RetrogeneDB ID: retro_btau_1175

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 29:20913362..20914124(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000000853
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: G3PDH
• Ensembl ID: ENSBTAG00000014731
• Aliases: GAPDH, GAPD
• Description: Glyceraldehyde-3-phosphate dehydrogenase [Source:UniProtKB/Swiss-Prot;Acc:P10096]

Sequence

>retro_btau_1175
ATGGTGAAGGTTGGAGTGAACGGATTTGGCCTGTTTGGGCGCCTGGCCACCAGGGCTGCTTTTAACTCTGGCAAAGTGGA
CATCATCGCCATCAATGACCCCCTTCATTGACCTTCACTACATGGTCTACATGTTCCAGTATGATTCCATCCATGGTGAG
TTTCACGACACAGTCAAGGCAGAGAATGGGAAGCTCGTCATTGATGGAAAGGCCATCACCATTTTCCAGGAGCAAGATCC
TGCCATCATCAAGTGCGGTGATGCTGGTGCTGCGTATGTGGTGGAGTCCACTGGTGTCTTCACTACCATGGAGAAGGCTA
GGGCTTACTTGAAGGGTGGAAACCAAGAGGGTCATCATCTCTGCACCTTCTACCGATCCCCCCAAGTTTGTGATGGGCGT
GAACCACGAGAGGTATGACAACTCCCTCAAGATTGTCAGCAATGCCTCCTGCACCACCAACTGCTTGGCCGCCCTGGCAA
AAGTCATCCATAACTACTTTGGCATCGTGGAGGGACTCATGACCACCATCCACGTCATCACTGCCACCCAGAAGACCGTG
GATGGGCCCTCCGGGATGCTATGGCGTGATGGCCGAGGGGCTGCCCAGAAAATCATCCCTACTTCTACCAGTGCTGCCAA
GGCCATGGGCAAGGTCCTCCCTGAGTTCAATGGGAATCTCCCCTGCGTGGCCTTCCATCCCCACCCCCAAGGTGTCCATT
GTGGATCTGACCTGCCACCTAAAGAAACCTGCCAAGTATAAT

Alignment

ORF - retro_btau_1175 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.93 %
• Parental protein coverage: 76.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MVKVGVNGFGRIGRLVTRAAFNSGKVDIVAINDP-FIDLHYMVYMFQYDSTHGKFNGTVKAENGKLVING
          MVKVGVNGFG..GRL.TRAAFNSGKVDI.AINDP.FIDLHYMVYMFQYDS.HG.F..TVKAENGKLVI.G
Retrocopy MVKVGVNGFGLFGRLATRAAFNSGKVDIIAINDP>FIDLHYMVYMFQYDSIHGEFHDTVKAENGKLVIDG

Parental  KAITIFQERDPANIKWGDAGAEYVVESTGVFTTMEKAGAHLKGG-AKRVIISAPSADAPMFVMGVNHEKY
          KAITIFQE.DPA.IK.GDAGA.YVVESTGVFTTMEKA.A.LKGG..KRVIISAPS.D.P.FVMGVNHE.Y
Retrocopy KAITIFQEQDPAIIKCGDAGAAYVVESTGVFTTMEKARAYLKGG>TKRVIISAPSTDPPKFVMGVNHERY

Parental  NNTLKIVSNASCTTNCLAPLAKVIHDHFGIVEGLMTTVHAITATQKTVDGPSGKLWRDGRGAAQNIIPAS
          .N.LKIVSNASCTTNCLA.LAKVIH..FGIVEGLMTT.H.ITATQKTVDGPSG.LWRDGRGAAQ.IIP.S
Retrocopy DNSLKIVSNASCTTNCLAALAKVIHNYFGIVEGLMTTIHVITATQKTVDGPSGMLWRDGRGAAQKIIPTS

Parental  TGAAKAVGKVIPELNGKLTGMAFRVPTP-NVSVVDLTCRLEKPAKYD
          T.AAKA.GKV.PE.NG.L...AF..P.P..VS.VDLTC.L.KPAKY.
Retrocopy TSAAKAMGKVLPEFNGNLPCVAFH-PHP>KVSIVDLTCHLKKPAKYN

