RetrogeneDB ID: retro_sscr_498

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 15:80266033..80266572(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000014540
• Aliases: None
• Description: Sus scrofa ferritin, heavy polypeptide 1 (FTH1), mRNA. [Source:RefSeq mRNA;Acc:NM_213975]

Sequence

>retro_sscr_498
ACGACCTCGTGCTCCTGGCAGGTGTGCCAGAACTACCACCAGGACTCGGAAGCGGCCATCAACCGCCAGATCAACCTGGA
GCTCTATGCCTCCTGCATGTACCTGTCCGTGTCATACTATTTTGACTGCGATGATGTGGCTTTGAAGAACTTTGCCAGAT
ACTTTCTTCACCAATCTCCTGAGGAGAGGGAACATCTGAAAAACTGATGAAGGTGCAGAACCAATGAGGTATCCAAATCC
TCCTTCAGGATATCAAGAAACCAGAGTGTGATGACTGGGAGAATGGGCTGATGTAATGGAATGTGCGCTACACCTGGAAA
AATACCATGGATCAGTCTCTACTGGAACTGCACAAACTGGCCACTGACAAAAATGACCCCCATTTGTGTGACTTCATTGA
GATGCATTATCTGGATGAGCAGGTGAAATCCATCAAAGAATTGGGTGACCACATTACCAACTTGTGCATGATGGGGGCCC
CCAAATATGGCCTGGCCGAGTATCTCTTTAACAAGCACACACTGAGAAGCAGTGAGAGC

Alignment

ORF - retro_sscr_498 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.06 %
• Parental protein coverage: 99.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TTSCSSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQSHEEREH-AEKL
          TTSCS.QV.QNYHQDSEAAINRQINLELYAS..YLS.SYYFD.DDVALKNFA.YFLHQS.EEREH..EKL
Retrocopy TTSCSWQVCQNYHQDSEAAINRQINLELYASCMYLSVSYYFDCDDVALKNFARYFLHQSPEEREH<SEKL

Parental  MKLQNQRGGRIFLQDIKKPERDDWENGLT-AMECALHLEK-NVNQSLLELHKLATDKNDPHLCDFIETHY
          MK.QNQ.G..I.LQDIKKPE.DDWENGL...MECALHLEK....QSLLELHKLATDKNDPHLCDFIE.HY
Retrocopy MKVQNQ*GIQILLQDIKKPECDDWENGLM<VMECALHLEK>TMDQSLLELHKLATDKNDPHLCDFIEMHY

Parental  LDEQVKAIKELGDHITNLHRMGAPEYGMAEYLFDKHTLGSSES
          LDEQVK.IKELGDHITNL..MGAP.YG.AEYLF.KHTL.SSES
Retrocopy LDEQVKSIKELGDHITNLCMMGAPKYGLAEYLFNKHTLRSSES

