmur_1599, retro_mmur_1600, retro_mmur_1611, retro_mmur_166, retro_mmur_241, retro_mmur_281, retro_mmur_289, retro_mmur_293, retro_mmur_347, retro_mmur_363, retro_mmur_390, retro_mmur_510, retro_mmur_511, retro_mmur_521, retro_mmur_523, retro_mmur_530, retro_mmur_54, retro_mmur_551, retro_mmur_591, retro_mmur_609, retro_mmur_619, retro_mmur_663, retro_mmur_665, retro_mmur_687, retro_mmur_767, retro_mmur_784, retro_mmur_828, retro_mmur_840, retro_mmur_917, retro_mmur_918, retro_mmur_931, retro_mmur_943, retro_mmur_946, retro_mmur_949, retro_mmur_96, retro_mmur_995,
Monodelphis domestica	ENSMODG00000011070	1 retrocopy	retro_mdom_238,
Mustela putorius furo	ENSMPUG00000005294	11 retrocopies	retro_mputfur_1044, retro_mputfur_1176, retro_mputfur_1325, retro_mputfur_1326, retro_mputfur_1393, retro_mputfur_160, retro_mputfur_205, retro_mputfur_48, retro_mputfur_725, retro_mputfur_876, retro_mputfur_988,
Mus musculus	ENSMUSG00000031320	13 retrocopies	retro_mmus_1092, retro_mmus_1686, retro_mmus_2052, retro_mmus_2197, retro_mmus_2487, retro_mmus_2541, retro_mmus_2916, retro_mmus_3025, retro_mmus_3702, retro_mmus_499, retro_mmus_797, retro_mmus_92, retro_mmus_987,
Nomascus leucogenys	ENSNLEG00000018121	25 retrocopies	retro_nleu_1127, retro_nleu_1226, retro_nleu_1361, retro_nleu_142, retro_nleu_1442, retro_nleu_1907, retro_nleu_1908, retro_nleu_2089, retro_nleu_2256, retro_nleu_244, retro_nleu_2461, retro_nleu_2495, retro_nleu_2587, retro_nleu_2613, retro_nleu_2640, retro_nleu_2646, retro_nleu_2776, retro_nleu_2801, retro_nleu_2932, retro_nleu_2967, retro_nleu_2968, retro_nleu_486, retro_nleu_500, retro_nleu_560, retro_nleu_947,
Otolemur garnettii	ENSOGAG00000011808	2 retrocopies	retro_ogar_121, retro_ogar_229,
Procavia capensis	ENSPCAG00000000761	3 retrocopies	retro_pcap_334, retro_pcap_35, retro_pcap_360,
Pongo abelii	ENSPPYG00000020462	24 retrocopies	retro_pabe_1005, retro_pabe_1401, retro_pabe_1472, retro_pabe_1524, retro_pabe_1586, retro_pabe_1657, retro_pabe_1673, retro_pabe_1702, retro_pabe_1784, retro_pabe_1948, retro_pabe_2455, retro_pabe_2629, retro_pabe_2836, retro_pabe_2923, retro_pabe_3275, retro_pabe_3325 , retro_pabe_340, retro_pabe_493, retro_pabe_579, retro_pabe_580, retro_pabe_679, retro_pabe_891, retro_pabe_921, retro_pabe_954,
Pan troglodytes	ENSPTRG00000022025	9 retrocopies	retro_ptro_1280, retro_ptro_131, retro_ptro_1366, retro_ptro_1367, retro_ptro_1408, retro_ptro_2276, retro_ptro_3032, retro_ptro_728, retro_ptro_784,
Pan troglodytes	ENSPTRG00000022470	1 retrocopy	retro_ptro_1153,
Pteropus vampyrus	ENSPVAG00000012882	21 retrocopies	retro_pvam_1021, retro_pvam_1082, retro_pvam_1158, retro_pvam_1264, retro_pvam_1298, retro_pvam_1312, retro_pvam_1327, retro_pvam_1364, retro_pvam_1419, retro_pvam_177, retro_pvam_191, retro_pvam_214, retro_pvam_219, retro_pvam_335, retro_pvam_473, retro_pvam_628, retro_pvam_714, retro_pvam_809, retro_pvam_835, retro_pvam_921, retro_pvam_930,
Rattus norvegicus	ENSRNOG00000003201	1 retrocopy	retro_rnor_135,
Sus scrofa	ENSSSCG00000012405	5 retrocopies	retro_sscr_1070, retro_sscr_563, retro_sscr_580, retro_sscr_665, retro_sscr_973,
Ictidomys tridecemlineatus	ENSSTOG00000028692	8 retrocopies	retro_itri_1179, retro_itri_1607, retro_itri_291, retro_itri_306, retro_itri_368, retro_itri_495, retro_itri_738, retro_itri_985,
Vicugna pacos	ENSVPAG00000010952	4 retrocopies	retro_vpac_244, retro_vpac_460, retro_vpac_604, retro_vpac_653,