RetrogeneDB ID: retro_sscr_353

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:188482132..188482526(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS8
• Ensembl ID: ENSSSCG00000003930
• Aliases: None
• Description: ribosomal protein S8 [Source:HGNC Symbol;Acc:10441]

Sequence

>retro_sscr_353
CGCAAGACGAGGATTATTGATATTGTGTGCAGTGCATCCAACAATGAACTGCTCTGTGCCAAGGCCCTGGTGAAAAACTG
CATCATGCTCATTTCCAGCACACCGTACCAACAGTGGTACGAGTCCCACTCTGCCCTGCCCCTGGGCCGCCAGAAGGGGG
CCAAGCTGACTCCTGAGGAGGAAGAGATTTTAAACCAAAAGCAATGAAAGAAAATTTAGTAAGTATGACAAAAGGAAAAA
GAATGCCCAAATCAGCAGTCTCCTAGAGGAGCAGTTCAAGCAGGGCAAGCTTCTTGCATGCATGACTTCAAGACCAGACA
GAGCAGATGGCTCTTCTCTAGAGGGCAAGGAGCTATAGTTCTATCTGAGAAAAATCAAGGTCTAGAAAGGCAAA

Alignment

ORF - retro_sscr_353 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.38 %
• Parental protein coverage: 64.9 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALPLGRKKGAKLTPEEEEILNKKRSK
          RKTRIID.V..ASNNEL...K.LVKNCI.LI.STPY.QWYESH.ALPLGR.KGAKLTPEEEEILN.K..K
Retrocopy RKTRIIDIVCSASNNELLCAKALVKNCIMLISSTPYQQWYESHSALPLGRQKGAKLTPEEEEILNQKQ*K

Parental  KI-QKKYDERKKNAKISSLLEEQFQQGKLLACIASRPGQCGRADGYVLEGKELEFYLRKIKARKGK
          KI..K.....K.....S.L.E..F.QGKLLAC..SRP....RADG..LEGKEL.FYLRKIK..KGK
Retrocopy KI>SKYDKRKKNAQISSLLEEQ-FKQGKLLACMTSRP---DRADGSSLEGKEL*FYLRKIKV*KGK

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	1463.63 RPM
SRP014902_testis	0.00 RPM	1361.14 RPM
SRP018288_heart	0.00 RPM	687.58 RPM
SRP018288_kidney	0.00 RPM	536.86 RPM
SRP018288_liver	0.00 RPM	556.33 RPM
SRP018288_lung	0.00 RPM	667.98 RPM
SRP018856_adipose	0.00 RPM	3099.43 RPM
SRP035408_brain	0.10 RPM	769.65 RPM
SRP035408_liver	0.03 RPM	753.56 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_353 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_353 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_353 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 121 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014147	3 retrocopies	retro_amel_1883, retro_amel_373, retro_amel_972,
Canis familiaris	ENSCAFG00000004745	8 retrocopies	retro_cfam_1336, retro_cfam_1662, retro_cfam_1730, retro_cfam_2139, retro_cfam_2177, retro_cfam_261, retro_cfam_589, retro_cfam_791,
Callithrix jacchus	ENSCJAG00000004197	5 retrocopies	retro_cjac_1068, retro_cjac_181, retro_cjac_3138, retro_cjac_6, retro_cjac_951,
Dipodomys ordii	ENSDORG00000009287	1 retrocopy	retro_dord_429,
Felis catus	ENSFCAG00000022996	4 retrocopies	retro_fcat_1222, retro_fcat_200, retro_fcat_456, retro_fcat_962,
Gorilla gorilla	ENSGGOG00000005645	5 retrocopies	retro_ggor_1127, retro_ggor_1170, retro_ggor_1357, retro_ggor_1465, retro_ggor_556,
Macropus eugenii	ENSMEUG00000001388	1 retrocopy	retro_meug_119,
Myotis lucifugus	ENSMLUG00000001559	30 retrocopies	retro_mluc_1114, retro_mluc_1132, retro_mluc_1165, retro_mluc_1277, retro_mluc_1288, retro_mluc_1418, retro_mluc_1467, retro_mluc_1476, retro_mluc_1486, retro_mluc_1634, retro_mluc_1656, retro_mluc_1689, retro_mluc_1808, retro_mluc_1911, retro_mluc_1938, retro_mluc_2043, retro_mluc_2055, retro_mluc_2085, retro_mluc_2111, retro_mluc_2153, retro_mluc_2182, retro_mluc_2209, retro_mluc_2414, retro_mluc_460, retro_mluc_662, retro_mluc_730, retro_mluc_773, retro_mluc_820, retro_mluc_821, retro_mluc_906,
Macaca mulatta	ENSMMUG00000015270	2 retrocopies	retro_mmul_275, retro_mmul_70,
Mustela putorius furo	ENSMPUG00000013485	6 retrocopies	retro_mputfur_334, retro_mputfur_337, retro_mputfur_493, retro_mputfur_780, retro_mputfur_908, retro_mputfur_986,
Nomascus leucogenys	ENSNLEG00000014147	1 retrocopy	retro_nleu_34,
Oryctolagus cuniculus	ENSOCUG00000012476	1 retrocopy	retro_ocun_168,
Otolemur garnettii	ENSOGAG00000006922	16 retrocopies	retro_ogar_1156, retro_ogar_1746, retro_ogar_1895, retro_ogar_2501, retro_ogar_2529, retro_ogar_2556, retro_ogar_2699, retro_ogar_2723, retro_ogar_2947, retro_ogar_308, retro_ogar_3291, retro_ogar_3436, retro_ogar_394, retro_ogar_521, retro_ogar_730, retro_ogar_805,
Pongo abelii	ENSPPYG00000001426	1 retrocopy	retro_pabe_147,
Pan troglodytes	ENSPTRG00000000659	1 retrocopy	retro_ptro_30,
Rattus norvegicus	ENSRNOG00000018768	2 retrocopies	retro_rnor_222, retro_rnor_235,
Sarcophilus harrisii	ENSSHAG00000000111	5 retrocopies	retro_shar_408, retro_shar_472, retro_shar_480, retro_shar_636, retro_shar_667,
Sus scrofa	ENSSSCG00000003930	4 retrocopies	retro_sscr_353 , retro_sscr_550, retro_sscr_607, retro_sscr_919,
Tupaia belangeri	ENSTBEG00000000418	20 retrocopies	retro_tbel_1066, retro_tbel_1537, retro_tbel_1538, retro_tbel_163, retro_tbel_1699, retro_tbel_2356, retro_tbel_244, retro_tbel_2580, retro_tbel_3058, retro_tbel_3230, retro_tbel_3478, retro_tbel_3905, retro_tbel_3950, retro_tbel_4241, retro_tbel_4250, retro_tbel_4530, retro_tbel_552, retro_tbel_803, retro_tbel_827, retro_tbel_934,
Tarsius syrichta	ENSTSYG00000005525	5 retrocopies	retro_tsyr_1412, retro_tsyr_1507, retro_tsyr_2176, retro_tsyr_552, retro_tsyr_734,