RetrogeneDB ID: retro_ptro_1513

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 22:39382470..39383393(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GAPDH
• Ensembl ID: ENSPTRG00000004577
• Aliases: GAPDH, GAPD
• Description: glyceraldehyde-3-phosphate dehydrogenase [Source:HGNC Symbol;Acc:4141]

Sequence

>retro_ptro_1513
GGAAAAGCGAAGGCTGGAGTAAACAGATTTGGACATATTGGGTGCCTGGTCACCAGGGCTGCTTTTAACTCTAGCACAAT
GGATATTGTTGCCATCAATGACCCCTTCATTGACCTCAGCTAAATGGTCTACATGTTCGAGTATGATTCCACCCATGGCA
AGTTCCACAGCACCATCAGGCTGAAAACGCGAAGCTTGTCACCAATGGAAATCCCATCACCATCTTCCAGGAATGAGATC
CCACCAAAATCAAAGGAGGTGATGCTGGTGCTGATTATGTTATGGAGCCCACCAGTGTCTTCACTACCATGGAGAAGGCT
GGGACTTACTTAGATGGGGGAGCCAAAAGAGTCACCATCTCTGCCCCTTCTGATGCCCCCATGTTTGTGATGGGTGTGAA
TCATGAGAAGTATGGAGACAGCCTCAAGATTATCAGCAATGCCTCCTGCACCACCAGTTGCTTAACCCCCCTGGCCAAGG
TCATCCATGACAACTTTGGCACCATGGAAGGACTCATGACCACAGTTCATGCCTTCAGTGCCACCCAGAAGACTACTGAT
GGTACCTCTGGGAAATTGTAGTGTGATGGCTGCAGGGCTCTCTAGAACATCATTCCTGCCAAGCCTGTGGGCAAAGTCAT
CCCCGAGCTGAATGGGAAGCTCACTGGCATGGCCTTCCATGTCCCCACCACCAACATGTTGGTCATGGACCTGACCTGCC
ATCTGGAGAAACCTGCCAAATACAGTGACATCAAGAGGATGGTGAAGCAGGCATTGAGGGAGATCCTCAAGGGCATCCTG
GGCTGTACTGAGCACAAGGTCGTCTCCTCTGACTTTGACAGTGACACCCATTCTTCCACCTTCAATGCTGGGGCTGGCAT
TGCCCTCGACAATGACTTTGTCAAGCTCATTTCCTGGTATGAC

Alignment

ORF - retro_ptro_1513 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.97 %
• Parental protein coverage: 93.73 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GKVKVGVNGFGRIGRLVTRAAFNSGKVDIVAINDPFIDLNYMVYMFQYDSTHGKFHGTVK-AENGKLVIN
          GK.K.GVN.FG.IG.LVTRAAFNS...DIVAINDPFIDL..MVYMF.YDSTHGKFH.T...AEN.KLV.N
Retrocopy GKAKAGVNRFGHIGCLVTRAAFNSSTMDIVAINDPFIDLS*MVYMFEYDSTHGKFHSTIR<AENAKLVTN

Parental  GNPITIFQERDPSKIKWGDAGAEYVVESTGVFTTMEKAGAHLQGGAKRVIISAPSADAPMFVMGVNHEKY
          GNPITIFQE.DP.KIK.GDAGA.YV.E.T.VFTTMEKAG..L.GGAKRV.ISAPS.DAPMFVMGVNHEKY
Retrocopy GNPITIFQE*DPTKIKGGDAGADYVMEPTSVFTTMEKAGTYLDGGAKRVTISAPS-DAPMFVMGVNHEKY

Parental  DNSLKIISNASCTTNCLAPLAKVIHDNFGIVEGLMTTVHAITATQKTVDGPSGKLWRDGRGALQNIIPAS
          ..SLKIISNASCTT.CL.PLAKVIHDNFG..EGLMTTVHA..ATQKT.DG.SGKL..DG..AL.NIIPA.
Retrocopy GDSLKIISNASCTTSCLTPLAKVIHDNFGTMEGLMTTVHAFSATQKTTDGTSGKL*CDGCRAL*NIIPAK

Parental  TGAAKAVGKVIPELNGKLTGMAFRVPTANVSVVDLTCRLEKPAKYDDIKKVVKQASEGPLKGILGYTEHQ
          ....K........L.G....MAF.VPT.N..V.DLTC.LEKPAKY.DIK..VKQA....LKGILG.TEH.
Retrocopy P-VGKVIPELNGKLTG----MAFHVPTTNMLVMDLTCHLEKPAKYSDIKRMVKQALREILKGILGCTEHK

Parental  VVSSDFNSDTHSSTFDAGAGIALNDHFVKLISWYD
          VVSSDF.SDTHSSTF.AGAGIAL...FVKLISWYD
Retrocopy VVSSDFDSDTHSSTFNAGAGIALDNDFVKLISWYD

