RetrogeneDB ID: retro_sscr_115

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:83324472..83324777(+)
• Located in intron of: ENSSSCG00000004382

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL23A
• Ensembl ID: ENSSSCG00000029802
• Aliases: None
• Description: ribosomal protein L23a [Source:HGNC Symbol;Acc:10317]

Sequence

>retro_sscr_115
ACCTTCTGGTGGCCCAAGACACTCCAAAGGCAGCCCAATTATGCTTGGAAGAGCAAGAATCTTAACAACTATGTCATCCT
CAAGTTCCCCCTGAGCACTGAGTGGCCAGGAAGGAGACAGAGACAGCAACACATTTGTGTTCATTAAGGATACCAAAGCC
AACAAGCACCAGAACAAACAGACTGTGAAGAAGCTCTACATCACTGATAAGGCCAAGGTCAACACCCTGGATCAGGCCTG
ATGGAGAGAAGAAAGTATATGTTTGACTGGTTCCTGACTATGATGCTTTGCATGTTGCCAAAAGA

Alignment

ORF - retro_sscr_115 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.06 %
• Parental protein coverage: 69.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TFRRPKTLRLRRQPKYPRKSAPRRNKLDHYAIIKFPLTTE-SAMKKIE-DNNTLVFIVDVKANKHQIKQA
          TF..PKTL...RQP.Y..KS......L..Y.I.KFPL.TE..A.K..E.D.NT.VFI.D.KANKHQ.KQ.
Retrocopy TFWWPKTLQ--RQPNYAWKS----KNLNNYVILKFPLSTE<VARKETE<DSNTFVFIKDTKANKHQNKQT

Parental  VKKLYDIDVAKVNTL-IRPDGEKKAYVRLAPDYDALDVANK
          VKKLY..D.AKVNTL.IRPDGEKK.YV.L.PDYDAL.VA..
Retrocopy VKKLYITDKAKVNTL>IRPDGEKKVYV*LVPDYDALHVAKR

