RetrogeneDB ID: retro_sscr_485

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 15:3935225..3935618(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000028850
• Aliases: None
• Description: Sus scrofa ribosomal protein L26 (RPL26), mRNA. [Source:RefSeq mRNA;Acc:NM_001243458]

Sequence

>retro_sscr_485
ATGAAATACAATCCCTTTGTTTCTTGTGACCAGAGTGAGAACCATAAAAATCATTTCAACTCACCTTCCCACATTTGCAC
AAAGATTGTCTTTTCCCGAGAGCTGAGAGAGAAGTACAATGTCTAGACCATGTCCATCTGAACGGATGATGAATCTTGAG
TTGTATGAGGAGACTACAAATATCAGCAGACTGGCAAAGTAGTTCAAGTTTTCAGGAAGAAATGTATCATCTACCCTAGA
CATATGCAACCAGAGAAGCCAATGGCACAACTGTCCATGTGGGCATTCAGCCCAGCAAGGTGGTTATAACCAGGCTGAAA
GTGGACACTGGTGGCAAAAAAGACCTTTGGATGTAAAGCCAGATCTTGCAAAGTAGGAAGGGAAAAGGGCCAA

Alignment

ORF - retro_sscr_485 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.5 %
• Parental protein coverage: 92.41 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKFNPFVTSDRSKNRKRHFNAPSHIRRKIMSSPLSKELRQKYNVRSMPIRKDDEVQVVRGHYKGQQIGKV
          MK.NPFV..D.S.N.K.HFN.PSHI..KI.....S.ELR.KYNV..M.I..DDE..VV.G.YK.QQ.GKV
Retrocopy MKYNPFVSCDQSENHKNHFNSPSHICTKIV---FSRELREKYNV*TMSI*TDDES*VV*GDYKYQQTGKV

Parental  VQVYRKKYVIYIERVQREK-ANGTTVHVGIHPSKVVITRLKLDKDRKKILER-KAKSRQVGKEKGK
          VQV.RKK..IY....Q.EK.ANGTTVHVGI.PSKVVITRLK.D...KK.L...KA.S..VG.EKG.
Retrocopy VQVFRKKCIIYPRHMQPEK<ANGTTVHVGIQPSKVVITRLKVDTGGKKDLWM>KARSCKVGREKGQ

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	676.53 RPM
SRP014902_testis	0.00 RPM	767.35 RPM
SRP018288_heart	0.00 RPM	547.76 RPM
SRP018288_kidney	0.00 RPM	308.62 RPM
SRP018288_liver	0.00 RPM	284.16 RPM
SRP018288_lung	0.00 RPM	878.45 RPM
SRP018856_adipose	0.00 RPM	1432.76 RPM
SRP035408_brain	0.00 RPM	1221.76 RPM
SRP035408_liver	0.00 RPM	962.96 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_485 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_485 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_485 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2165
Macaca mulatta	retro_mmul_903
Equus caballus	retro_ecab_429

---

Parental genes homology:

