RetrogeneDB ID: retro_pabe_2662

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:89145002..89145358(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: H3F3B
• Ensembl ID: ENSPPYG00000008636
• Aliases: None
• Description: histone H3.3 [Source:RefSeq peptide;Acc:NP_001127304]

Sequence

>retro_pabe_2662
AAGCGGACTGCACGCAAATCCACCGGTGGTAAAGCACCCGGGAAGCAACTGGCTACAAAAGCCTTTTGCAAGAGTGCGCC
CTCTACTGGACGGGCGAATACACTGCATTTTTACAGGCCTTGTACGGAGGCACGATTCGCAAACTTCCCTTCCAGCGTCT
GGTGTGAGAAATTGCTCAGGATTTTAAAACAGATCTGTGCTTCCAGAGTGCAGCTATTGGTGCTTTGCAGGAGGCAATTA
AGGCCTAACTGGTTGGCCTTTTTGAAGGCACCCACCTGTGTGCCATCCATGCCAAACGTGTAACAATTATGCCAAAAGAC
ATCGAGCTAGCATGCCGCACACGTGGAGAACGTGCT

Alignment

ORF - retro_pabe_2662 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.33 %
• Parental protein coverage: 96.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KQTARKSTGGKAPRKQLATKAARK---SAPSTGGIRRYQKSTEL-LIRKLPFQRLVREIAQDFKTDLRFQ
          K.TARKSTGGKAP.KQLATKA..K...S.........Y...TE...IRKLPFQRLV.EIAQDFKTDL.FQ
Retrocopy KRTARKSTGGKAPGKQLATKAFCKSAPSTGRANTLHFYRPCTEA<TIRKLPFQRLV*EIAQDFKTDLCFQ

Parental  SAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
          SAAIGALQEA..A.LVGLFE.T.LCAIHAKRVTIMPKDI.LA.R.RGERA
Retrocopy SAAIGALQEAIKA*LVGLFEGTHLCAIHAKRVTIMPKDIELACRTRGERA

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	139.66 RPM
SRP007412_cerebellum	0.12 RPM	270.08 RPM
SRP007412_heart	0.00 RPM	95.49 RPM
SRP007412_kidney	0.00 RPM	182.77 RPM
SRP007412_liver	0.00 RPM	244.42 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2662 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2662 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2662 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3214
Pan troglodytes	retro_ptro_2238
Gorilla gorilla	retro_ggor_2181

---

Parental genes homology:

