RetrogeneDB ID: retro_sscr_408

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 14:21591651..21591954(+)
• Located in intron of: ENSSSCG00000009714

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS17
• Ensembl ID: ENSSSCG00000027358
• Aliases: None
• Description: Sus scrofa ribosomal protein S17 (RPS17), mRNA. [Source:RefSeq mRNA;Acc:NM_001001634]

Sequence

>retro_sscr_408
TGCGAGGAGATTGCCATTATTTCCAGCAAGAAGCTCTGCAATAAGATCGCAGGCTATGTCACACATCTGATGAAGCGGAT
TCAGAGAGGACCAGTGAGAGATATCTCCATCAAGCTGCAGGAGGAGGAGAGAGAGAGGAGAGATAACTATGTGCCTGAGG
TCTCAGCCCTGGATCAGGAGATCATTGAAGTAGATCCTGACACTAAGGAGATGCTGAAACTCTTGGACTTTAGCGGTCTG
TCCAACCTGCAAGTCACTCAGCCTACAGTTGCGATGAATTTCAAAACACCACGTGGAGCCGTT

Alignment

ORF - retro_sscr_408 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.15 %
• Parental protein coverage: 74.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CEEIAIIPSKKLRNKIAGYVTHLMKRIQRGPVRGISIKLQEEERERRDNYVPEVSALDQEIIEVDPDTKE
          CEEIAII.SKKL.NKIAGYVTHLMKRIQRGPVR.ISIKL.........NYVPEVSALDQEIIEVDPDTKE
Retrocopy CEEIAIISSKKLCNKIAGYVTHLMKRIQRGPVRDISIKLXXXXXXXXXNYVPEVSALDQEIIEVDPDTKE

Parental  MLKLLDFGSLSNLQVTQPTVGMNFKTPRGAV
          MLKLLDF..LSNLQVTQPTV.MNFKTPRGAV
Retrocopy MLKLLDFSGLSNLQVTQPTVAMNFKTPRGAV

