RetrogeneDB ID: retro_sscr_889

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 6:130801206..130801579(-)
• Located in intron of: ENSSSCG00000025085

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000011676
• Aliases: None
• Description: None

Sequence

>retro_sscr_889
ATGCTTCAGACCCTGAACCATGAGGTTCCAAAATATCGTGACCAGATTTCTAGTCCAGGACTTAACGGTTTTTCCAAAAC
CAGTGTAAGTGTTGGATTATTCGTTGTGTCTGATCCAGAGTCCTATAAAGGGTACATTGATGACCTTAAGAAATTTCTAA
AGCCATATGACTTAGAAGAACAGAAGAATCTCACAGATTGTCCCTATGGAACATTTTTTTGAACAGAAGGGACCAGATTA
TGATGCATGTCGGTTTCTTCCTCACTTACTTGAAACATGCAGTGTTGTGATTGATCCCCAGTTTGGCTACTCCAGAGGAA
ACCCTTGTATTCTTGTGAAAATGAACAGAGTAATTGGATTAAAGCCTCAAGGA

Alignment

ORF - retro_sscr_889 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.57 %
• Parental protein coverage: 51.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLQTLNDEVPKYRDQISSPGLMVFPKPVSALDYSFSVSDPDSYKGYIDDLKKFLKPYDLEEQKNLTDCTD
          MLQTLN.EVPKYRDQISSPGL..F.K........F.VSDP.SYKGYIDDLKKFLKPYDLEEQKNLTDC..
Retrocopy MLQTLNHEVPKYRDQISSPGLNGFSKTSVSVGL-FVVSDPESYKGYIDDLKKFLKPYDLEEQKNLTDCPY

Parental  GKFL-EQKGPHYDACRFPLNLLEACSGEIDPQFGYSRGNPCILVKMNRIIGLKPQG
          G.F..EQKGP.YDACRF...LLE.CS..IDPQFGYSRGNPCILVKMNR.IGLKPQG
Retrocopy GTFF>EQKGPDYDACRFLPHLLETCSVVIDPQFGYSRGNPCILVKMNRVIGLKPQG

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	4.65 RPM
SRP014902_testis	0.00 RPM	31.12 RPM
SRP018288_heart	0.00 RPM	13.78 RPM
SRP018288_kidney	0.00 RPM	26.30 RPM
SRP018288_liver	0.16 RPM	5.44 RPM
SRP018288_lung	0.00 RPM	29.22 RPM
SRP018856_adipose	0.00 RPM	16.85 RPM
SRP035408_brain	0.00 RPM	29.82 RPM
SRP035408_liver	0.00 RPM	5.61 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_889 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_889 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_889 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014140	5 retrocopies	retro_btau_1136, retro_btau_1322, retro_btau_1743, retro_btau_318, retro_btau_920,
Choloepus hoffmanni	ENSCHOG00000007515	4 retrocopies	retro_chof_1000, retro_chof_1421, retro_chof_2393, retro_chof_2445,
Callithrix jacchus	ENSCJAG00000001981	1 retrocopy	retro_cjac_309,
Cavia porcellus	ENSCPOG00000003739	4 retrocopies	retro_cpor_1181, retro_cpor_1468, retro_cpor_1506, retro_cpor_222,
Equus caballus	ENSECAG00000019885	2 retrocopies	retro_ecab_1084, retro_ecab_468,
Homo sapiens	ENSG00000069849	2 retrocopies	retro_hsap_1387, retro_hsap_2263,
Loxodonta africana	ENSLAFG00000010553	1 retrocopy	retro_lafr_815,
Mus musculus	ENSMUSG00000032412	2 retrocopies	retro_mmus_2174, retro_mmus_3427,
Nomascus leucogenys	ENSNLEG00000004663	1 retrocopy	retro_nleu_1286,
Otolemur garnettii	ENSOGAG00000008662	1 retrocopy	retro_ogar_2284,
Procavia capensis	ENSPCAG00000013927	1 retrocopy	retro_pcap_350,
Pongo abelii	ENSPPYG00000014169	1 retrocopy	retro_pabe_1953,
Pan troglodytes	ENSPTRG00000015476	2 retrocopies	retro_ptro_1603, retro_ptro_951,
Rattus norvegicus	ENSRNOG00000011501	2 retrocopies	retro_rnor_2571, retro_rnor_789,
Sus scrofa	ENSSSCG00000011676	3 retrocopies	retro_sscr_889 , retro_sscr_945, retro_sscr_95,
Ictidomys tridecemlineatus	ENSSTOG00000013235	1 retrocopy	retro_itri_1663,
Tupaia belangeri	ENSTBEG00000001004	1 retrocopy	retro_tbel_3620,
Tarsius syrichta	ENSTSYG00000000222	1 retrocopy	retro_tsyr_330,
Tursiops truncatus	ENSTTRG00000012038	1 retrocopy	retro_ttru_333,