RetrogeneDB ID: retro_sscr_723

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 3:13442433..13442782(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS16
• Ensembl ID: ENSSSCG00000020817
• Aliases: None
• Description: Sus scrofa ribosomal protein S16 (RPS16), mRNA. [Source:RefSeq mRNA;Acc:NM_001137620]

Sequence

>retro_sscr_723
ATGCTGTCCAAGGGCCCTCCACCGTTGGTGCAGGTCTTTGGACGCAAAAAGACATCCACAGCCGTGGGGCACTGCACACG
AGGTAATGGCCTCATCCAAGTGAAAGGGTGGCCCCCGGAGATGATCAAACCACACAGGCTGCAGTACAAGCTTCTGGAAC
CTTTTCTGCTTCTGGGCAAGGAGTGGTTTGCTGGTGTGCACATCCTCGACTGAGTGAAGGGTGGCGGTCACGTGGCCCAG
ATTTACGCAACCTGCCAGTCCATCTCCGAAGCCTTGGTGGCCTATTACCAGAAATAACATGGACGAGGCTTCCAAGGAGG
AGATCAAAGACATCCCCATCCTGTATGAC

Alignment

ORF - retro_sscr_723 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.21 %
• Parental protein coverage: 79.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPSKGPLQSVQVFGRKKTATAVAHCKRGNGLIKVNGRPLEMIEPRTLQYKLLEPVLLLGKERFAGVDIRV
          M.SKGP...VQVFGRKKT.TAV.HC.RGNGLI.V.G.P.EMI.P..LQYKLLEP.LLLGKE.FAGV.I..
Retrocopy MLSKGPPPLVQVFGRKKTSTAVGHCTRGNGLIQVKGWPPEMIKPHRLQYKLLEPFLLLGKEWFAGVHILD

Parental  RVKGGGHVAQIYAIRQSISKALVAYYQK-YVDEASKKEIKDILIQYD
          .VKGGGHVAQIYA..QSIS.ALVAYYQK...DEASK.EIKDI.I.YD
Retrocopy *VKGGGHVAQIYATCQSISEALVAYYQK>NMDEASKEEIKDIPILYD

