RetrogeneDB ID: retro_hsap_3268

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 5:173940310..173941307(+)
• Located in intron of: ENSG00000249306

Retrocopy information

• Ensembl ID: ENSG00000213376
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GAPDH
• Ensembl ID: ENSG00000111640
• Aliases: GAPDH, G3PD, GAPD, HEL-S-162eP
• Description: glyceraldehyde-3-phosphate dehydrogenase [Source:HGNC Symbol;Acc:4141]

Sequence

>retro_hsap_3268
AAGGTGAAGGCTGGAGTCAATGGATTTGGTCGTATTGAACACCTGGTAACCAAGCCTGCTTTTAACTCTGGTAAAGTGGA
TATTGTCACCATCAATGACCCCTTCGTTGACCTCAACAACATGGTCTACATGTTCCAGTATGATTCCACCCATGGCAAAT
TCTGTGGCACCGTCAAGGCTGAGAACAGGAAGCTTGTCGCCAGTGGAAATCCCATCACCGTCTTCCAGGGCGAGATCCCT
CCAAAATCAAATGGGGTGATGCTGGTGCTCAGTACATTGCGGAGTCCACTTGTATCTTCACCACCATGGAGAAGGCTGGG
GCTGACTTGCAGGGAGGAGCCAAAAGGGTCATCATCTCTGCCCCCTCTGCTGATGCCCCCATGTTCGTGATGGATGTGAA
CCACGAGAAGTATGACAACAGCCTCAAGATCGTCAGCAATGCCTCCTGCATCACCAACTGCTTAGCGCCCCTGGCCAACG
TCATCCACAACTTTGGTATCGTGGAAGGACCCATGACCACAGTCCATGCTATCACTGCCACCCAGAAGATTGTGGATGGC
CCCTCCGGGAAACTGGCATAACGGCCGTGGAGCTCTCCAGAACATCATCCCTGCCTCTACTGGCACTGCCAAAGCTGTGG
GCAAGGTCATCCCTGAGCTGAACAGGAAGCTTACTGGCATGGGATTCTGTGTCCTCACTGCCAATGTGTTGGTCATGGAC
CTGACATGCCATCTGGAAAAACCTGCCAAATACAATGACATCAAGAAGGTAGTAAAGCAGGCATCCAACGCCCCCTCAAG
GGCATCCTGGGCTACACGAGCACCAGGTGGTCTCCTCTGACTTCAACAGCGACACCCACACCTACTCTTCCACCTTCAAT
GCTGGGGCTGGCACTGCCCTCGATGGCCACTTTGTCAAGCTCGTTTCCTGGTATGACAATGAATTTGGCTACAGCAACAG
GGTGGTGAACCTCAGGGCCCACATGGCCGCCAAGGAG

Alignment

ORF - retro_hsap_3268 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.19 %
• Parental protein coverage: 99.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KVKVGVNGFGRIGRLVTRAAFNSGKVDIVAINDPFIDLNYMVYMFQYDSTHGKFHGTVKAENGKLVINGN
          KVK.GVNGFGRI..LVT..AFNSGKVDIV.INDPF.DLN.MVYMFQYDSTHGKF.GTVKAEN.KLV..GN
Retrocopy KVKAGVNGFGRIEHLVTKPAFNSGKVDIVTINDPFVDLNNMVYMFQYDSTHGKFCGTVKAENRKLVASGN

Parental  PITIFQE-RDPSKIKWGDAGAEYVVESTGVFTTMEKAGAHLQGGAKRVIISAPSADAPMFVMGVNHEKYD
          PIT.FQ..RDPSKIKWGDAGA.Y..EST..FTTMEKAGA.LQGGAKRVIISAPSADAPMFVM.VNHEKYD
Retrocopy PITVFQG<RDPSKIKWGDAGAQYIAESTCIFTTMEKAGADLQGGAKRVIISAPSADAPMFVMDVNHEKYD

Parental  NSLKIISNASCTTNCLAPLAKVIHDNFGIVEGLMTTVHAITATQKTVDG-PSGKLWRDGRGALQNIIPAS
          NSLKI.SNASC.TNCLAPLA.VIH.NFGIVEG.MTTVHAITATQK.VDG.P.G..W..GRGALQNIIPAS
Retrocopy NSLKIVSNASCITNCLAPLANVIH-NFGIVEGPMTTVHAITATQKIVDG>PPGN-WHNGRGALQNIIPAS

Parental  TGAAKAVGKVIPELNGKLTGMAFRVPTANVSVVDLTCRLEKPAKYDDIKKVVKQAS-EGPLKGILGYT-E
          TG.AKAVGKVIPELN.KLTGM.F.V.TANV.V.DLTC.LEKPAKY.DIKKVVKQAS...PLKGILGYT.E
Retrocopy TGTAKAVGKVIPELNRKLTGMGFCVLTANVLVMDLTCHLEKPAKYNDIKKVVKQAS<QRPLKGILGYT<E

Parental  HQVVSSDFNSDTH--SSTFDAGAGIALNDHFVKLISWYDNEFGYSNRVVDLMAHMASKE
          HQVVSSDFNSDTH..SSTF.AGAG.AL..HFVKL.SWYDNEFGYSNRVV.L.AHMA.KE
Retrocopy HQVVSSDFNSDTHTYSSTFNAGAGTALDGHFVKLVSWYDNEFGYSNRVVNLRAHMAAKE

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
bodymap2_adipose	0.00 RPM	800.01 RPM
bodymap2_adrenal	0.00 RPM	711.44 RPM
bodymap2_brain	0.12 RPM	829.45 RPM
bodymap2_breast	0.00 RPM	897.25 RPM
bodymap2_colon	0.00 RPM	863.73 RPM
bodymap2_heart	0.00 RPM	1155.35 RPM
bodymap2_kidney	0.00 RPM	639.42 RPM
bodymap2_liver	0.00 RPM	488.97 RPM
bodymap2_lung	0.00 RPM	494.01 RPM
bodymap2_lymph_node	0.00 RPM	593.75 RPM
bodymap2_ovary	0.00 RPM	502.99 RPM
bodymap2_prostate	0.00 RPM	865.61 RPM
bodymap2_skeletal_muscle	0.04 RPM	3644.85 RPM
bodymap2_testis	0.00 RPM	728.86 RPM
bodymap2_thyroid	0.00 RPM	1157.16 RPM
bodymap2_white_blood_cells	0.00 RPM	735.54 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3268 was not detected

EST

No EST(s) were mapped for retro_hsap_3268 retrocopy.

TSS

No TSS is located nearby retro_hsap_3268 retrocopy 5' end.

Lab

retro_hsap_3268 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3268 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2211
Gorilla gorilla	retro_ggor_2224
Pongo abelii	retro_pabe_2706
Macaca mulatta	retro_mmul_2056

---

Parental genes homology:

Parental genes homology involve 20 parental genes, and 509 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,
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,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 RPM
CEU_NA11843	0.03 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.04 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.09 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.03 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.03 RPM
FIN_HG00277	0.04 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.04 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.04 RPM
GBR_HG00099	0.03 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.03 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.02 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.03 RPM
TSI_NA20512	0.03 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.06 RPM
TSI_NA20532	0.10 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.02 RPM
TSI_NA20771	0.06 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.03 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).