RetrogeneDB ID: retro_nleu_1712

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397306.1:5272008..5272621(+)
• Located in intron of: ENSNLEG00000005533

Retrocopy information

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

Parental gene information

• Parental gene symbol: GAPDH
• Ensembl ID: ENSNLEG00000003825
• Aliases: None
• Description: Glyceraldehyde-3-phosphate dehydrogenase [Source:UniProtKB/TrEMBL;Acc:G1QVR0]

Sequence

>retro_nleu_1712
TTGATGGGCATGAACCATGAGAAGTACGAAAGCAACCCCACAATCATCAGCATTGCCTCCTGCACCACCAACTGCTTAGC
ATTCTCTGACCAAGATCATCCATGACAGCTCTGGCATCATGGAGGGACTCATGACCACAGTCCCTGCCATCACTGCCACC
CAGGAGACCTATGGATGGCTCTTCTGGGAAACTGTGACGTCATGGTTGTGGGGCTCTCCAAAACATTATTCCTGCATCTA
CTGGAACTTCCATGGCTGTGGGCAAGGACATCCTCGAGCTGAATGGGGAGATCATTGGCATGGCCTTCCTCATACCTACC
ACCAGTGTGTCAATTGTGGACCTGACCTGCTGTCTGGAGTAACCTGCCAAATATGATGACTTCAAGAAGATGGTGAAGCA
GGCATCGGAAGGCCCTTCGGGGACACACTGGGCTACACTGAACACCAAGTTGTCCCCTGTGACTTTAACGATGACACTCC
CTCTTCCACTTTTAATTCTGGGGCTAGCATTGACCTCAGCAACCGTTTTGTCAAGTTAATTTCCTGGTATGACAATTAGT
TTTGCTACAGCAACGGGGTGGTGGACCTCATGGTCCACATGGCCTCCAAGGAA

Alignment

ORF - retro_nleu_1712 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.53 %
• Parental protein coverage: 60.9 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VMGVNHEKYDNSLKIVSNASCTTNCLA-PLAKVIHDNFGIVEGLMTTVHAITATQKT-VDGPSGKLWRDG
          .MG.NHEKY.....I.S.ASCTTNCLA..L.K.IHD..GI.EGLMTTV.AITATQ.T..DG.SGKL.R.G
Retrocopy LMGMNHEKYESNPTIISIASCTTNCLA>SLTKIIHDSSGIMEGLMTTVPAITATQET>MDGSSGKL*RHG

Parental  RGALQNIIPASTGAAKAVGKVIPELNGKLTGMAFRVPTANVSVVDLTCRLEKPAKYDDIKKVVKQASEG-
          .GALQNIIPASTG...AVGK.I.ELNG...GMAF..PT..VS.VDLTC.LE.PAKYDD.KK.VKQASEG.
Retrocopy CGALQNIIPASTGTSMAVGKDILELNGEIIGMAFLIPTTSVSIVDLTCCLE*PAKYDDFKKMVKQASEG<

Parental  PLKGILGYTEHQVVSSDFNSDTHSSTFDAGAGIALNDHFVKLISWYDNEFGYSNRVVDLMSHMASKE
          P....LGYTEHQVV..DFN.DT.SSTF..GA.I.L...FVKLISWYDN.F.YSN.VVDLM.HMASKE
Retrocopy PFGDTLGYTEHQVVPCDFNDDTPSSTFNSGASIDLSNRFVKLISWYDN*FCYSNGVVDLMVHMASKE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_1712 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 367 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,
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,
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,
Nomascus leucogenys	ENSNLEG00000003825	44 retrocopies	retro_nleu_1017, retro_nleu_1146, retro_nleu_1302, retro_nleu_1516, retro_nleu_1522, retro_nleu_155, retro_nleu_1562, retro_nleu_1583, retro_nleu_1605, retro_nleu_164, retro_nleu_1641, retro_nleu_1711, retro_nleu_1712 , retro_nleu_1760, retro_nleu_1877, retro_nleu_1879, retro_nleu_1880, retro_nleu_1881, retro_nleu_1882, retro_nleu_1883, retro_nleu_1884, retro_nleu_1916, retro_nleu_1951, retro_nleu_2113, retro_nleu_2181, retro_nleu_2195, retro_nleu_223, retro_nleu_2272, retro_nleu_2427, retro_nleu_2459, retro_nleu_2673, retro_nleu_2685, retro_nleu_2744, retro_nleu_2981, retro_nleu_346, retro_nleu_374, retro_nleu_434, retro_nleu_465, retro_nleu_519, retro_nleu_596, retro_nleu_630, retro_nleu_784, retro_nleu_808, retro_nleu_999,
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,