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	277.41 RPM
SRP014902_testis	0.00 RPM	297.04 RPM
SRP018288_heart	0.00 RPM	147.37 RPM
SRP018288_kidney	0.00 RPM	154.16 RPM
SRP018288_liver	0.00 RPM	120.57 RPM
SRP018288_lung	0.00 RPM	244.89 RPM
SRP018856_adipose	0.00 RPM	383.58 RPM
SRP035408_brain	0.00 RPM	30.20 RPM
SRP035408_liver	0.00 RPM	28.59 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_723 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_723 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_723 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 32 parental genes, and 141 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014176	1 retrocopy	retro_acar_194,
Bos taurus	ENSBTAG00000021093	3 retrocopies	retro_btau_1509, retro_btau_167, retro_btau_441,
Canis familiaris	ENSCAFG00000005501	6 retrocopies	retro_cfam_1349, retro_cfam_1754, retro_cfam_2142, retro_cfam_2147, retro_cfam_799, retro_cfam_908,
Callithrix jacchus	ENSCJAG00000014170	6 retrocopies	retro_cjac_2641, retro_cjac_2737, retro_cjac_3019, retro_cjac_885, retro_cjac_905, retro_cjac_949,
Cavia porcellus	ENSCPOG00000011359	3 retrocopies	retro_cpor_1266, retro_cpor_1408, retro_cpor_1515,
Dasypus novemcinctus	ENSDNOG00000001527	3 retrocopies	retro_dnov_2260, retro_dnov_2315, retro_dnov_308,
Equus caballus	ENSECAG00000004311	2 retrocopies	retro_ecab_186, retro_ecab_779,
Echinops telfairi	ENSETEG00000015290	4 retrocopies	retro_etel_1825, retro_etel_1834, retro_etel_193, retro_etel_351,
Felis catus	ENSFCAG00000010743	4 retrocopies	retro_fcat_1258, retro_fcat_1709, retro_fcat_1806, retro_fcat_1976,
Homo sapiens	ENSG00000105193	11 retrocopies	retro_hsap_118, retro_hsap_1658, retro_hsap_1736, retro_hsap_1977, retro_hsap_2064, retro_hsap_2230, retro_hsap_2327, retro_hsap_3593, retro_hsap_4209, retro_hsap_787, retro_hsap_813,
Gorilla gorilla	ENSGGOG00000014414	10 retrocopies	retro_ggor_110, retro_ggor_1250, retro_ggor_1344, retro_ggor_1664, retro_ggor_1766, retro_ggor_193, retro_ggor_2423, retro_ggor_2819, retro_ggor_652, retro_ggor_667,
Loxodonta africana	ENSLAFG00000001541	1 retrocopy	retro_lafr_1191,
Macropus eugenii	ENSMEUG00000010380	2 retrocopies	retro_meug_1306, retro_meug_612,
Microcebus murinus	ENSMICG00000006110	4 retrocopies	retro_mmur_1006, retro_mmur_1058, retro_mmur_375, retro_mmur_798,
Myotis lucifugus	ENSMLUG00000029089	5 retrocopies	retro_mluc_1906, retro_mluc_2096, retro_mluc_2174, retro_mluc_2529, retro_mluc_481,
Macaca mulatta	ENSMMUG00000019370	8 retrocopies	retro_mmul_1018, retro_mmul_1080, retro_mmul_1175, retro_mmul_1219, retro_mmul_1403, retro_mmul_20, retro_mmul_767, retro_mmul_862,
Monodelphis domestica	ENSMODG00000013545	4 retrocopies	retro_mdom_1668, retro_mdom_1823, retro_mdom_815, retro_mdom_856,
Mustela putorius furo	ENSMPUG00000017722	5 retrocopies	retro_mputfur_283, retro_mputfur_322, retro_mputfur_447, retro_mputfur_701, retro_mputfur_985,
Mus musculus	ENSMUSG00000037563	11 retrocopies	retro_mmus_1780, retro_mmus_2058, retro_mmus_2125, retro_mmus_2697, retro_mmus_2727, retro_mmus_3091, retro_mmus_3173, retro_mmus_3198, retro_mmus_3202, retro_mmus_700, retro_mmus_771,
Nomascus leucogenys	ENSNLEG00000014388	3 retrocopies	retro_nleu_1266, retro_nleu_248, retro_nleu_46,
Oryctolagus cuniculus	ENSOCUG00000002150	14 retrocopies	retro_ocun_1028, retro_ocun_1073, retro_ocun_1394, retro_ocun_1430, retro_ocun_1436, retro_ocun_1774, retro_ocun_371, retro_ocun_580, retro_ocun_632, retro_ocun_645, retro_ocun_670, retro_ocun_837, retro_ocun_906, retro_ocun_986,
Otolemur garnettii	ENSOGAG00000004497	4 retrocopies	retro_ogar_1229, retro_ogar_1309, retro_ogar_1313, retro_ogar_98,
Oreochromis niloticus	ENSONIG00000000006	1 retrocopy	retro_onil_52,
Pelodiscus sinensis	ENSPSIG00000016930	1 retrocopy	retro_psin_55,
Pan troglodytes	ENSPTRG00000010970	11 retrocopies	retro_ptro_1223, retro_ptro_1318, retro_ptro_1376, retro_ptro_1577, retro_ptro_1699, retro_ptro_2432, retro_ptro_2857, retro_ptro_2953, retro_ptro_2957, retro_ptro_548, retro_ptro_565,
Rattus norvegicus	ENSRNOG00000019578	3 retrocopies	retro_rnor_10, retro_rnor_1823, retro_rnor_302,
Sorex araneus	ENSSARG00000000852	1 retrocopy	retro_sara_595,
Sus scrofa	ENSSSCG00000010712	1 retrocopy	retro_sscr_731,
Sus scrofa	ENSSSCG00000020817	3 retrocopies	retro_sscr_478, retro_sscr_5, retro_sscr_723 ,
Ictidomys tridecemlineatus	ENSSTOG00000006794	1 retrocopy	retro_itri_321,
Tarsius syrichta	ENSTSYG00000005241	4 retrocopies	retro_tsyr_1115, retro_tsyr_1208, retro_tsyr_1492, retro_tsyr_1780,
Tursiops truncatus	ENSTTRG00000003571	1 retrocopy	retro_ttru_202,