RetrogeneDB ID: retro_sscr_108

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:63646192..63646747(+)
• Located in intron of: ENSSSCG00000025426

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL17
• Ensembl ID: ENSSSCG00000029642
• Aliases: None
• Description: ribosomal protein L17 [Source:HGNC Symbol;Acc:10307]

Sequence

>retro_sscr_108
ATGGTTTGCTATTCACTTGACCCATAAAAACCCCATAAAATCATGAGAATCAAGAGGTTCAAATCTTCATGTTCACTTTA
AGAACACCCATGACACTGCCCAGGCCATTAAGGGTATGCATATTCGAAAAGCCACCAAGGATCTGAAGGATGTCACTCTA
CAGAAGCAATGTGTGCCATTTCGTCATTACAATGGTGGAGCTGGTAGGTGTGCCCATACCAAATAGGCCTGGGGCTAGAC
ACAGGGTCAGTGACCCAAAAAGAGTGAATTTTTATTGCACATGCTCAAAAATGCAGAGAGTAATGCTGAACTGAAGGGCT
TGGATGTAGAGTCTCCGGTCATTCAGCACATCCAGGTGAACAAAGCCCCTAAAATGCAGCGCAGGACTTATAATAGAGCT
CTGGCCAGATCAATCCTTACCTGAGTTCTCCCTGCCACATTAAGATGATCCTTACTGAAAAAGAGCAGATTGTTCCTAAG
CCAGAAGAGGAGGTTGCATAGAAGAAAAAGATATCCCAGAAGAAACTGAAGAAACAAAAACTTATGGCCCGGGAA

Alignment

ORF - retro_sscr_108 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.45 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVRYSLDP-ENPTKSCKSRGSNLRVHFKNTRETAQAIKGMHIRKATKYLKDFTLQKQCVPFRRYN-GVGR
          MV.YSLDP..NP.KS..SRGSNL.VHFKNT..TAQAIKGMHIRKATK.LKD.TLQKQCVPFR.YN.G.GR
Retrocopy MVCYSLDP>KNPIKS*ESRGSNLHVHFKNTHDTAQAIKGMHIRKATKDLKDVTLQKQCVPFRHYNGGAGR

Parental  CAQAK-QWGWTQGRWPKKSAEFLLHMLKNAESNAELKGLDVDSLVIEHIQVNKAPKMRRRTY-RA-HGRI
          CA..K..WG.TQG..PKKS.EFLLHMLKNAESNAELKGLDV.S.VI.HIQVNKAPKM.RRTY.RA..G.I
Retrocopy CAHTK*AWG*TQGQ*PKKS-EFLLHMLKNAESNAELKGLDVESPVIQHIQVNKAPKMQRRTYNRA<SGQI

Parental  NPYMSSPCHIEMILTEKEQIVPKPEEEVAQKKKISQKKLKKQKLMARE
          NPY.SSPCHI.MILTEKEQIVPKPEEEVA.KKKISQKKLKKQKLMARE
Retrocopy NPYLSSPCHIKMILTEKEQIVPKPEEEVA*KKKISQKKLKKQKLMARE