Parental genes homology involve 29 parental genes, and 280 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002453	7 retrocopies	retro_amel_1175, retro_amel_1535, retro_amel_1885, retro_amel_1934, retro_amel_360, retro_amel_499, retro_amel_900,
Bos taurus	ENSBTAG00000012344	2 retrocopies	retro_btau_1090, retro_btau_230,
Choloepus hoffmanni	ENSCHOG00000004703	10 retrocopies	retro_chof_149, retro_chof_1893, retro_chof_2147, retro_chof_2276, retro_chof_2333, retro_chof_2383, retro_chof_244, retro_chof_312, retro_chof_816, retro_chof_942,
Callithrix jacchus	ENSCJAG00000014372	8 retrocopies	retro_cjac_110, retro_cjac_119, retro_cjac_240, retro_cjac_250, retro_cjac_270, retro_cjac_297, retro_cjac_321, retro_cjac_362,
Cavia porcellus	ENSCPOG00000001315	10 retrocopies	retro_cpor_1009, retro_cpor_1161, retro_cpor_1346, retro_cpor_1421, retro_cpor_1503, retro_cpor_1526, retro_cpor_167, retro_cpor_522, retro_cpor_585, retro_cpor_858,
Dasypus novemcinctus	ENSDNOG00000002470	3 retrocopies	retro_dnov_2054, retro_dnov_2174, retro_dnov_378,
Equus caballus	ENSECAG00000015757	4 retrocopies	retro_ecab_429, retro_ecab_473, retro_ecab_515, retro_ecab_609,
Felis catus	ENSFCAG00000011259	13 retrocopies	retro_fcat_1090, retro_fcat_1151, retro_fcat_1198, retro_fcat_1236, retro_fcat_1257, retro_fcat_1309, retro_fcat_1412, retro_fcat_1652, retro_fcat_1801, retro_fcat_1845, retro_fcat_1965, retro_fcat_497, retro_fcat_801,
Homo sapiens	ENSG00000161970	27 retrocopies	retro_hsap_1137, retro_hsap_1309, retro_hsap_1376, retro_hsap_1394, retro_hsap_191, retro_hsap_2108, retro_hsap_2165, retro_hsap_2253, retro_hsap_253, retro_hsap_267, retro_hsap_2946, retro_hsap_3118, retro_hsap_3260, retro_hsap_3324, retro_hsap_3490, retro_hsap_3700, retro_hsap_3803, retro_hsap_3813, retro_hsap_3914, retro_hsap_4043, retro_hsap_4061, retro_hsap_4874, retro_hsap_4932, retro_hsap_642, retro_hsap_691, retro_hsap_915, retro_hsap_998,
Gorilla gorilla	ENSGGOG00000023944	4 retrocopies	retro_ggor_2565, retro_ggor_270, retro_ggor_51, retro_ggor_974,
Macropus eugenii	ENSMEUG00000009891	7 retrocopies	retro_meug_1239, retro_meug_1538, retro_meug_1607, retro_meug_1827, retro_meug_262, retro_meug_322, retro_meug_534,
Myotis lucifugus	ENSMLUG00000002176	1 retrocopy	retro_mluc_232,
Macaca mulatta	ENSMMUG00000003448	22 retrocopies	retro_mmul_1117, retro_mmul_1361, retro_mmul_1398, retro_mmul_1497, retro_mmul_1710, retro_mmul_1773, retro_mmul_1899, retro_mmul_1986, retro_mmul_2052, retro_mmul_2163, retro_mmul_2332, retro_mmul_2344, retro_mmul_325, retro_mmul_360, retro_mmul_398, retro_mmul_405, retro_mmul_448, retro_mmul_548, retro_mmul_805, retro_mmul_903, retro_mmul_920, retro_mmul_992,
Monodelphis domestica	ENSMODG00000006201	2 retrocopies	retro_mdom_36, retro_mdom_64,
Mustela putorius furo	ENSMPUG00000007988	12 retrocopies	retro_mputfur_1003, retro_mputfur_1146, retro_mputfur_1385, retro_mputfur_1428, retro_mputfur_1595, retro_mputfur_251, retro_mputfur_365, retro_mputfur_395, retro_mputfur_488, retro_mputfur_522, retro_mputfur_643, retro_mputfur_685,