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	1.99 RPM
SRP014902_testis	0.00 RPM	9.90 RPM
SRP018288_heart	0.03 RPM	0.79 RPM
SRP018288_kidney	0.00 RPM	3.94 RPM
SRP018288_liver	0.00 RPM	6.08 RPM
SRP018288_lung	0.10 RPM	1.93 RPM
SRP018856_adipose	0.00 RPM	0.52 RPM
SRP035408_brain	0.03 RPM	0.44 RPM
SRP035408_liver	0.00 RPM	0.53 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_115 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_115 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_115 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 313 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005311	2 retrocopies	retro_acar_152, retro_acar_173,
Bos taurus	ENSBTAG00000046394	6 retrocopies	retro_btau_132, retro_btau_159, retro_btau_169, retro_btau_178, retro_btau_237, retro_btau_8,
Dasypus novemcinctus	ENSDNOG00000019487	65 retrocopies	retro_dnov_1018, retro_dnov_1065, retro_dnov_1069, retro_dnov_1082, retro_dnov_1169, retro_dnov_120, retro_dnov_123, retro_dnov_1238, retro_dnov_127, retro_dnov_1283, retro_dnov_1365, retro_dnov_1460, retro_dnov_1514, retro_dnov_1538, retro_dnov_1541, retro_dnov_1597, retro_dnov_171, retro_dnov_1781, retro_dnov_1793, retro_dnov_1816, retro_dnov_183, retro_dnov_1835, retro_dnov_1837, retro_dnov_1873, retro_dnov_1926, retro_dnov_203, retro_dnov_2046, retro_dnov_2051, retro_dnov_2089, retro_dnov_2178, retro_dnov_2256, retro_dnov_2278, retro_dnov_2284, retro_dnov_2343, retro_dnov_2368, retro_dnov_246, retro_dnov_2493, retro_dnov_2563, retro_dnov_2573, retro_dnov_267, retro_dnov_372, retro_dnov_401, retro_dnov_429, retro_dnov_470, retro_dnov_499, retro_dnov_556, retro_dnov_581, retro_dnov_591, retro_dnov_611, retro_dnov_625, retro_dnov_636, retro_dnov_64, retro_dnov_67, retro_dnov_683, retro_dnov_704, retro_dnov_718, retro_dnov_731, retro_dnov_736, retro_dnov_749, retro_dnov_769, retro_dnov_813, retro_dnov_832, retro_dnov_903, retro_dnov_929, retro_dnov_972,
Gorilla gorilla	ENSGGOG00000016736	26 retrocopies	retro_ggor_1027, retro_ggor_1028, retro_ggor_1123, retro_ggor_120, retro_ggor_123, retro_ggor_1284, retro_ggor_140, retro_ggor_1431, retro_ggor_158, retro_ggor_1650, retro_ggor_1743, retro_ggor_1789, retro_ggor_1911, retro_ggor_1948, retro_ggor_2164, retro_ggor_2239, retro_ggor_2285, retro_ggor_229, retro_ggor_2409, retro_ggor_2475, retro_ggor_2568, retro_ggor_2764, retro_ggor_2773, retro_ggor_580, retro_ggor_611, retro_ggor_642,
Loxodonta africana	ENSLAFG00000013387	16 retrocopies	retro_lafr_1176, retro_lafr_153, retro_lafr_237, retro_lafr_33, retro_lafr_335, retro_lafr_442, retro_lafr_510, retro_lafr_525, retro_lafr_551, retro_lafr_557, retro_lafr_643, retro_lafr_78, retro_lafr_891, retro_lafr_908, retro_lafr_957, retro_lafr_96,
Myotis lucifugus	ENSMLUG00000012448	4 retrocopies	retro_mluc_175, retro_mluc_2375, retro_mluc_353, retro_mluc_91,
Monodelphis domestica	ENSMODG00000019297	3 retrocopies	retro_mdom_120, retro_mdom_870, retro_mdom_912,
Mustela putorius furo	ENSMPUG00000014179	12 retrocopies	retro_mputfur_102, retro_mputfur_106, retro_mputfur_123, retro_mputfur_159, retro_mputfur_168, retro_mputfur_179, retro_mputfur_3, retro_mputfur_333, retro_mputfur_42, retro_mputfur_52, retro_mputfur_599, retro_mputfur_91,
Mus musculus	ENSMUSG00000058546	8 retrocopies	retro_mmus_1, retro_mmus_126, retro_mmus_130, retro_mmus_184, retro_mmus_224, retro_mmus_64, retro_mmus_84, retro_mmus_95,
Nomascus leucogenys	ENSNLEG00000002872	60 retrocopies	retro_nleu_1004, retro_nleu_1216, retro_nleu_1273, retro_nleu_1290, retro_nleu_1398, retro_nleu_1448, retro_nleu_145, retro_nleu_1544, retro_nleu_158, retro_nleu_160, retro_nleu_161, retro_nleu_1775, retro_nleu_1782, retro_nleu_2004, retro_nleu_2010, retro_nleu_203, retro_nleu_211, retro_nleu_2115, retro_nleu_213, retro_nleu_2312, retro_nleu_2339, retro_nleu_2406, retro_nleu_2413, retro_nleu_2455, retro_nleu_2468, retro_nleu_2474, retro_nleu_2492, retro_nleu_2514, retro_nleu_2594, retro_nleu_2661, retro_nleu_2664, retro_nleu_2784, retro_nleu_2788, retro_nleu_2925, retro_nleu_2943, retro_nleu_2960, retro_nleu_2964, retro_nleu_3026, retro_nleu_3031, retro_nleu_3037, retro_nleu_3056, retro_nleu_3096, retro_nleu_3101, retro_nleu_3107, retro_nleu_3108, retro_nleu_3110, retro_nleu_3114, retro_nleu_3118, retro_nleu_3123, retro_nleu_3124, retro_nleu_328, retro_nleu_355, retro_nleu_356, retro_nleu_401, retro_nleu_473, retro_nleu_518, retro_nleu_641, retro_nleu_902, retro_nleu_938, retro_nleu_966,
Procavia capensis	ENSPCAG00000017002	30 retrocopies	retro_pcap_103, retro_pcap_122, retro_pcap_131, retro_pcap_187, retro_pcap_213, retro_pcap_215, retro_pcap_221, retro_pcap_233, retro_pcap_246, retro_pcap_279, retro_pcap_320, retro_pcap_321, retro_pcap_331, retro_pcap_336, retro_pcap_342, retro_pcap_347, retro_pcap_368, retro_pcap_372, retro_pcap_382, retro_pcap_390, retro_pcap_392, retro_pcap_396, retro_pcap_437, retro_pcap_450, retro_pcap_453, retro_pcap_460, retro_pcap_61, retro_pcap_70, retro_pcap_82, retro_pcap_96,
Pteropus vampyrus	ENSPVAG00000002922	32 retrocopies	retro_pvam_1002, retro_pvam_1004, retro_pvam_1083, retro_pvam_1113, retro_pvam_113, retro_pvam_1211, retro_pvam_1226, retro_pvam_1268, retro_pvam_1300, retro_pvam_1329, retro_pvam_1350, retro_pvam_1363, retro_pvam_1456, retro_pvam_159, retro_pvam_249, retro_pvam_385, retro_pvam_425, retro_pvam_436, retro_pvam_445, retro_pvam_511, retro_pvam_526, retro_pvam_537, retro_pvam_564, retro_pvam_593, retro_pvam_72, retro_pvam_729, retro_pvam_752, retro_pvam_840, retro_pvam_897, retro_pvam_927, retro_pvam_947, retro_pvam_95,
Sarcophilus harrisii	ENSSHAG00000014549	13 retrocopies	retro_shar_188, retro_shar_373, retro_shar_407, retro_shar_448, retro_shar_498, retro_shar_564, retro_shar_624, retro_shar_630, retro_shar_685, retro_shar_698, retro_shar_824, retro_shar_829, retro_shar_835,
Sus scrofa	ENSSSCG00000017768	9 retrocopies	retro_sscr_1025, retro_sscr_1047, retro_sscr_1133, retro_sscr_239, retro_sscr_356, retro_sscr_418, retro_sscr_598, retro_sscr_638, retro_sscr_952,
Sus scrofa	ENSSSCG00000029802	4 retrocopies	retro_sscr_115 , retro_sscr_170, retro_sscr_248, retro_sscr_430,
Ictidomys tridecemlineatus	ENSSTOG00000011328	23 retrocopies	retro_itri_1022, retro_itri_1035, retro_itri_1051, retro_itri_1059, retro_itri_1071, retro_itri_1150, retro_itri_1261, retro_itri_1327, retro_itri_1347, retro_itri_1460, retro_itri_1507, retro_itri_217, retro_itri_225, retro_itri_304, retro_itri_360, retro_itri_494, retro_itri_626, retro_itri_627, retro_itri_734, retro_itri_761, retro_itri_791, retro_itri_965, retro_itri_972,