RetrogeneDB ID: retro_sscr_54

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 6:33613002..33613350(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000002850
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000012842
• Aliases: None
• Description: 60S acidic ribosomal protein P2 [Source:UniProtKB/TrEMBL;Acc:F1RYZ0]

Sequence

>retro_sscr_54
ATGCATTACATCACTTCCTACCTGCTGGCCGCCCTTGAGGGCAATACCTCTCCTAGCACCAAGGACATCAAGAAGATCCT
GGACAGTGTGGGCATCAAGGCGGGCGATGATCGGCTCAACAAGTTCATCAGTGAGTTGAACGAGAAGAACATTGAGGACG
TCATTGCCCAGGGCATTGGCAAGGTGGCCAGCAGACCTGCTGGCAGGGTTGTGTCCATCACTGCTGCCCCAGGGTCTGCA
GCTCCTGCTGCAGGTTCTGCCCCAGCTGCAGCAGAGGAGAAGAAAGAAGAGAAGAAGGAGGAGTCAGAGGAGTCAGACGA
CGACATGGGCTTCGGCTTGTTTGACTAG

Alignment

ORF - retro_sscr_54 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.22 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRYVASYLLAALGGNTSPSAKDIKKILDSVGIEADDDRLNKVISELNGKNIEDVIAQGIGKLASVPSGGA
          M.Y..SYLLAAL.GNTSPS.KDIKKILDSVGI.A.DDRLNK.ISELN.KNIEDVIAQGIGK.AS.P.G..
Retrocopy MHYITSYLLAALEGNTSPSTKDIKKILDSVGIKAGDDRLNKFISELNEKNIEDVIAQGIGKVASRPAGRV

Parental  VAVAAAPGSAAPAAGSAPAAAEEKKEEKKEESEESDDDMGFGLFD
          V...AAPGSAAPAAGSAPAAAEEKKEEKKEESEESDDDMGFGLFD
Retrocopy VSITAAPGSAAPAAGSAPAAAEEKKEEKKEESEESDDDMGFGLFD

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	0.40 RPM	809.39 RPM
SRP014902_testis	1.84 RPM	542.73 RPM
SRP018288_heart	0.05 RPM	272.18 RPM
SRP018288_kidney	0.79 RPM	396.98 RPM
SRP018288_liver	0.48 RPM	306.55 RPM
SRP018288_lung	0.00 RPM	325.44 RPM
SRP018856_adipose	0.38 RPM	1355.87 RPM
SRP035408_brain	0.29 RPM	848.35 RPM
SRP035408_liver	0.15 RPM	750.04 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_54 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_54 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_54 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 73 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006935	1 retrocopy	retro_amel_197,
Bos taurus	ENSBTAG00000001777	2 retrocopies	retro_btau_117, retro_btau_1399,
Canis familiaris	ENSCAFG00000009523	1 retrocopy	retro_cfam_18,
Ciona intestinalis	ENSCING00000000626	1 retrocopy	retro_cint_34,
Callithrix jacchus	ENSCJAG00000011838	6 retrocopies	retro_cjac_2399, retro_cjac_2497, retro_cjac_2539, retro_cjac_2745, retro_cjac_3097, retro_cjac_3859,
Dasypus novemcinctus	ENSDNOG00000011513	12 retrocopies	retro_dnov_143, retro_dnov_1464, retro_dnov_1498, retro_dnov_1522, retro_dnov_1655, retro_dnov_1693, retro_dnov_1768, retro_dnov_200, retro_dnov_2104, retro_dnov_2293, retro_dnov_335, retro_dnov_366,
Dipodomys ordii	ENSDORG00000016458	3 retrocopies	retro_dord_705, retro_dord_706, retro_dord_707,
Echinops telfairi	ENSETEG00000010240	4 retrocopies	retro_etel_1206, retro_etel_1458, retro_etel_1640, retro_etel_455,
Felis catus	ENSFCAG00000008417	1 retrocopy	retro_fcat_860,
Homo sapiens	ENSG00000177600	5 retrocopies	retro_hsap_1777, retro_hsap_3395, retro_hsap_3440, retro_hsap_821, retro_hsap_982,
Gorilla gorilla	ENSGGOG00000010789	5 retrocopies	retro_ggor_2238, retro_ggor_2298, retro_ggor_2323, retro_ggor_672, retro_ggor_784,
Macaca mulatta	ENSMMUG00000020627	2 retrocopies	retro_mmul_221, retro_mmul_311,
Mustela putorius furo	ENSMPUG00000009049	1 retrocopy	retro_mputfur_254,
Mus musculus	ENSMUSG00000025508	4 retrocopies	retro_mmus_1364, retro_mmus_2111, retro_mmus_2282, retro_mmus_330,
Nomascus leucogenys	ENSNLEG00000026860	5 retrocopies	retro_nleu_1948, retro_nleu_2144, retro_nleu_2296, retro_nleu_2762, retro_nleu_85,
Otolemur garnettii	ENSOGAG00000016296	2 retrocopies	retro_ogar_156, retro_ogar_275,
Petromyzon marinus	ENSPMAG00000009576	1 retrocopy	retro_pmar_15,
Pongo abelii	ENSPPYG00000002885	6 retrocopies	retro_pabe_1537, retro_pabe_1543, retro_pabe_2789, retro_pabe_2844, retro_pabe_732, retro_pabe_830,
Pan troglodytes	ENSPTRG00000003137	5 retrocopies	retro_ptro_1189, retro_ptro_2307, retro_ptro_2332, retro_ptro_572, retro_ptro_764,
Rattus norvegicus	ENSRNOG00000002116	3 retrocopies	retro_rnor_257, retro_rnor_320, retro_rnor_388,
Sarcophilus harrisii	ENSSHAG00000001056	1 retrocopy	retro_shar_321,
Sus scrofa	ENSSSCG00000012842	1 retrocopy	retro_sscr_54 ,
Tursiops truncatus	ENSTTRG00000012450	1 retrocopy	retro_ttru_1420,