Mus musculus	ENSMUSG00000060938	21 retrocopies	retro_mmus_1325, retro_mmus_1444, retro_mmus_1506, retro_mmus_1642, retro_mmus_1866, retro_mmus_1978, retro_mmus_2011, retro_mmus_2218, retro_mmus_2435, retro_mmus_2540, retro_mmus_2673, retro_mmus_3078, retro_mmus_3174, retro_mmus_320, retro_mmus_3270, retro_mmus_3291, retro_mmus_3361, retro_mmus_384, retro_mmus_556, retro_mmus_900, retro_mmus_939,
Nomascus leucogenys	ENSNLEG00000009981	1 retrocopy	retro_nleu_76,
Oryctolagus cuniculus	ENSOCUG00000006538	11 retrocopies	retro_ocun_1125, retro_ocun_1290, retro_ocun_1442, retro_ocun_1484, retro_ocun_1515, retro_ocun_1621, retro_ocun_1917, retro_ocun_529, retro_ocun_542, retro_ocun_589, retro_ocun_803,
Otolemur garnettii	ENSOGAG00000017070	3 retrocopies	retro_ogar_118, retro_ogar_255, retro_ogar_66,
Pan troglodytes	ENSPTRG00000008742	3 retrocopies	retro_ptro_1546, retro_ptro_2510, retro_ptro_73,
Rattus norvegicus	ENSRNOG00000004214	3 retrocopies	retro_rnor_213, retro_rnor_260, retro_rnor_273,
Sorex araneus	ENSSARG00000005798	13 retrocopies	retro_sara_172, retro_sara_208, retro_sara_228, retro_sara_273, retro_sara_319, retro_sara_334, retro_sara_393, retro_sara_527, retro_sara_578, retro_sara_627, retro_sara_641, retro_sara_656, retro_sara_740,
Sarcophilus harrisii	ENSSHAG00000006890	1 retrocopy	retro_shar_458,
Sus scrofa	ENSSSCG00000016989	3 retrocopies	retro_sscr_1104, retro_sscr_462, retro_sscr_685,
Sus scrofa	ENSSSCG00000028850	9 retrocopies	retro_sscr_261, retro_sscr_363, retro_sscr_426, retro_sscr_427, retro_sscr_471, retro_sscr_485 , retro_sscr_508, retro_sscr_609, retro_sscr_736,
Ictidomys tridecemlineatus	ENSSTOG00000021923	6 retrocopies	retro_itri_1113, retro_itri_1145, retro_itri_1206, retro_itri_1262, retro_itri_1670, retro_itri_811,
Tupaia belangeri	ENSTBEG00000007749	53 retrocopies	retro_tbel_1053, retro_tbel_1088, retro_tbel_1103, retro_tbel_1140, retro_tbel_1366, retro_tbel_1389, retro_tbel_1390, retro_tbel_1391, retro_tbel_1433, retro_tbel_1497, retro_tbel_1512, retro_tbel_1767, retro_tbel_1793, retro_tbel_1928, retro_tbel_1930, retro_tbel_2005, retro_tbel_2033, retro_tbel_2053, retro_tbel_2057, retro_tbel_2099, retro_tbel_2105, retro_tbel_2332, retro_tbel_2416, retro_tbel_2465, retro_tbel_2500, retro_tbel_268, retro_tbel_2727, retro_tbel_2778, retro_tbel_2806, retro_tbel_2884, retro_tbel_3020, retro_tbel_3187, retro_tbel_3300, retro_tbel_3332, retro_tbel_3704, retro_tbel_3711, retro_tbel_3790, retro_tbel_3964, retro_tbel_404, retro_tbel_4162, retro_tbel_4200, retro_tbel_4381, retro_tbel_4416, retro_tbel_446, retro_tbel_4480, retro_tbel_470, retro_tbel_474, retro_tbel_495, retro_tbel_573, retro_tbel_863, retro_tbel_906, retro_tbel_964, retro_tbel_99,
Tarsius syrichta	ENSTSYG00000001483	17 retrocopies	retro_tsyr_1273, retro_tsyr_1274, retro_tsyr_1499, retro_tsyr_153, retro_tsyr_1705, retro_tsyr_1858, retro_tsyr_1869, retro_tsyr_2152, retro_tsyr_262, retro_tsyr_327, retro_tsyr_346, retro_tsyr_600, retro_tsyr_636, retro_tsyr_684, retro_tsyr_808, retro_tsyr_865, retro_tsyr_905,
Vicugna pacos	ENSVPAG00000000279	4 retrocopies	retro_vpac_214, retro_vpac_255, retro_vpac_26, retro_vpac_357,