RetrogeneDB ID: retro_sscr_289

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 11:81827715..81828106(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000016840
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000010328
• Aliases: LOC100155012, RPS24
• Description: 40S ribosomal protein S24 [Source:UniProtKB/TrEMBL;Acc:F1S2E5]

Sequence

>retro_sscr_289
ATGAATGACACAGCAACGATTGGGAGCAGGAAGTTCATGACCAACCAACCACTTGAGCAGAAACAAATGGTCATTGATGT
CCTTCACCCTGGGAAGGCAACAGTACCAAAGACAGAAATTCGGGAAAAACTAGCCAAAATGTACAAGACTACACCAGACA
TCATCTTTGTCTTTGGATTCAGAACCCATTTTTGTGGTGGCAAGGCAACCGGCTTTGGCCTGATTTATGATTCCTTGGAT
TACGCAAAGAAAAATGAGCCCAAACACAGCCTTGCAAGACACAGCTTGAATGAGAAGAGAAAGACCTCAAGAAAACAGAG
AAAAGAAGAAATCCAGGATGAAGAAATCCAGGGGAACTGCAAAGGCCAATGTTGGTGCTGGCAAAAAGAAG

Alignment

ORF - retro_sscr_289 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.06 %
• Parental protein coverage: 99.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNDTVTIRTRKFMTNRLLQRKQMVIDVLHPGKATVPKTEIREKLAKMYKTTPDVIFVFGFRTHFGGGKTT
          MNDT.TI..RKFMTN..L..KQMVIDVLHPGKATVPKTEIREKLAKMYKTTPD.IFVFGFRTHF.GGK.T
Retrocopy MNDTATIGSRKFMTNQPLEQKQMVIDVLHPGKATVPKTEIREKLAKMYKTTPDIIFVFGFRTHFCGGKAT

Parental  GFGMIYDSLDYAKKNEPKHRLARHGLYEKKKTSRKQRKERKNRMKKVRG-TAKANVGAGKKK
          GFG.IYDSLDYAKKNEPKH.LARH.L.EK.KTSRKQRKE.........G.TAKANVGAGKKK
Retrocopy GFGLIYDSLDYAKKNEPKHSLARHSLNEKRKTSRKQRKE-EIQDEEIQG>TAKANVGAGKKK

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	21.77 RPM	307.01 RPM
SRP014902_testis	4.81 RPM	543.58 RPM
SRP018288_heart	0.13 RPM	921.88 RPM
SRP018288_kidney	0.49 RPM	281.92 RPM
SRP018288_liver	0.16 RPM	248.50 RPM
SRP018288_lung	0.10 RPM	655.56 RPM
SRP018856_adipose	0.81 RPM	472.27 RPM
SRP035408_brain	0.67 RPM	1032.12 RPM
SRP035408_liver	31.59 RPM	794.19 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_289 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_289 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_289 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 100 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000010243	18 retrocopies	retro_dnov_1299, retro_dnov_1305, retro_dnov_1394, retro_dnov_1444, retro_dnov_1470, retro_dnov_1471, retro_dnov_168, retro_dnov_1889, retro_dnov_1920, retro_dnov_1985, retro_dnov_2074, retro_dnov_2357, retro_dnov_288, retro_dnov_309, retro_dnov_551, retro_dnov_73, retro_dnov_782, retro_dnov_92,
Dipodomys ordii	ENSDORG00000000189	4 retrocopies	retro_dord_248, retro_dord_498, retro_dord_717, retro_dord_766,
Equus caballus	ENSECAG00000016939	5 retrocopies	retro_ecab_239, retro_ecab_398, retro_ecab_422, retro_ecab_514, retro_ecab_746,
Echinops telfairi	ENSETEG00000007481	32 retrocopies	retro_etel_1119, retro_etel_1242, retro_etel_1274, retro_etel_1339, retro_etel_1395, retro_etel_1663, retro_etel_1688, retro_etel_1783, retro_etel_1800, retro_etel_1806, retro_etel_183, retro_etel_1901, retro_etel_1934, retro_etel_1978, retro_etel_1991, retro_etel_2040, retro_etel_2104, retro_etel_223, retro_etel_287, retro_etel_289, retro_etel_369, retro_etel_422, retro_etel_476, retro_etel_503, retro_etel_523, retro_etel_67, retro_etel_744, retro_etel_752, retro_etel_815, retro_etel_904, retro_etel_91, retro_etel_94,
Gadus morhua	ENSGMOG00000012595	1 retrocopy	retro_gmor_15,
Microcebus murinus	ENSMICG00000005951	7 retrocopies	retro_mmur_1308, retro_mmur_132, retro_mmur_1338, retro_mmur_1636, retro_mmur_217, retro_mmur_583, retro_mmur_902,
Monodelphis domestica	ENSMODG00000025091	3 retrocopies	retro_mdom_1303, retro_mdom_1706, retro_mdom_1914,
Mus musculus	ENSMUSG00000025290	13 retrocopies	retro_mmus_1101, retro_mmus_1462, retro_mmus_1589, retro_mmus_1592, retro_mmus_1599, retro_mmus_2134, retro_mmus_2332, retro_mmus_2497, retro_mmus_2984, retro_mmus_3162, retro_mmus_321, retro_mmus_3233, retro_mmus_602,
Ornithorhynchus anatinus	ENSOANG00000006329	1 retrocopy	retro_oana_54,
Pongo abelii	ENSPPYG00000002304	1 retrocopy	retro_pabe_184,
Sarcophilus harrisii	ENSSHAG00000008090	3 retrocopies	retro_shar_276, retro_shar_303, retro_shar_697,
Sus scrofa	ENSSSCG00000010328	8 retrocopies	retro_sscr_1212, retro_sscr_14, retro_sscr_242, retro_sscr_289 , retro_sscr_491, retro_sscr_564, retro_sscr_718, retro_sscr_902,
Tarsius syrichta	ENSTSYG00000006715	1 retrocopy	retro_tsyr_1919,
Tursiops truncatus	ENSTTRG00000007845	3 retrocopies	retro_ttru_1462, retro_ttru_740, retro_ttru_86,