RetrogeneDB ID: retro_pabe_1406

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 16_random:2969502..2969912(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACP1
• Ensembl ID: ENSPPYG00000012694
• Aliases: None
• Description: Low molecular weight phosphotyrosine protein phosphatase [Source:UniProtKB/Swiss-Prot;Acc:Q5REM7]

Sequence

>retro_pabe_1406
GAACAGGGGCCCGTAGTGGGGCTGTTTGTGTGTTCCGGGTGACATCTGGCAATCCCCCACTGCAGAGGCGATTTTAAGAA
AATCTGCAGATAATAAAAACGTTTCAGGTAATTGGATCGTTGACAGTGGAGTGGCCTTGGACTAAGAATGTGGGCTAGCC
CTTAAAAGCAAGAGCTCTAAGCTGCCTAAGAAACTGTGGCATTAACCAGGCCATCAAATAAGTCAGGATTATCAAAGACG
TCTTCCTTGCTTGTGATTATATATAATACATGGATGAAAGCAAACTGGGAGACTGGAACAGAAAAGGTAATTAAGTTAAA
AAATGCAAAGCTAAAATTGAACTCCTTGGGAGGTAGGAGCCACAAATGTAACTTATAACTGAAAAGCCCTATTAAGGTAA
TGATTCAGAT

Alignment

ORF - retro_pabe_1406 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.35 %
• Parental protein coverage: 86.62 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EQSTKSVLFVCLG-NICRSPIAEAVFRKLVTDQNISENWVIDSGAVSD-WNVGRSPDPRAVSCLRNHGIH
          EQ.....LFVC.G..I..SP.AEA..RK.....N.S.NW..DSG...D..NVG.....RA.SCLRN.GI.
Retrocopy EQGPVVGLFVCSG>DIWQSPTAEAILRKSADNKNVSGNWIVDSGVALD>KNVG*PLKARALSCLRNCGIN

Parental  TAHKARQITREDFATFDYILCMDESNLRDLNRKSNQVKTCKAKIELLGSYDPQKQLIIEDPYYGNDSD
          .A.K...I....F...DYI..MDES.L.D.NRK.N.VK.CKAKIELLG...PQ..LI.E.PY.GNDSD
Retrocopy QAIK*VRIIKDVFLACDYI*YMDESKLGDWNRKGN*VKKCKAKIELLGR*EPQM*LITEKPY*GNDSD