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
SRP014902_placenta	0.00 RPM	409.48 RPM
SRP014902_testis	0.85 RPM	1086.45 RPM
SRP018288_heart	0.03 RPM	699.89 RPM
SRP018288_kidney	0.00 RPM	518.83 RPM
SRP018288_liver	0.32 RPM	468.70 RPM
SRP018288_lung	0.31 RPM	447.73 RPM
SRP018856_adipose	0.09 RPM	2235.01 RPM
SRP035408_brain	1.68 RPM	1765.53 RPM
SRP035408_liver	0.56 RPM	949.78 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_108 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_108 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_108 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 256 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009498	40 retrocopies	retro_amel_1147, retro_amel_1150, retro_amel_1252, retro_amel_1273, retro_amel_132, retro_amel_1422, retro_amel_1435, retro_amel_1487, retro_amel_1541, retro_amel_156, retro_amel_1567, retro_amel_1582, retro_amel_1599, retro_amel_1622, retro_amel_1624, retro_amel_1652, retro_amel_1703, retro_amel_1704, retro_amel_1743, retro_amel_1757, retro_amel_184, retro_amel_1908, retro_amel_1922, retro_amel_208, retro_amel_359, retro_amel_401, retro_amel_425, retro_amel_426, retro_amel_452, retro_amel_486, retro_amel_589, retro_amel_731, retro_amel_736, retro_amel_780, retro_amel_820, retro_amel_834, retro_amel_865, retro_amel_950, retro_amel_953, retro_amel_980,
Canis familiaris	ENSCAFG00000019044	7 retrocopies	retro_cfam_102, retro_cfam_171, retro_cfam_175, retro_cfam_189, retro_cfam_2, retro_cfam_239, retro_cfam_34,
Callithrix jacchus	ENSCJAG00000004779	4 retrocopies	retro_cjac_122, retro_cjac_248, retro_cjac_360, retro_cjac_376,
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,
Felis catus	ENSFCAG00000011342	43 retrocopies	retro_fcat_1002, retro_fcat_1004, retro_fcat_1019, retro_fcat_1050, retro_fcat_1065, retro_fcat_1196, retro_fcat_1235, retro_fcat_1300, retro_fcat_1322, retro_fcat_1426, retro_fcat_1427, retro_fcat_1432, retro_fcat_1516, retro_fcat_1525, retro_fcat_1539, retro_fcat_1552, retro_fcat_1588, retro_fcat_1655, retro_fcat_1692, retro_fcat_1699, retro_fcat_1703, retro_fcat_1740, retro_fcat_1746, retro_fcat_1821, retro_fcat_1864, retro_fcat_1892, retro_fcat_1917, retro_fcat_2023, retro_fcat_211, retro_fcat_264, retro_fcat_360, retro_fcat_461, retro_fcat_481, retro_fcat_488, retro_fcat_532, retro_fcat_607, retro_fcat_734, retro_fcat_791, retro_fcat_808, retro_fcat_855, retro_fcat_900, retro_fcat_917, retro_fcat_988,
Homo sapiens	ENSG00000215472	1 retrocopy	retro_hsap_2367,
Gorilla gorilla	ENSGGOG00000026697	1 retrocopy	retro_ggor_167,
Latimeria chalumnae	ENSLACG00000008835	1 retrocopy	retro_lcha_38,
Loxodonta africana	ENSLAFG00000005569	16 retrocopies	retro_lafr_1001, retro_lafr_1036, retro_lafr_1060, retro_lafr_1130, retro_lafr_177, retro_lafr_186, retro_lafr_207, retro_lafr_213, retro_lafr_256, retro_lafr_293, retro_lafr_354, retro_lafr_721, retro_lafr_731, retro_lafr_773, retro_lafr_860, retro_lafr_933,
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,
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,
Mustela putorius furo	ENSMPUG00000000801	7 retrocopies	retro_mputfur_1008, retro_mputfur_126, retro_mputfur_1349, retro_mputfur_16, retro_mputfur_184, retro_mputfur_40, retro_mputfur_536,
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,
Sus scrofa	ENSSSCG00000029642	30 retrocopies	retro_sscr_1002, retro_sscr_1003, retro_sscr_1033, retro_sscr_1067, retro_sscr_108 , retro_sscr_110, retro_sscr_1106, retro_sscr_111, retro_sscr_1151, retro_sscr_1170, retro_sscr_121, retro_sscr_180, retro_sscr_340, retro_sscr_370, retro_sscr_386, retro_sscr_403, retro_sscr_413, retro_sscr_442, retro_sscr_460, retro_sscr_481, retro_sscr_496, retro_sscr_502, retro_sscr_592, retro_sscr_613, retro_sscr_768, retro_sscr_823, retro_sscr_848, retro_sscr_857, retro_sscr_881, retro_sscr_931,
Vicugna pacos	ENSVPAG00000009568	1 retrocopy	retro_vpac_10,