RetrogeneDB ID: retro_sscr_1188

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:34866004..34866472(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000012217
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL21
• Ensembl ID: ENSSSCG00000009303
• Aliases: None
• Description: ribosomal protein L21 [Source:HGNC Symbol;Acc:10313]

Sequence

>retro_sscr_1188
ATGACCAACACAAAGGGAAAGAGGAGGGGCACTCTAGGCCTTTTAGAAAACATGGACTTGTTCCTTTGGCTGCATACACA
CAAATCTATAGTAAGAAAGGTAATATTGCAGACATCCAGGGAACAGGCACTGTTCAAAAAGGAATGTCGCACAAATGTTT
CCATGGCAAAAGCGGAAGAGTCTACAATGTAACCCAGCATGCTACTGGCACTGCTGTAAACAAACAAGCTGAGGGCCAGA
TTCTTGCCAGAGCATTAATGTGCCTAGTGAGCATATTAAGCACTCTAAGAGCCAAGGCAACTTCCTGAAACATGTGAAGG
AAAATGATCAGAAAAAGAAGGAAGCCAAAGAGAAAGGTACTTGGGTTCAGCTCAAGAGCCAGCCTGCTCCACTCAGAGAA
GCACCCCTCGGGAAAACCAAGGGAAAGGAGCCTGAGCTGTTGGAACCCAATCCCATGAATTCGTGGCA

Alignment

ORF - retro_sscr_1188 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.95 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MTNTK-GKRRGTRYMFSRPFRKHGVVPLATYMRIY-KKGDIVDIKGMGTVQKGMPHKCYHGKTGRVYNVT
          MTNTK.GK..G.....SRPFRKHG.VPLA.Y..IY.KKG.I.DI.G.GTVQKGM.HKC.HGK.GRVYNVT
Retrocopy MTNTK<GKEEG----HSRPFRKHGLVPLAAYTQIYSKKGNIADIQGTGTVQKGMSHKCFHGKSGRVYNVT

Parental  QHAVGIVVNKQVKGKILAKR-INVRIEHIKHSKSRDSFLKRVKENDQKKKEAKEKGTWVQLKRQPAPPRE
          QHA.G..VNKQ..G.ILA...INV..EHIKHSKS...FLK.VKENDQKKKEAKEKGTWVQLK.QPAP.RE
Retrocopy QHATGTAVNKQAEGQILARA<INVPSEHIKHSKSQGNFLKHVKENDQKKKEAKEKGTWVQLKSQPAPLRE