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	0.27 RPM	466.28 RPM
SRP014902_testis	2.83 RPM	1446.43 RPM
SRP018288_heart	0.00 RPM	425.38 RPM
SRP018288_kidney	0.20 RPM	391.66 RPM
SRP018288_liver	0.00 RPM	341.73 RPM
SRP018288_lung	0.10 RPM	469.21 RPM
SRP018856_adipose	0.06 RPM	1145.77 RPM
SRP035408_brain	0.13 RPM	484.41 RPM
SRP035408_liver	0.15 RPM	557.61 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_408 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_408 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_408 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 149 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012225	4 retrocopies	retro_acar_128, retro_acar_154, retro_acar_177, retro_acar_81,
Bos taurus	ENSBTAG00000000622	4 retrocopies	retro_btau_1014, retro_btau_568, retro_btau_731, retro_btau_884,
Canis familiaris	ENSCAFG00000013053	9 retrocopies	retro_cfam_1032, retro_cfam_1234, retro_cfam_1680, retro_cfam_1707, retro_cfam_217, retro_cfam_240, retro_cfam_307, retro_cfam_491, retro_cfam_82,
Dasypus novemcinctus	ENSDNOG00000012633	6 retrocopies	retro_dnov_1183, retro_dnov_1296, retro_dnov_2140, retro_dnov_2636, retro_dnov_416, retro_dnov_673,
Equus caballus	ENSECAG00000024902	1 retrocopy	retro_ecab_92,
Echinops telfairi	ENSETEG00000008035	10 retrocopies	retro_etel_1279, retro_etel_1375, retro_etel_1501, retro_etel_1658, retro_etel_1950, retro_etel_592, retro_etel_619, retro_etel_673, retro_etel_851, retro_etel_984,
Felis catus	ENSFCAG00000002358	7 retrocopies	retro_fcat_1060, retro_fcat_1354, retro_fcat_1419, retro_fcat_1549, retro_fcat_288, retro_fcat_436, retro_fcat_710,
Homo sapiens	ENSG00000182774	11 retrocopies	retro_hsap_1516, retro_hsap_1743, retro_hsap_2150, retro_hsap_2702, retro_hsap_3172, retro_hsap_3477, retro_hsap_3570, retro_hsap_3588, retro_hsap_3719, retro_hsap_464, retro_hsap_925,
Homo sapiens	ENSG00000184779	5 retrocopies	retro_hsap_2559, retro_hsap_2854, retro_hsap_3233, retro_hsap_3909, retro_hsap_4110,
Myotis lucifugus	ENSMLUG00000022830	3 retrocopies	retro_mluc_1202, retro_mluc_1347, retro_mluc_1949,
Macaca mulatta	ENSMMUG00000011327	6 retrocopies	retro_mmul_116, retro_mmul_194, retro_mmul_200, retro_mmul_266, retro_mmul_67, retro_mmul_99,
Monodelphis domestica	ENSMODG00000002011	9 retrocopies	retro_mdom_1482, retro_mdom_1923, retro_mdom_1928, retro_mdom_330, retro_mdom_342, retro_mdom_422, retro_mdom_425, retro_mdom_645, retro_mdom_762,
Mus musculus	ENSMUSG00000061787	12 retrocopies	retro_mmus_1095, retro_mmus_1396, retro_mmus_1630, retro_mmus_2457, retro_mmus_2805, retro_mmus_2852, retro_mmus_3382, retro_mmus_3608, retro_mmus_549, retro_mmus_697, retro_mmus_909, retro_mmus_972,
Oryctolagus cuniculus	ENSOCUG00000006370	1 retrocopy	retro_ocun_90,
Otolemur garnettii	ENSOGAG00000024107	16 retrocopies	retro_ogar_1342, retro_ogar_14, retro_ogar_1632, retro_ogar_174, retro_ogar_1902, retro_ogar_2146, retro_ogar_2221, retro_ogar_2392, retro_ogar_2547, retro_ogar_2686, retro_ogar_2744, retro_ogar_3059, retro_ogar_439, retro_ogar_579, retro_ogar_647, retro_ogar_752,
Ochotona princeps	ENSOPRG00000004728	7 retrocopies	retro_opri_108, retro_opri_189, retro_opri_27, retro_opri_616, retro_opri_802, retro_opri_901, retro_opri_926,
Procavia capensis	ENSPCAG00000006035	3 retrocopies	retro_pcap_164, retro_pcap_439, retro_pcap_72,
Pongo abelii	ENSPPYG00000006888	3 retrocopies	retro_pabe_108, retro_pabe_194, retro_pabe_72,
Pteropus vampyrus	ENSPVAG00000012022	8 retrocopies	retro_pvam_1172, retro_pvam_1263, retro_pvam_332, retro_pvam_411, retro_pvam_413, retro_pvam_603, retro_pvam_739, retro_pvam_823,
Rattus norvegicus	ENSRNOG00000019106	6 retrocopies	retro_rnor_19, retro_rnor_23, retro_rnor_276, retro_rnor_285, retro_rnor_289, retro_rnor_84,
Sorex araneus	ENSSARG00000013001	2 retrocopies	retro_sara_246, retro_sara_388,
Sarcophilus harrisii	ENSSHAG00000014004	10 retrocopies	retro_shar_174, retro_shar_203, retro_shar_230, retro_shar_312, retro_shar_326, retro_shar_376, retro_shar_392, retro_shar_500, retro_shar_647, retro_shar_702,
Sus scrofa	ENSSSCG00000027358	2 retrocopies	retro_sscr_408 , retro_sscr_91,
Ictidomys tridecemlineatus	ENSSTOG00000006298	2 retrocopies	retro_itri_769, retro_itri_841,
Tursiops truncatus	ENSTTRG00000013011	2 retrocopies	retro_ttru_1467, retro_ttru_683,