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	0.16 RPM	2168.65 RPM
SRP007412_cerebellum	0.07 RPM	1166.58 RPM
SRP007412_heart	0.00 RPM	1898.41 RPM
SRP007412_kidney	0.03 RPM	1211.09 RPM
SRP007412_liver	0.00 RPM	1233.46 RPM
SRP007412_testis	0.00 RPM	203.39 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1513 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1513 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1513 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2589
Macaca mulatta	retro_mmul_650

---

Parental genes homology:

Parental genes homology involve 21 parental genes, and 510 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006675	5 retrocopies	retro_amel_1189, retro_amel_146, retro_amel_1792, retro_amel_1826, retro_amel_549,
Ailuropoda melanoleuca	ENSAMEG00000014329	35 retrocopies	retro_amel_1050, retro_amel_1082, retro_amel_1134, retro_amel_1174, retro_amel_1229, retro_amel_1235, retro_amel_1253, retro_amel_1308, retro_amel_1538, retro_amel_1550, retro_amel_1598, retro_amel_1605, retro_amel_1614, retro_amel_1658, retro_amel_1776, retro_amel_1801, retro_amel_1802, retro_amel_187, retro_amel_1900, retro_amel_1904, retro_amel_268, retro_amel_294, retro_amel_387, retro_amel_443, retro_amel_471, retro_amel_601, retro_amel_605, retro_amel_641, retro_amel_738, retro_amel_750, retro_amel_762, retro_amel_852, retro_amel_899, retro_amel_961, retro_amel_992,
Canis familiaris	ENSCAFG00000015077	4 retrocopies	retro_cfam_122, retro_cfam_214, retro_cfam_3, retro_cfam_7,
Cavia porcellus	ENSCPOG00000026350	1 retrocopy	retro_cpor_125,
Erinaceus europaeus	ENSEEUG00000011444	3 retrocopies	retro_eeur_427, retro_eeur_569, retro_eeur_677,
Homo sapiens	ENSG00000111640	42 retrocopies	retro_hsap_1014, retro_hsap_1183, retro_hsap_1188, retro_hsap_1489, retro_hsap_1490, retro_hsap_1582, retro_hsap_1672, retro_hsap_188, retro_hsap_2006, retro_hsap_2094, retro_hsap_2225, retro_hsap_2414, retro_hsap_2589, retro_hsap_2711, retro_hsap_2733, retro_hsap_2852, retro_hsap_2956, retro_hsap_307, retro_hsap_3096, retro_hsap_3268, retro_hsap_3398, retro_hsap_3491, retro_hsap_3543, retro_hsap_3599, retro_hsap_3618, retro_hsap_364, retro_hsap_3665, retro_hsap_3697, retro_hsap_4093, retro_hsap_421, retro_hsap_439, retro_hsap_441, retro_hsap_442, retro_hsap_443, retro_hsap_444, retro_hsap_445, retro_hsap_4806, retro_hsap_4820, retro_hsap_489, retro_hsap_4927, retro_hsap_710, retro_hsap_954,
Gorilla gorilla	ENSGGOG00000009553	30 retrocopies	retro_ggor_1142, retro_ggor_1143, retro_ggor_1260, retro_ggor_1450, retro_ggor_1621, retro_ggor_1659, retro_ggor_1889, retro_ggor_1902, retro_ggor_1982, retro_ggor_2126, retro_ggor_2224, retro_ggor_2443, retro_ggor_2477, retro_ggor_2500, retro_ggor_2991, retro_ggor_3004, retro_ggor_341, retro_ggor_376, retro_ggor_412, retro_ggor_424, retro_ggor_427, retro_ggor_428, retro_ggor_429, retro_ggor_430, retro_ggor_431, retro_ggor_459, retro_ggor_804, retro_ggor_921, retro_ggor_922, retro_ggor_926,
Loxodonta africana	ENSLAFG00000002780	3 retrocopies	retro_lafr_421, retro_lafr_46, retro_lafr_954,