Parental  AHFVRTNGKEPELLEPIP-YEFMA
          A....T.GKEPELLEP.P..EF.A
Retrocopy APLGKTKGKEPELLEPNP<HEFVA

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	78.71 RPM
SRP014902_testis	0.00 RPM	260.12 RPM
SRP018288_heart	0.00 RPM	401.86 RPM
SRP018288_kidney	0.00 RPM	331.87 RPM
SRP018288_liver	0.00 RPM	309.27 RPM
SRP018288_lung	0.00 RPM	406.69 RPM
SRP018856_adipose	0.00 RPM	620.58 RPM
SRP035408_brain	0.16 RPM	438.42 RPM
SRP035408_liver	0.23 RPM	389.99 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1188 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1188 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1188 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 275 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001648	5 retrocopies	retro_btau_1383, retro_btau_194, retro_btau_209, retro_btau_93, retro_btau_976,
Callithrix jacchus	ENSCJAG00000019355	1 retrocopy	retro_cjac_152,
Cavia porcellus	ENSCPOG00000008784	3 retrocopies	retro_cpor_2, retro_cpor_26, retro_cpor_41,
Felis catus	ENSFCAG00000006750	1 retrocopy	retro_fcat_64,
Latimeria chalumnae	ENSLACG00000012678	1 retrocopy	retro_lcha_32,
Loxodonta africana	ENSLAFG00000003677	11 retrocopies	retro_lafr_1167, retro_lafr_308, retro_lafr_331, retro_lafr_583, retro_lafr_63, retro_lafr_652, retro_lafr_738, retro_lafr_740, retro_lafr_856, retro_lafr_89, retro_lafr_97,
Microcebus murinus	ENSMICG00000014754	54 retrocopies	retro_mmur_1011, retro_mmur_1019, retro_mmur_1078, retro_mmur_1200, retro_mmur_1232, retro_mmur_1276, retro_mmur_1293, retro_mmur_1329, retro_mmur_1337, retro_mmur_1348, retro_mmur_1395, retro_mmur_1448, retro_mmur_1451, retro_mmur_146, retro_mmur_1464, retro_mmur_1524, retro_mmur_1533, retro_mmur_1587, retro_mmur_1598, retro_mmur_1616, retro_mmur_1623, retro_mmur_1632, retro_mmur_177, retro_mmur_234, retro_mmur_251, retro_mmur_296, retro_mmur_310, retro_mmur_328, retro_mmur_385, retro_mmur_405, retro_mmur_418, retro_mmur_434, retro_mmur_437, retro_mmur_438, retro_mmur_478, retro_mmur_489, retro_mmur_539, retro_mmur_541, retro_mmur_547, retro_mmur_627, retro_mmur_645, retro_mmur_655, retro_mmur_719, retro_mmur_73, retro_mmur_774, retro_mmur_790, retro_mmur_801, retro_mmur_805, retro_mmur_847, retro_mmur_865, retro_mmur_867, retro_mmur_869, retro_mmur_94, retro_mmur_964,
Myotis lucifugus	ENSMLUG00000010093	46 retrocopies	retro_mluc_1066, retro_mluc_1079, retro_mluc_1138, retro_mluc_1164, retro_mluc_1171, retro_mluc_1219, retro_mluc_1274, retro_mluc_1279, retro_mluc_1307, retro_mluc_1323, retro_mluc_1379, retro_mluc_1382, retro_mluc_1409, retro_mluc_1413, retro_mluc_1469, retro_mluc_1481, retro_mluc_1525, retro_mluc_162, retro_mluc_1647, retro_mluc_1753, retro_mluc_1803, retro_mluc_1849, retro_mluc_1862, retro_mluc_1929, retro_mluc_1969, retro_mluc_1981, retro_mluc_2044, retro_mluc_2077, retro_mluc_2109, retro_mluc_2121, retro_mluc_2212, retro_mluc_230, retro_mluc_2335, retro_mluc_2338, retro_mluc_2436, retro_mluc_2592, retro_mluc_27, retro_mluc_279, retro_mluc_360, retro_mluc_503, retro_mluc_554, retro_mluc_620, retro_mluc_631, retro_mluc_806, retro_mluc_961, retro_mluc_97,
Macaca mulatta	ENSMMUG00000023368	2 retrocopies	retro_mmul_288, retro_mmul_45,
Monodelphis domestica	ENSMODG00000008923	1 retrocopy	retro_mdom_156,
Mus musculus	ENSMUSG00000041453	101 retrocopies	retro_mmus_1012, retro_mmus_1046, retro_mmus_1057, retro_mmus_1083, retro_mmus_1123, retro_mmus_1199, retro_mmus_1287, retro_mmus_1354, retro_mmus_1461, retro_mmus_1475, retro_mmus_1529, retro_mmus_1561, retro_mmus_1572, retro_mmus_1596, retro_mmus_1617, retro_mmus_1641, retro_mmus_1644, retro_mmus_17, retro_mmus_1714, retro_mmus_1739, retro_mmus_1762, retro_mmus_1797, retro_mmus_1848, retro_mmus_1860, retro_mmus_1862, retro_mmus_1875, retro_mmus_1897, retro_mmus_1915, retro_mmus_1931, retro_mmus_1936, retro_mmus_1994, retro_mmus_2042, retro_mmus_2049, retro_mmus_2101, retro_mmus_2130, retro_mmus_2176, retro_mmus_2179, retro_mmus_2185, retro_mmus_2214, retro_mmus_2233, retro_mmus_2237, retro_mmus_2238, retro_mmus_2279, retro_mmus_2309, retro_mmus_2312, retro_mmus_2335, retro_mmus_2344, retro_mmus_2395, retro_mmus_2447, retro_mmus_2517, retro_mmus_2567, retro_mmus_2585, retro_mmus_2598, retro_mmus_266, retro_mmus_2662, retro_mmus_2698, retro_mmus_2707, retro_mmus_2778, retro_mmus_2808, retro_mmus_2853, retro_mmus_2874, retro_mmus_2945, retro_mmus_2980, retro_mmus_3035, retro_mmus_3055, retro_mmus_3085, retro_mmus_3103, retro_mmus_3112, retro_mmus_3220, retro_mmus_3252, retro_mmus_3261, retro_mmus_3295, retro_mmus_3318, retro_mmus_3328, retro_mmus_333, retro_mmus_3341, retro_mmus_3446, retro_mmus_3545, retro_mmus_3581, retro_mmus_3712, retro_mmus_397, retro_mmus_400, retro_mmus_401, retro_mmus_598, retro_mmus_601, retro_mmus_606, retro_mmus_663, retro_mmus_734, retro_mmus_735, retro_mmus_758, retro_mmus_782, retro_mmus_806, retro_mmus_835, retro_mmus_862, retro_mmus_883, retro_mmus_918, retro_mmus_932, retro_mmus_940, retro_mmus_957, retro_mmus_993, retro_mmus_998,
Nomascus leucogenys	ENSNLEG00000000327	6 retrocopies	retro_nleu_112, retro_nleu_1144, retro_nleu_26, retro_nleu_713, retro_nleu_95, retro_nleu_951,
Oryctolagus cuniculus	ENSOCUG00000002506	10 retrocopies	retro_ocun_104, retro_ocun_122, retro_ocun_125, retro_ocun_159, retro_ocun_163, retro_ocun_186, retro_ocun_198, retro_ocun_209, retro_ocun_232, retro_ocun_86,
Rattus norvegicus	ENSRNOG00000000957	13 retrocopies	retro_rnor_227, retro_rnor_298, retro_rnor_319, retro_rnor_329, retro_rnor_330, retro_rnor_333, retro_rnor_365, retro_rnor_366, retro_rnor_416, retro_rnor_5, retro_rnor_79, retro_rnor_81, retro_rnor_82,
Sarcophilus harrisii	ENSSHAG00000000845	11 retrocopies	retro_shar_224, retro_shar_446, retro_shar_499, retro_shar_531, retro_shar_534, retro_shar_601, retro_shar_664, retro_shar_67, retro_shar_683, retro_shar_729, retro_shar_757,
Sus scrofa	ENSSSCG00000009303	9 retrocopies	retro_sscr_1144, retro_sscr_1188 , retro_sscr_336, retro_sscr_343, retro_sscr_624, retro_sscr_674, retro_sscr_741, retro_sscr_837, retro_sscr_863,