Parental genes homology involve 54 parental genes, and 332 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009765	3 retrocopies	retro_amel_1636, retro_amel_1794, retro_amel_192,
Ailuropoda melanoleuca	ENSAMEG00000014588	7 retrocopies	retro_amel_1023, retro_amel_1026, retro_amel_144, retro_amel_570, retro_amel_687, retro_amel_711, retro_amel_903,
Bos taurus	ENSBTAG00000024561	3 retrocopies	retro_btau_156, retro_btau_204, retro_btau_47,
Canis familiaris	ENSCAFG00000004916	2 retrocopies	retro_cfam_1117, retro_cfam_622,
Canis familiaris	ENSCAFG00000016119	4 retrocopies	retro_cfam_168, retro_cfam_1845, retro_cfam_650, retro_cfam_673,
Choloepus hoffmanni	ENSCHOG00000009661	10 retrocopies	retro_chof_1580, retro_chof_1635, retro_chof_1911, retro_chof_2281, retro_chof_2294, retro_chof_2343, retro_chof_2546, retro_chof_454, retro_chof_517, retro_chof_530,
Callithrix jacchus	ENSCJAG00000012702	10 retrocopies	retro_cjac_145, retro_cjac_198, retro_cjac_201, retro_cjac_224, retro_cjac_235, retro_cjac_238, retro_cjac_307, retro_cjac_334, retro_cjac_366, retro_cjac_68,
Cavia porcellus	ENSCPOG00000004707	7 retrocopies	retro_cpor_1059, retro_cpor_1390, retro_cpor_1524, retro_cpor_432, retro_cpor_695, retro_cpor_842, retro_cpor_853,
Dasypus novemcinctus	ENSDNOG00000024843	2 retrocopies	retro_dnov_1624, retro_dnov_775,
Dipodomys ordii	ENSDORG00000008132	9 retrocopies	retro_dord_238, retro_dord_283, retro_dord_43, retro_dord_589, retro_dord_678, retro_dord_685, retro_dord_719, retro_dord_765, retro_dord_774,
Equus caballus	ENSECAG00000006904	1 retrocopy	retro_ecab_916,
Equus caballus	ENSECAG00000016948	1 retrocopy	retro_ecab_266,
Erinaceus europaeus	ENSEEUG00000013796	1 retrocopy	retro_eeur_2,
Felis catus	ENSFCAG00000003617	4 retrocopies	retro_fcat_1085, retro_fcat_1953, retro_fcat_592, retro_fcat_830,
Felis catus	ENSFCAG00000030424	5 retrocopies	retro_fcat_1251, retro_fcat_1532, retro_fcat_1533, retro_fcat_2011, retro_fcat_674,
Homo sapiens	ENSG00000132475	11 retrocopies	retro_hsap_1212, retro_hsap_1552, retro_hsap_2180, retro_hsap_24, retro_hsap_2971, retro_hsap_3231, retro_hsap_3294, retro_hsap_3299, retro_hsap_389, retro_hsap_4236, retro_hsap_911,
Homo sapiens	ENSG00000163041	5 retrocopies	retro_hsap_2825, retro_hsap_2889, retro_hsap_3102, retro_hsap_3214, retro_hsap_4800,
Gorilla gorilla	ENSGGOG00000022526	11 retrocopies	retro_ggor_1179, retro_ggor_1809, retro_ggor_1837, retro_ggor_1919, retro_ggor_2003, retro_ggor_2837, retro_ggor_2956, retro_ggor_3082, retro_ggor_393, retro_ggor_736, retro_ggor_944,
Gorilla gorilla	ENSGGOG00000022928	7 retrocopies	retro_ggor_1964, retro_ggor_2181, retro_ggor_2198, retro_ggor_2357, retro_ggor_2805, retro_ggor_2905, retro_ggor_2987,
Gadus morhua	ENSGMOG00000014306	1 retrocopy	retro_gmor_9,
Latimeria chalumnae	ENSLACG00000004118	1 retrocopy	retro_lcha_104,
Loxodonta africana	ENSLAFG00000008083	3 retrocopies	retro_lafr_837, retro_lafr_959, retro_lafr_99,
Loxodonta africana	ENSLAFG00000021624	4 retrocopies	retro_lafr_172, retro_lafr_410, retro_lafr_546, retro_lafr_832,
Macropus eugenii	ENSMEUG00000004090	5 retrocopies	retro_meug_1041, retro_meug_1065, retro_meug_1819, retro_meug_281, retro_meug_573,
Microcebus murinus	ENSMICG00000002139	2 retrocopies	retro_mmur_36, retro_mmur_371,
Microcebus murinus	ENSMICG00000010469	6 retrocopies	retro_mmur_1185, retro_mmur_1243, retro_mmur_1249, retro_mmur_1543, retro_mmur_827, retro_mmur_83,
Myotis lucifugus	ENSMLUG00000015447	10 retrocopies	retro_mluc_146, retro_mluc_1571, retro_mluc_2286, retro_mluc_2344, retro_mluc_2364, retro_mluc_246, retro_mluc_2468, retro_mluc_2500, retro_mluc_392, retro_mluc_613,
Macaca mulatta	ENSMMUG00000031483	9 retrocopies	retro_mmul_108, retro_mmul_147, retro_mmul_201, retro_mmul_213, retro_mmul_215, retro_mmul_286, retro_mmul_337, retro_mmul_346, retro_mmul_7,
Monodelphis domestica	ENSMODG00000005983	3 retrocopies	retro_mdom_1037, retro_mdom_1132, retro_mdom_175,
Mustela putorius furo	ENSMPUG00000004555	4 retrocopies	retro_mputfur_389, retro_mputfur_82, retro_mputfur_99, retro_mputfur_990,
Mustela putorius furo	ENSMPUG00000013811	3 retrocopies	retro_mputfur_1159, retro_mputfur_787, retro_mputfur_881,