Macropus eugenii	ENSMEUG00000015273	67 retrocopies	retro_meug_1057, retro_meug_1066, retro_meug_1080, retro_meug_1086, retro_meug_1197, retro_meug_1206, retro_meug_1249, retro_meug_1286, retro_meug_1310, retro_meug_1319, retro_meug_1352, retro_meug_1369, retro_meug_1377, retro_meug_1390, retro_meug_1423, retro_meug_1429, retro_meug_1542, retro_meug_1595, retro_meug_1646, retro_meug_165, retro_meug_1686, retro_meug_1759, retro_meug_1776, retro_meug_180, retro_meug_185, retro_meug_1870, retro_meug_1884, retro_meug_1889, retro_meug_2039, retro_meug_2046, retro_meug_2047, retro_meug_2085, retro_meug_2088, retro_meug_2113, retro_meug_2141, retro_meug_2178, retro_meug_239, retro_meug_374, retro_meug_382, retro_meug_383, retro_meug_393, retro_meug_416, retro_meug_421, retro_meug_450, retro_meug_453, retro_meug_460, retro_meug_50, retro_meug_595, retro_meug_602, retro_meug_630, retro_meug_643, retro_meug_661, retro_meug_678, retro_meug_680, retro_meug_70, retro_meug_720, retro_meug_731, retro_meug_739, retro_meug_758, retro_meug_761, retro_meug_777, retro_meug_79, retro_meug_834, retro_meug_844, retro_meug_866, retro_meug_879, retro_meug_890,
Microcebus murinus	ENSMICG00000006546	16 retrocopies	retro_mmur_1049, retro_mmur_1064, retro_mmur_1084, retro_mmur_1255, retro_mmur_1431, retro_mmur_1446, retro_mmur_145, retro_mmur_1463, retro_mmur_1553, retro_mmur_1567, retro_mmur_329, retro_mmur_429, retro_mmur_464, retro_mmur_670, retro_mmur_780, retro_mmur_873,
Macaca mulatta	ENSMMUG00000018679	33 retrocopies	retro_mmul_1016, retro_mmul_1469, retro_mmul_1529, retro_mmul_1535, retro_mmul_1713, retro_mmul_1776, retro_mmul_1812, retro_mmul_1833, retro_mmul_1839, retro_mmul_1893, retro_mmul_2056, retro_mmul_2116, retro_mmul_2133, retro_mmul_2134, retro_mmul_2220, retro_mmul_2252, retro_mmul_2253, retro_mmul_2413, retro_mmul_2430, retro_mmul_2461, retro_mmul_2562, retro_mmul_2572, retro_mmul_480, retro_mmul_494, retro_mmul_513, retro_mmul_523, retro_mmul_524, retro_mmul_525, retro_mmul_526, retro_mmul_605, retro_mmul_650, retro_mmul_776, retro_mmul_784,
Monodelphis domestica	ENSMODG00000018066	41 retrocopies	retro_mdom_1060, retro_mdom_1089, retro_mdom_1104, retro_mdom_1137, retro_mdom_1161, retro_mdom_1184, retro_mdom_1233, retro_mdom_1241, retro_mdom_1317, retro_mdom_1358, retro_mdom_1384, retro_mdom_142, retro_mdom_1494, retro_mdom_1544, retro_mdom_1610, retro_mdom_1631, retro_mdom_1661, retro_mdom_1691, retro_mdom_1698, retro_mdom_1743, retro_mdom_1810, retro_mdom_1908, retro_mdom_2022, retro_mdom_275, retro_mdom_310, retro_mdom_354, retro_mdom_382, retro_mdom_497, retro_mdom_531, retro_mdom_552, retro_mdom_584, retro_mdom_590, retro_mdom_591, retro_mdom_628, retro_mdom_678, retro_mdom_766, retro_mdom_816, retro_mdom_828, retro_mdom_832, retro_mdom_835, retro_mdom_863,
Mustela putorius furo	ENSMPUG00000016891	28 retrocopies	retro_mputfur_1027, retro_mputfur_105, retro_mputfur_1051, retro_mputfur_1091, retro_mputfur_1152, retro_mputfur_1197, retro_mputfur_1198, retro_mputfur_1229, retro_mputfur_1278, retro_mputfur_1422, retro_mputfur_1461, retro_mputfur_1483, retro_mputfur_1630, retro_mputfur_244, retro_mputfur_300, retro_mputfur_31, retro_mputfur_317, retro_mputfur_380, retro_mputfur_481, retro_mputfur_513, retro_mputfur_555, retro_mputfur_612, retro_mputfur_717, retro_mputfur_789, retro_mputfur_817, retro_mputfur_842, retro_mputfur_88, retro_mputfur_925,