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	36.49 RPM
SRP007412_cerebellum	0.00 RPM	27.48 RPM
SRP007412_heart	0.00 RPM	14.09 RPM
SRP007412_kidney	0.00 RPM	29.47 RPM
SRP007412_liver	0.00 RPM	23.32 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1406 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1406 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1406 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 25 parental genes, and 250 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009554	2 retrocopies	retro_amel_705, retro_amel_761,
Bos taurus	ENSBTAG00000020498	4 retrocopies	retro_btau_1085, retro_btau_1099, retro_btau_1695, retro_btau_421,
Choloepus hoffmanni	ENSCHOG00000003891	94 retrocopies	retro_chof_1010, retro_chof_1053, retro_chof_1073, retro_chof_1099, retro_chof_1100, retro_chof_1144, retro_chof_119, retro_chof_1190, retro_chof_121, retro_chof_1259, retro_chof_1265, retro_chof_1275, retro_chof_1330, retro_chof_1351, retro_chof_1359, retro_chof_1389, retro_chof_1390, retro_chof_1412, retro_chof_142, retro_chof_1444, retro_chof_1447, retro_chof_1508, retro_chof_1567, retro_chof_1570, retro_chof_1593, retro_chof_1632, retro_chof_1633, retro_chof_1658, retro_chof_1684, retro_chof_169, retro_chof_1698, retro_chof_17, retro_chof_1716, retro_chof_174, retro_chof_1799, retro_chof_1802, retro_chof_1815, retro_chof_1833, retro_chof_1838, retro_chof_1864, retro_chof_1941, retro_chof_1956, retro_chof_1993, retro_chof_2012, retro_chof_2041, retro_chof_2044, retro_chof_2091, retro_chof_2165, retro_chof_2192, retro_chof_2208, retro_chof_2228, retro_chof_2259, retro_chof_2344, retro_chof_2378, retro_chof_2384, retro_chof_2443, retro_chof_245, retro_chof_2478, retro_chof_2512, retro_chof_2532, retro_chof_2542, retro_chof_2551, retro_chof_261, retro_chof_262, retro_chof_2622, retro_chof_2636, retro_chof_2643, retro_chof_2653, retro_chof_2654, retro_chof_2678, retro_chof_2701, retro_chof_2705, retro_chof_2707, retro_chof_319, retro_chof_377, retro_chof_460, retro_chof_598, retro_chof_603, retro_chof_649, retro_chof_650, retro_chof_66, retro_chof_727, retro_chof_80, retro_chof_803, retro_chof_83, retro_chof_842, retro_chof_934, retro_chof_939, retro_chof_958, retro_chof_962, retro_chof_986, retro_chof_991, retro_chof_994, retro_chof_999,
Callithrix jacchus	ENSCJAG00000011663	5 retrocopies	retro_cjac_1226, retro_cjac_2082, retro_cjac_2162, retro_cjac_405, retro_cjac_609,
Dasypus novemcinctus	ENSDNOG00000017382	32 retrocopies	retro_dnov_1166, retro_dnov_1213, retro_dnov_1234, retro_dnov_1255, retro_dnov_1302, retro_dnov_136, retro_dnov_1373, retro_dnov_1393, retro_dnov_1499, retro_dnov_1553, retro_dnov_1601, retro_dnov_1685, retro_dnov_1709, retro_dnov_1732, retro_dnov_1895, retro_dnov_1937, retro_dnov_1950, retro_dnov_2320, retro_dnov_2349, retro_dnov_2509, retro_dnov_2582, retro_dnov_297, retro_dnov_312, retro_dnov_355, retro_dnov_474, retro_dnov_501, retro_dnov_535, retro_dnov_650, retro_dnov_768, retro_dnov_81, retro_dnov_830, retro_dnov_987,
Equus caballus	ENSECAG00000010079	1 retrocopy	retro_ecab_135,
Echinops telfairi	ENSETEG00000013764	18 retrocopies	retro_etel_100, retro_etel_1034, retro_etel_110, retro_etel_1204, retro_etel_1655, retro_etel_1718, retro_etel_1824, retro_etel_1861, retro_etel_1940, retro_etel_2133, retro_etel_230, retro_etel_343, retro_etel_398, retro_etel_420, retro_etel_679, retro_etel_797, retro_etel_82, retro_etel_958,
Felis catus	ENSFCAG00000026717	1 retrocopy	retro_fcat_1472,
Homo sapiens	ENSG00000143727	5 retrocopies	retro_hsap_1627, retro_hsap_1666, retro_hsap_1667, retro_hsap_529, retro_hsap_603,
Gorilla gorilla	ENSGGOG00000015577	5 retrocopies	retro_ggor_1228, retro_ggor_1256, retro_ggor_485, retro_ggor_532, retro_ggor_72,
Loxodonta africana	ENSLAFG00000002966	4 retrocopies	retro_lafr_1053, retro_lafr_1227, retro_lafr_336, retro_lafr_916,
Macropus eugenii	ENSMEUG00000010733	3 retrocopies	retro_meug_1736, retro_meug_706, retro_meug_806,
Myotis lucifugus	ENSMLUG00000017707	4 retrocopies	retro_mluc_133, retro_mluc_1970, retro_mluc_548, retro_mluc_686,
Macaca mulatta	ENSMMUG00000017097	2 retrocopies	retro_mmul_1575, retro_mmul_2447,
Monodelphis domestica	ENSMODG00000025764	3 retrocopies	retro_mdom_236, retro_mdom_292, retro_mdom_364,
Mustela putorius furo	ENSMPUG00000012787	2 retrocopies	retro_mputfur_1420, retro_mputfur_1619,
Mus musculus	ENSMUSG00000044573	11 retrocopies	retro_mmus_1041, retro_mmus_1103, retro_mmus_1230, retro_mmus_1261, retro_mmus_2133, retro_mmus_2143, retro_mmus_2155, retro_mmus_2969, retro_mmus_3690, retro_mmus_455, retro_mmus_717,
Nomascus leucogenys	ENSNLEG00000008359	6 retrocopies	retro_nleu_1784, retro_nleu_2230, retro_nleu_2683, retro_nleu_2792, retro_nleu_2821, retro_nleu_2915,
Oryctolagus cuniculus	ENSOCUG00000012876	11 retrocopies	retro_ocun_1192, retro_ocun_1302, retro_ocun_1328, retro_ocun_1347, retro_ocun_1358, retro_ocun_1501, retro_ocun_1610, retro_ocun_1743, retro_ocun_1744, retro_ocun_1859, retro_ocun_1860,
Otolemur garnettii	ENSOGAG00000000301	5 retrocopies	retro_ogar_1665, retro_ogar_2357, retro_ogar_3182, retro_ogar_426, retro_ogar_471,
Pongo abelii	ENSPPYG00000012694	6 retrocopies	retro_pabe_1374, retro_pabe_1406 , retro_pabe_1748, retro_pabe_220, retro_pabe_543, retro_pabe_588,
Pan troglodytes	ENSPTRG00000011605	5 retrocopies	retro_ptro_1129, retro_ptro_2959, retro_ptro_3050, retro_ptro_3080, retro_ptro_446,
Rattus norvegicus	ENSRNOG00000005260	11 retrocopies	retro_rnor_1201, retro_rnor_1302, retro_rnor_1303, retro_rnor_1476, retro_rnor_1802, retro_rnor_2079, retro_rnor_2382, retro_rnor_2569, retro_rnor_2772, retro_rnor_449, retro_rnor_457,
Ictidomys tridecemlineatus	ENSSTOG00000002520	3 retrocopies	retro_itri_1010, retro_itri_1581, retro_itri_821,
Tarsius syrichta	ENSTSYG00000004864	7 retrocopies	retro_tsyr_1013, retro_tsyr_1214, retro_tsyr_1477, retro_tsyr_1482, retro_tsyr_209, retro_tsyr_444, retro_tsyr_523,