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	2803.55 RPM
SRP014902_testis	0.14 RPM	1553.08 RPM
SRP018288_heart	0.00 RPM	1380.53 RPM
SRP018288_kidney	0.10 RPM	4845.69 RPM
SRP018288_liver	0.16 RPM	3195.47 RPM
SRP018288_lung	6.52 RPM	1533.50 RPM
SRP018856_adipose	0.32 RPM	6323.18 RPM
SRP035408_brain	0.00 RPM	1830.93 RPM
SRP035408_liver	0.00 RPM	1346.58 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_498 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_498 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_498 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 28 parental genes, and 328 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016831	1 retrocopy	retro_amel_115,
Bos taurus	ENSBTAG00000011184	10 retrocopies	retro_btau_1151, retro_btau_121, retro_btau_1255, retro_btau_1473, retro_btau_1708, retro_btau_1745, retro_btau_256, retro_btau_595, retro_btau_673, retro_btau_959,
Canis familiaris	ENSCAFG00000015901	1 retrocopy	retro_cfam_150,
Callithrix jacchus	ENSCJAG00000019089	16 retrocopies	retro_cjac_1570, retro_cjac_1634, retro_cjac_2115, retro_cjac_2233, retro_cjac_230, retro_cjac_232, retro_cjac_2320, retro_cjac_2531, retro_cjac_278, retro_cjac_2843, retro_cjac_2857, retro_cjac_485, retro_cjac_519, retro_cjac_699, retro_cjac_767, retro_cjac_804,
Cavia porcellus	ENSCPOG00000026586	3 retrocopies	retro_cpor_1309, retro_cpor_15, retro_cpor_157,
Dasypus novemcinctus	ENSDNOG00000017128	83 retrocopies	retro_dnov_1017, retro_dnov_1074, retro_dnov_1078, retro_dnov_110, retro_dnov_1179, retro_dnov_1188, retro_dnov_1196, retro_dnov_1201, retro_dnov_1205, retro_dnov_1271, retro_dnov_1352, retro_dnov_1356, retro_dnov_1369, retro_dnov_1397, retro_dnov_1415, retro_dnov_1425, retro_dnov_1446, retro_dnov_1489, retro_dnov_1526, retro_dnov_1535, retro_dnov_1554, retro_dnov_1565, retro_dnov_162, retro_dnov_1627, retro_dnov_1640, retro_dnov_1777, retro_dnov_1787, retro_dnov_1792, retro_dnov_1827, retro_dnov_1851, retro_dnov_1865, retro_dnov_1875, retro_dnov_189, retro_dnov_197, retro_dnov_2005, retro_dnov_2065, retro_dnov_2093, retro_dnov_2097, retro_dnov_2109, retro_dnov_2124, retro_dnov_2136, retro_dnov_2154, retro_dnov_2173, retro_dnov_220, retro_dnov_2216, retro_dnov_2231, retro_dnov_2241, retro_dnov_2251, retro_dnov_2356, retro_dnov_2388, retro_dnov_2399, retro_dnov_242, retro_dnov_2443, retro_dnov_2444, retro_dnov_2454, retro_dnov_2476, retro_dnov_2483, retro_dnov_2489, retro_dnov_2511, retro_dnov_2528, retro_dnov_2554, retro_dnov_2579, retro_dnov_2607, retro_dnov_2626, retro_dnov_2646, retro_dnov_304, retro_dnov_383, retro_dnov_409, retro_dnov_422, retro_dnov_471, retro_dnov_517, retro_dnov_52, retro_dnov_55, retro_dnov_589, retro_dnov_61, retro_dnov_661, retro_dnov_675, retro_dnov_722, retro_dnov_726, retro_dnov_810, retro_dnov_864, retro_dnov_890, retro_dnov_994,
Felis catus	ENSFCAG00000007382	1 retrocopy	retro_fcat_887,
Homo sapiens	ENSG00000167996	20 retrocopies	retro_hsap_1243, retro_hsap_139, retro_hsap_1432, retro_hsap_2240, retro_hsap_2351, retro_hsap_2662, retro_hsap_2835, retro_hsap_2985, retro_hsap_2996, retro_hsap_316, retro_hsap_3208, retro_hsap_3293, retro_hsap_3589, retro_hsap_4083, retro_hsap_4232, retro_hsap_4671, retro_hsap_484, retro_hsap_81, retro_hsap_87, retro_hsap_898,
Gorilla gorilla	ENSGGOG00000027722	7 retrocopies	retro_ggor_1313, retro_ggor_153, retro_ggor_1671, retro_ggor_1858, retro_ggor_2835, retro_ggor_64, retro_ggor_726,
Latimeria chalumnae	ENSLACG00000017426	1 retrocopy	retro_lcha_75,
Loxodonta africana	ENSLAFG00000004824	12 retrocopies	retro_lafr_106, retro_lafr_1080, retro_lafr_1129, retro_lafr_138, retro_lafr_321, retro_lafr_433, retro_lafr_523, retro_lafr_53, retro_lafr_624, retro_lafr_717, retro_lafr_760, retro_lafr_966,