Mus musculus	ENSMUSG00000057666	109 retrocopies	retro_mmus_1029, retro_mmus_1082, retro_mmus_1136, retro_mmus_1193, retro_mmus_1249, retro_mmus_1319, retro_mmus_1328, retro_mmus_136, retro_mmus_1365, retro_mmus_1371, retro_mmus_1467, retro_mmus_1474, retro_mmus_1480, retro_mmus_1615, retro_mmus_1692, retro_mmus_1721, retro_mmus_1728, retro_mmus_1886, retro_mmus_1922, retro_mmus_1957, retro_mmus_1983, retro_mmus_1985, retro_mmus_2009, retro_mmus_2020, retro_mmus_2030, retro_mmus_2100, retro_mmus_211, retro_mmus_2119, retro_mmus_2122, retro_mmus_2148, retro_mmus_2158, retro_mmus_2175, retro_mmus_2206, retro_mmus_2216, retro_mmus_2248, retro_mmus_2298, retro_mmus_2370, retro_mmus_2371, retro_mmus_2389, retro_mmus_2463, retro_mmus_2477, retro_mmus_2481, retro_mmus_2512, retro_mmus_2556, retro_mmus_2587, retro_mmus_2623, retro_mmus_2626, retro_mmus_2647, retro_mmus_2681, retro_mmus_2755, retro_mmus_2761, retro_mmus_2764, retro_mmus_2848, retro_mmus_2872, retro_mmus_2911, retro_mmus_2912, retro_mmus_2913, retro_mmus_2914, retro_mmus_2915, retro_mmus_2920, retro_mmus_2932, retro_mmus_2943, retro_mmus_300, retro_mmus_3036, retro_mmus_3064, retro_mmus_3120, retro_mmus_3137, retro_mmus_3140, retro_mmus_3148, retro_mmus_3151, retro_mmus_3188, retro_mmus_3193, retro_mmus_3197, retro_mmus_3216, retro_mmus_3228, retro_mmus_3306, retro_mmus_3335, retro_mmus_3336, retro_mmus_3357, retro_mmus_3377, retro_mmus_3445, retro_mmus_3514, retro_mmus_3575, retro_mmus_3650, retro_mmus_3658, retro_mmus_3693, retro_mmus_3716, retro_mmus_3814, retro_mmus_416, retro_mmus_437, retro_mmus_48, retro_mmus_553, retro_mmus_608, retro_mmus_619, retro_mmus_628, retro_mmus_635, retro_mmus_698, retro_mmus_745, retro_mmus_765, retro_mmus_766, retro_mmus_787, retro_mmus_811, retro_mmus_893, retro_mmus_914, retro_mmus_921, retro_mmus_946, retro_mmus_952, retro_mmus_976, retro_mmus_996,
Pongo abelii	ENSPPYG00000004189	38 retrocopies	retro_pabe_1238, retro_pabe_1239, retro_pabe_1303, retro_pabe_1377, retro_pabe_1458, retro_pabe_1641, retro_pabe_1767, retro_pabe_1779, retro_pabe_1975, retro_pabe_2003, retro_pabe_2262, retro_pabe_2272, retro_pabe_2360, retro_pabe_2452, retro_pabe_2706, retro_pabe_2793, retro_pabe_284, retro_pabe_285, retro_pabe_286, retro_pabe_287, retro_pabe_2883, retro_pabe_2927, retro_pabe_2969, retro_pabe_298, retro_pabe_2981, retro_pabe_3007, retro_pabe_3038, retro_pabe_3154, retro_pabe_3355, retro_pabe_341, retro_pabe_373, retro_pabe_3735, retro_pabe_3748, retro_pabe_444, retro_pabe_542, retro_pabe_614, retro_pabe_785, retro_pabe_852,
Pan troglodytes	ENSPTRG00000004577	43 retrocopies	retro_ptro_1008, retro_ptro_1009, retro_ptro_1065, retro_ptro_1133, retro_ptro_1337, retro_ptro_1390, retro_ptro_1513 , retro_ptro_1539, retro_ptro_1573, retro_ptro_173, retro_ptro_1832, retro_ptro_1847, retro_ptro_186, retro_ptro_187, retro_ptro_188, retro_ptro_189, retro_ptro_190, retro_ptro_191, retro_ptro_1932, retro_ptro_2001, retro_ptro_2092, retro_ptro_2309, retro_ptro_2365, retro_ptro_2409, retro_ptro_2447, retro_ptro_2459, retro_ptro_248, retro_ptro_2487, retro_ptro_2506, retro_ptro_2777, retro_ptro_285, retro_ptro_2939, retro_ptro_2986, retro_ptro_3196, retro_ptro_3209, retro_ptro_322, retro_ptro_3310, retro_ptro_369, retro_ptro_507, retro_ptro_661, retro_ptro_748, retro_ptro_811, retro_ptro_815,
Pan troglodytes	ENSPTRG00000010848	1 retrocopy	retro_ptro_2211,
Rattus norvegicus	ENSRNOG00000018630	4 retrocopies	retro_rnor_107, retro_rnor_335, retro_rnor_407, retro_rnor_91,
Rattus norvegicus	ENSRNOG00000030638	2 retrocopies	retro_rnor_1571, retro_rnor_1777,
Sarcophilus harrisii	ENSSHAG00000014953	4 retrocopies	retro_shar_178, retro_shar_330, retro_shar_40, retro_shar_533,
Xenopus tropicalis	ENSXETG00000033975	1 retrocopy	retro_xtro_70,