RetrogeneDB ID: retro_ecab_939

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 7:79460420..79460972(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL17
• Ensembl ID: ENSECAG00000011547
• Aliases: None
• Description: ribosomal protein L17 [Source:HGNC Symbol;Acc:10307]

Sequence

>retro_ecab_939
AAAAGGGCTCCCTACTCACTTGACCCAGAAAACCCTACAAAATCATGCAAATCAAGAGATTCAAATCTTCATATTCATAT
TAAGAACACTGTGAAACTTCCCAGGCCATAAAGGGTGTGCATATCTGAAAAGCCCCCAAGTATCTGAAGGATGTCACTTG
AAAGAAGCAGCATGTGCCATTCTGTCATCACAATGATGGAGTTGGTAGGCGCGCCCAGGCCAAGCAGTGGGGCTGGACAT
AGGCTCGATGGCCCAAAAAGAGTGCTGAATTTTTGCTGCACATGCTGAAAAATGCAGAGTAATGCTGAACTTAAGGGCTT
GGATGTAGATTCTCTGGTTAGTGAGCACATCCAGGTGAACAAAGCCCCCAAGATGCGGCGCAGAACCTACAGAGCTCCCG
GGAGGACTAACCCCTACGTGAGCCGGCCCTGCCACACTGAGATGGCCTTTCCTGAAAAAGAGCAGATCGTTCCTAGACCG
GAAGAGGAGGTTGCAGAGAAGAAAGGGATATCCCAGAAGAAACTGAAGAAACAAAAACTTATGGCCTGGGAA

Alignment

ORF - retro_ecab_939 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.33 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KMVRYSLDPENPTKSCKSRGSNLRVHFKNTR-ETAQAIKGMHIRKATKYLKDVTLKKQCVPFRRYNGGVG
          K...YSLDPENPTKSCKSR.SNL..H.KNT..ET.QAIKG.HI.KA.KYLKDVT.KKQ.VPF...N.GVG
Retrocopy KRAPYSLDPENPTKSCKSRDSNLHIHIKNTV<ETSQAIKGVHI*KAPKYLKDVT*KKQHVPFCHHNDGVG

Parental  RCAQAKQWGWTQGRW-PKKSAEFLLHMLKNAESNAELKGLDVDSLVIEHIQVNKAPKMRRRTYRAHGRIN
          R.AQAKQWGWT..RW.PK....F.....K...SNAELKGLDVDSLV.EHIQVNKAPKMRRRTYRA.GR.N
Retrocopy RRAQAKQWGWT*ARW>PKRVLNFCCTC*K-MQSNAELKGLDVDSLVSEHIQVNKAPKMRRRTYRAPGRTN

Parental  PYMSSPCHIEMILTEKEQIVPKPEEEVAQKKKISQKKLKKQKLMARE
          PY.S.PCH.EM...EKEQIVP.PEEEVA.KK.ISQKKLKKQKLMA.E
Retrocopy PYVSRPCHTEMAFPEKEQIVPRPEEEVAEKKGISQKKLKKQKLMAWE