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
ERP005899_liver	0.00 RPM	289.18 RPM
ERP005899_muscle	0.00 RPM	925.23 RPM
SRP017611_brain	0.09 RPM	1087.67 RPM
SRP017611_kidney	0.00 RPM	775.63 RPM
SRP017611_liver	0.08 RPM	447.46 RPM
SRP030211_testis	0.03 RPM	113.68 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1175 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1175 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1175 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 20 parental genes, and 428 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,
Bos taurus	ENSBTAG00000014731	4 retrocopies	retro_btau_1175 , retro_btau_1417, retro_btau_834, retro_btau_887,
Canis familiaris	ENSCAFG00000015077	4 retrocopies	retro_cfam_122, retro_cfam_214, retro_cfam_3, retro_cfam_7,
Callithrix jacchus	ENSCJAG00000008234	1 retrocopy	retro_cjac_1548,
Cavia porcellus	ENSCPOG00000026350	1 retrocopy	retro_cpor_125,
Echinops telfairi	ENSETEG00000013749	118 retrocopies	retro_etel_1011, retro_etel_1037, retro_etel_1070, retro_etel_1117, retro_etel_1132, retro_etel_1153, retro_etel_1171, retro_etel_1183, retro_etel_1214, retro_etel_1215, retro_etel_1247, retro_etel_1249, retro_etel_1255, retro_etel_1257, retro_etel_1258, retro_etel_1266, retro_etel_127, retro_etel_1320, retro_etel_1349, retro_etel_1352, retro_etel_1381, retro_etel_1386, retro_etel_1389, retro_etel_1408, retro_etel_1419, retro_etel_1422, retro_etel_1431, retro_etel_1437, retro_etel_1470, retro_etel_1473, retro_etel_1490, retro_etel_150, retro_etel_1511, retro_etel_1538, retro_etel_1550, retro_etel_1563, retro_etel_1570, retro_etel_1588, retro_etel_1601, retro_etel_1608, retro_etel_1620, retro_etel_163, retro_etel_1635, retro_etel_1641, retro_etel_1674, retro_etel_1679, retro_etel_1702, retro_etel_1738, retro_etel_1746, retro_etel_1759, retro_etel_1769, retro_etel_1776, retro_etel_1780, retro_etel_180, retro_etel_184, retro_etel_1840, retro_etel_1869, retro_etel_1895, retro_etel_1897, retro_etel_1949, retro_etel_1970, retro_etel_1976, retro_etel_1982, retro_etel_1989, retro_etel_2033, retro_etel_2076, retro_etel_209, retro_etel_212, retro_etel_213, retro_etel_2152, retro_etel_2161, retro_etel_2173, retro_etel_2198, retro_etel_2202, retro_etel_2210, retro_etel_243, retro_etel_290, retro_etel_330, retro_etel_339, retro_etel_340, retro_etel_365, retro_etel_397, retro_etel_432, retro_etel_440, retro_etel_463, retro_etel_489, retro_etel_495, retro_etel_504, retro_etel_536, retro_etel_557, retro_etel_586, retro_etel_589, retro_etel_600, retro_etel_611, retro_etel_618, retro_etel_621, retro_etel_624, retro_etel_649, retro_etel_653, retro_etel_69, retro_etel_770, retro_etel_780, retro_etel_790, retro_etel_792, retro_etel_798, retro_etel_802, retro_etel_810, retro_etel_874, retro_etel_895, retro_etel_899, retro_etel_90, retro_etel_906, retro_etel_931, retro_etel_934, retro_etel_935, retro_etel_968, retro_etel_969, retro_etel_987,
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,
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,
Ornithorhynchus anatinus	ENSOANG00000004492	1 retrocopy	retro_oana_81,
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,
Sus scrofa	ENSSSCG00000000694	2 retrocopies	retro_sscr_1213, retro_sscr_572,
Tursiops truncatus	ENSTTRG00000016094	2 retrocopies	retro_ttru_654, retro_ttru_707,
Xenopus tropicalis	ENSXETG00000033975	1 retrocopy	retro_xtro_70,