Microcebus murinus	ENSMICG00000005851	6 retrocopies	retro_mmur_1227, retro_mmur_1303, retro_mmur_1370, retro_mmur_1609, retro_mmur_392, retro_mmur_509,
Myotis lucifugus	ENSMLUG00000025726	16 retrocopies	retro_mluc_1030, retro_mluc_1142, retro_mluc_1211, retro_mluc_1354, retro_mluc_1464, retro_mluc_1769, retro_mluc_1984, retro_mluc_2002, retro_mluc_2091, retro_mluc_212, retro_mluc_2635, retro_mluc_361, retro_mluc_532, retro_mluc_556, retro_mluc_850, retro_mluc_885,
Monodelphis domestica	ENSMODG00000007582	9 retrocopies	retro_mdom_1134, retro_mdom_122, retro_mdom_1294, retro_mdom_1407, retro_mdom_1742, retro_mdom_300, retro_mdom_564, retro_mdom_643, retro_mdom_809,
Mustela putorius furo	ENSMPUG00000014030	3 retrocopies	retro_mputfur_1642, retro_mputfur_36, retro_mputfur_408,
Mus musculus	ENSMUSG00000024661	4 retrocopies	retro_mmus_2856, retro_mmus_3417, retro_mmus_3660, retro_mmus_45,
Nomascus leucogenys	ENSNLEG00000003321	29 retrocopies	retro_nleu_1036, retro_nleu_1157, retro_nleu_136, retro_nleu_1411, retro_nleu_1503, retro_nleu_1532, retro_nleu_1732, retro_nleu_1886, retro_nleu_2049, retro_nleu_2143, retro_nleu_2162, retro_nleu_2163, retro_nleu_2281, retro_nleu_2356, retro_nleu_2357, retro_nleu_2358, retro_nleu_2359, retro_nleu_2360, retro_nleu_2361, retro_nleu_2417, retro_nleu_2433, retro_nleu_2962, retro_nleu_303, retro_nleu_383, retro_nleu_72, retro_nleu_738, retro_nleu_747, retro_nleu_78, retro_nleu_936,
Oryctolagus cuniculus	ENSOCUG00000014108	4 retrocopies	retro_ocun_1172, retro_ocun_1179, retro_ocun_1598, retro_ocun_93,
Otolemur garnettii	ENSOGAG00000025354	9 retrocopies	retro_ogar_1065, retro_ogar_1198, retro_ogar_1518, retro_ogar_2010, retro_ogar_2099, retro_ogar_2349, retro_ogar_2661, retro_ogar_2747, retro_ogar_3380,
Ochotona princeps	ENSOPRG00000010734	7 retrocopies	retro_opri_1219, retro_opri_292, retro_opri_558, retro_opri_689, retro_opri_816, retro_opri_818, retro_opri_936,
Procavia capensis	ENSPCAG00000010377	13 retrocopies	retro_pcap_177, retro_pcap_217, retro_pcap_248, retro_pcap_276, retro_pcap_344, retro_pcap_348, retro_pcap_374, retro_pcap_379, retro_pcap_383, retro_pcap_395, retro_pcap_447, retro_pcap_5, retro_pcap_62,
Pongo abelii	ENSPPYG00000003173	12 retrocopies	retro_pabe_1034, retro_pabe_1186, retro_pabe_2410, retro_pabe_2483, retro_pabe_2484, retro_pabe_249, retro_pabe_3351, retro_pabe_3406, retro_pabe_35, retro_pabe_3713, retro_pabe_47, retro_pabe_479,
Pteropus vampyrus	ENSPVAG00000013038	3 retrocopies	retro_pvam_1006, retro_pvam_136, retro_pvam_5,
Rattus norvegicus	ENSRNOG00000022619	9 retrocopies	retro_rnor_1197, retro_rnor_1280, retro_rnor_1356, retro_rnor_1832, retro_rnor_2060, retro_rnor_2163, retro_rnor_264, retro_rnor_427, retro_rnor_71,
Sus scrofa	ENSSSCG00000003153	33 retrocopies	retro_sscr_1040, retro_sscr_1095, retro_sscr_1101, retro_sscr_1142, retro_sscr_1189, retro_sscr_1214, retro_sscr_1215, retro_sscr_124, retro_sscr_197, retro_sscr_212, retro_sscr_224, retro_sscr_305, retro_sscr_331, retro_sscr_400, retro_sscr_531, retro_sscr_532, retro_sscr_533, retro_sscr_534, retro_sscr_535, retro_sscr_536, retro_sscr_559, retro_sscr_589, retro_sscr_605, retro_sscr_74, retro_sscr_747, retro_sscr_799, retro_sscr_817, retro_sscr_830, retro_sscr_833, retro_sscr_839, retro_sscr_840, retro_sscr_862, retro_sscr_898,
Sus scrofa	ENSSSCG00000014540	9 retrocopies	retro_sscr_1045, retro_sscr_168, retro_sscr_286, retro_sscr_359, retro_sscr_498 , retro_sscr_581, retro_sscr_78, retro_sscr_906, retro_sscr_949,
Ictidomys tridecemlineatus	ENSSTOG00000014521	1 retrocopy	retro_itri_250,
Vicugna pacos	ENSVPAG00000003956	6 retrocopies	retro_vpac_233, retro_vpac_300, retro_vpac_370, retro_vpac_505, retro_vpac_515, retro_vpac_643,