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
SRP021940_articular_cartilage	0.06 RPM	837.99 RPM
SRP021940_cerebellum	0.05 RPM	238.68 RPM
SRP021940_embryo	0.38 RPM	569.09 RPM
SRP021940_placental_villous	0.05 RPM	338.75 RPM
SRP021940_synovial_membrane	0.16 RPM	487.80 RPM
SRP021940_testis	0.58 RPM	215.62 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_939 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_939 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_939 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 288 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000019337	31 retrocopies	retro_cpor_1004, retro_cpor_1005, retro_cpor_1015, retro_cpor_1050, retro_cpor_1083, retro_cpor_1118, retro_cpor_1125, retro_cpor_1227, retro_cpor_1271, retro_cpor_1305, retro_cpor_1413, retro_cpor_1455, retro_cpor_1539, retro_cpor_159, retro_cpor_213, retro_cpor_238, retro_cpor_272, retro_cpor_319, retro_cpor_374, retro_cpor_50, retro_cpor_521, retro_cpor_662, retro_cpor_675, retro_cpor_776, retro_cpor_784, retro_cpor_792, retro_cpor_827, retro_cpor_872, retro_cpor_924, retro_cpor_943, retro_cpor_955,
Equus caballus	ENSECAG00000011547	9 retrocopies	retro_ecab_162, retro_ecab_331, retro_ecab_488, retro_ecab_584, retro_ecab_620, retro_ecab_678, retro_ecab_751, retro_ecab_939 , retro_ecab_977,
Echinops telfairi	ENSETEG00000011322	10 retrocopies	retro_etel_1787, retro_etel_1810, retro_etel_1900, retro_etel_1936, retro_etel_1954, retro_etel_207, retro_etel_396, retro_etel_470, retro_etel_565, retro_etel_831,
Homo sapiens	ENSG00000215472	1 retrocopy	retro_hsap_2367,
Latimeria chalumnae	ENSLACG00000008835	1 retrocopy	retro_lcha_38,
Macropus eugenii	ENSMEUG00000016709	26 retrocopies	retro_meug_1111, retro_meug_127, retro_meug_1285, retro_meug_1485, retro_meug_1821, retro_meug_188, retro_meug_1886, retro_meug_191, retro_meug_204, retro_meug_2159, retro_meug_2167, retro_meug_2183, retro_meug_257, retro_meug_326, retro_meug_355, retro_meug_373, retro_meug_410, retro_meug_413, retro_meug_509, retro_meug_58, retro_meug_703, retro_meug_738, retro_meug_740, retro_meug_779, retro_meug_81, retro_meug_934,
Myotis lucifugus	ENSMLUG00000025554	22 retrocopies	retro_mluc_1141, retro_mluc_1224, retro_mluc_1300, retro_mluc_1375, retro_mluc_1468, retro_mluc_1500, retro_mluc_1547, retro_mluc_1579, retro_mluc_1739, retro_mluc_1755, retro_mluc_1822, retro_mluc_1870, retro_mluc_1959, retro_mluc_2018, retro_mluc_2027, retro_mluc_2036, retro_mluc_2059, retro_mluc_2165, retro_mluc_2198, retro_mluc_719, retro_mluc_835, retro_mluc_929,
Myotis lucifugus	ENSMLUG00000029264	36 retrocopies	retro_mluc_1043, retro_mluc_1060, retro_mluc_1061, retro_mluc_1081, retro_mluc_1094, retro_mluc_1163, retro_mluc_1193, retro_mluc_1206, retro_mluc_123, retro_mluc_1230, retro_mluc_1241, retro_mluc_1416, retro_mluc_157, retro_mluc_1581, retro_mluc_1652, retro_mluc_1677, retro_mluc_1693, retro_mluc_170, retro_mluc_1711, retro_mluc_1848, retro_mluc_1890, retro_mluc_2003, retro_mluc_2064, retro_mluc_2095, retro_mluc_2125, retro_mluc_2387, retro_mluc_2636, retro_mluc_2637, retro_mluc_661, retro_mluc_734, retro_mluc_763, retro_mluc_779, retro_mluc_785, retro_mluc_807, retro_mluc_938, retro_mluc_977,
Macaca mulatta	ENSMMUG00000018837	26 retrocopies	retro_mmul_1015, retro_mmul_1046, retro_mmul_1205, retro_mmul_1216, retro_mmul_1225, retro_mmul_1441, retro_mmul_163, retro_mmul_172, retro_mmul_1784, retro_mmul_1858, retro_mmul_1952, retro_mmul_2006, retro_mmul_2008, retro_mmul_2257, retro_mmul_2268, retro_mmul_2284, retro_mmul_2304, retro_mmul_2512, retro_mmul_46, retro_mmul_474, retro_mmul_589, retro_mmul_652, retro_mmul_669, retro_mmul_825, retro_mmul_956, retro_mmul_971,
Mus musculus	ENSMUSG00000062328	80 retrocopies	retro_mmus_1002, retro_mmus_1004, retro_mmus_1011, retro_mmus_1024, retro_mmus_1032, retro_mmus_1040, retro_mmus_1042, retro_mmus_1087, retro_mmus_1138, retro_mmus_1205, retro_mmus_1208, retro_mmus_1218, retro_mmus_1222, retro_mmus_1226, retro_mmus_1259, retro_mmus_1263, retro_mmus_1308, retro_mmus_1346, retro_mmus_1395, retro_mmus_1404, retro_mmus_1484, retro_mmus_1499, retro_mmus_1502, retro_mmus_1710, retro_mmus_1840, retro_mmus_1842, retro_mmus_1935, retro_mmus_201, retro_mmus_2016, retro_mmus_2034, retro_mmus_2076, retro_mmus_2099, retro_mmus_2124, retro_mmus_2156, retro_mmus_2203, retro_mmus_2261, retro_mmus_2262, retro_mmus_2343, retro_mmus_2345, retro_mmus_243, retro_mmus_2468, retro_mmus_2550, retro_mmus_2613, retro_mmus_2634, retro_mmus_2724, retro_mmus_2759, retro_mmus_2773, retro_mmus_2775, retro_mmus_288, retro_mmus_2919, retro_mmus_3003, retro_mmus_302, retro_mmus_3037, retro_mmus_3049, retro_mmus_310, retro_mmus_311, retro_mmus_314, retro_mmus_327, retro_mmus_334, retro_mmus_3354, retro_mmus_337, retro_mmus_3490, retro_mmus_3601, retro_mmus_3687, retro_mmus_388, retro_mmus_419, retro_mmus_420, retro_mmus_523, retro_mmus_525, retro_mmus_529, retro_mmus_661, retro_mmus_673, retro_mmus_741, retro_mmus_773, retro_mmus_828, retro_mmus_871, retro_mmus_879, retro_mmus_922, retro_mmus_948, retro_mmus_966,
Oryctolagus cuniculus	ENSOCUG00000012485	2 retrocopies	retro_ocun_1433, retro_ocun_231,
Pongo abelii	ENSPPYG00000009151	43 retrocopies	retro_pabe_1177, retro_pabe_1178, retro_pabe_1179, retro_pabe_1197, retro_pabe_1373, retro_pabe_1408, retro_pabe_1448, retro_pabe_1464, retro_pabe_1531, retro_pabe_1565, retro_pabe_1574, retro_pabe_1725, retro_pabe_1807, retro_pabe_1832, retro_pabe_1902, retro_pabe_2052, retro_pabe_2053, retro_pabe_2088, retro_pabe_2102, retro_pabe_2164, retro_pabe_2231, retro_pabe_2317, retro_pabe_2520, retro_pabe_2635, retro_pabe_2638, retro_pabe_2871, retro_pabe_2917, retro_pabe_2921, retro_pabe_2971, retro_pabe_3020, retro_pabe_3029, retro_pabe_3103, retro_pabe_3187, retro_pabe_3248, retro_pabe_3253, retro_pabe_3262, retro_pabe_3277, retro_pabe_347, retro_pabe_3493, retro_pabe_539, retro_pabe_567, retro_pabe_617, retro_pabe_882,
Vicugna pacos	ENSVPAG00000009568	1 retrocopy	retro_vpac_10,