Mus musculus	ENSMUSG00000016559	18 retrocopies	retro_mmus_1058, retro_mmus_1188, retro_mmus_1269, retro_mmus_1535, retro_mmus_1635, retro_mmus_2021, retro_mmus_2083, retro_mmus_2377, retro_mmus_2771, retro_mmus_2867, retro_mmus_2972, retro_mmus_3002, retro_mmus_3144, retro_mmus_3477, retro_mmus_3667, retro_mmus_896, retro_mmus_961, retro_mmus_962,
Mus musculus	ENSMUSG00000060743	19 retrocopies	retro_mmus_1053, retro_mmus_1116, retro_mmus_1139, retro_mmus_1151, retro_mmus_1254, retro_mmus_2285, retro_mmus_2614, retro_mmus_2934, retro_mmus_3009, retro_mmus_3213, retro_mmus_3425, retro_mmus_395, retro_mmus_498, retro_mmus_808, retro_mmus_884, retro_mmus_885, retro_mmus_886, retro_mmus_959, retro_mmus_960,
Nomascus leucogenys	ENSNLEG00000001577	2 retrocopies	retro_nleu_25, retro_nleu_35,
Oryctolagus cuniculus	ENSOCUG00000024644	2 retrocopies	retro_ocun_185, retro_ocun_217,
Otolemur garnettii	ENSOGAG00000024312	11 retrocopies	retro_ogar_1086, retro_ogar_1790, retro_ogar_1863, retro_ogar_2364, retro_ogar_2463, retro_ogar_2581, retro_ogar_2746, retro_ogar_3415, retro_ogar_478, retro_ogar_842, retro_ogar_955,
Otolemur garnettii	ENSOGAG00000025933	14 retrocopies	retro_ogar_1285, retro_ogar_1364, retro_ogar_1449, retro_ogar_1575, retro_ogar_1576, retro_ogar_2200, retro_ogar_2316, retro_ogar_2449, retro_ogar_2634, retro_ogar_3235, retro_ogar_42, retro_ogar_733, retro_ogar_937, retro_ogar_952,
Oreochromis niloticus	ENSONIG00000015805	7 retrocopies	retro_onil_45, retro_onil_47, retro_onil_51, retro_onil_54, retro_onil_61, retro_onil_65, retro_onil_69,
Oreochromis niloticus	ENSONIG00000019975	5 retrocopies	retro_onil_41, retro_onil_46, retro_onil_56, retro_onil_60, retro_onil_63,
Ochotona princeps	ENSOPRG00000015952	2 retrocopies	retro_opri_1180, retro_opri_937,
Procavia capensis	ENSPCAG00000004484	2 retrocopies	retro_pcap_171, retro_pcap_95,
Pongo abelii	ENSPPYG00000000168	14 retrocopies	retro_pabe_1285, retro_pabe_2151, retro_pabe_2204, retro_pabe_2252, retro_pabe_2391, retro_pabe_2679, retro_pabe_2722, retro_pabe_2805, retro_pabe_2938, retro_pabe_3078, retro_pabe_323, retro_pabe_3420, retro_pabe_3637, retro_pabe_3697,
Pongo abelii	ENSPPYG00000008636	1 retrocopy	retro_pabe_2662 ,
Pan troglodytes	ENSPTRG00000002045	20 retrocopies	retro_ptro_1045, retro_ptro_1704, retro_ptro_1770, retro_ptro_1867, retro_ptro_1954, retro_ptro_2098, retro_ptro_2183, retro_ptro_2228, retro_ptro_2229, retro_ptro_2230, retro_ptro_2232, retro_ptro_2233, retro_ptro_2363, retro_ptro_279, retro_ptro_2834, retro_ptro_2936, retro_ptro_2978, retro_ptro_300, retro_ptro_3111, retro_ptro_3164,
Pan troglodytes	ENSPTRG00000009655	12 retrocopies	retro_ptro_1742, retro_ptro_1915, retro_ptro_2009, retro_ptro_2227, retro_ptro_2231, retro_ptro_2234, retro_ptro_2238, retro_ptro_2640, retro_ptro_2879, retro_ptro_631, retro_ptro_695, retro_ptro_830,
Pteropus vampyrus	ENSPVAG00000008459	2 retrocopies	retro_pvam_218, retro_pvam_52,
Rattus norvegicus	ENSRNOG00000003220	4 retrocopies	retro_rnor_121, retro_rnor_191, retro_rnor_336, retro_rnor_44,
Sarcophilus harrisii	ENSSHAG00000005807	1 retrocopy	retro_shar_565,
Sus scrofa	ENSSSCG00000023971	2 retrocopies	retro_sscr_31, retro_sscr_712,
Ictidomys tridecemlineatus	ENSSTOG00000024226	8 retrocopies	retro_itri_315, retro_itri_449, retro_itri_465, retro_itri_505, retro_itri_649, retro_itri_695, retro_itri_764, retro_itri_771,
Tupaia belangeri	ENSTBEG00000006177	13 retrocopies	retro_tbel_110, retro_tbel_1274, retro_tbel_15, retro_tbel_170, retro_tbel_2335, retro_tbel_3341, retro_tbel_3342, retro_tbel_3820, retro_tbel_391, retro_tbel_487, retro_tbel_592, retro_tbel_783, retro_tbel_978,
Tupaia belangeri	ENSTBEG00000016171	7 retrocopies	retro_tbel_3459, retro_tbel_3605, retro_tbel_3824, retro_tbel_3856, retro_tbel_4243, retro_tbel_4350, retro_tbel_674,
Tursiops truncatus	ENSTTRG00000015889	7 retrocopies	retro_ttru_1094, retro_ttru_1306, retro_ttru_18, retro_ttru_451, retro_ttru_738, retro_ttru_814, retro_ttru_92,
Vicugna pacos	ENSVPAG00000011531	5 retrocopies	retro_vpac_107, retro_vpac_637, retro_vpac_646, retro_vpac_76, retro_vpac_96,