RetrogeneDB ID: retro_sscr_542

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 16:27693735..27694292(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000027723
• Aliases: None
• Description: None

Sequence

>retro_sscr_542
ATGCTGACTCTGACAAGCAAACTAAAGCGGGTTGGAGGTCTCAAAGGGTCCCTGGCGTCAGCAGCAGCCTCCGACTCCAC
TCGGCGGATTTCTGTGGGGGACAGGCTGCTTGTTAAAGAGTTGCCGAACTTGAAGCTAATTTACCTTGTACGTATAAAGT
GCATTTTCCTGATCTAAACAAGCTTCACTGCTTTCAGCTAACTGTAGCCCCAGACGAGGGTTACTACCAAGGTGGAAAGT
TTCAGTTTGAAACTGAAGTTCCCGATGGGTACAACATGGTGTCCCCCAAAGTGAAATGCCTGACCAGAATCTGGCACCCC
AGCATCACAGAGACAGGCGAAATATGTCTCAGTTTACTGAGAGAACAGTCGATTGACGGCACCGGCTGGGCACCCACGAG
GACATTGAAGGATGTTGTTTGGGATTCAACTCTTTGTTTACTGTAAGATCTTTTGAATTTTGATGATCCGCTGAATATTG
CAGCTGCAGAGCATCATTTGCGGGTCAAGGAGGACTTCCAGAATAAGGTGGAAGACTGCATCAAGCGCTATGCCAGA

Alignment

ORF - retro_sscr_542 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.03 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLTLASKLKRDDGLKGSRASPAASDSTRRVSVRDRLLVKE-VAELEANLPCTCKVHFPDPNKLHCFQLTV
          MLTL.SKLKR..GLKGS.AS.AASDSTRR.SV.DRLLVKE.VAELEANLPCT.KVHFPD.NKLHCFQLTV
Retrocopy MLTLTSKLKRVGGLKGSLASAAASDSTRRISVGDRLLVKE<VAELEANLPCTYKVHFPDLNKLHCFQLTV

Parental  TPDEGYYQGGKFQFETEVPDAYNMVPPKVKCLTRIWHPNITETGEICLSLLREHSIDGTGWAPTRTLKDV
          .PDEGYYQGGKFQFETEVPD.YNMV.PKVKCLTRIWHP.ITETGEICLSLLRE.SIDGTGWAPTRTLKDV
Retrocopy APDEGYYQGGKFQFETEVPDGYNMVSPKVKCLTRIWHPSITETGEICLSLLREQSIDGTGWAPTRTLKDV

Parental  VWGLN-SLFTDLLNFDDPLNIEAAEHHLRDKEDFRSKVEDYIKRFAR
          VW.....L..DLLNFDDPLNI.AAEHHLR.KEDF..KVED.IKR.AR
Retrocopy VWDSTLCLL*DLLNFDDPLNIAAAEHHLRVKEDFQNKVEDCIKRYAR

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	33.18 RPM
SRP014902_testis	0.14 RPM	22.63 RPM
SRP018288_heart	0.08 RPM	14.04 RPM
SRP018288_kidney	0.20 RPM	34.58 RPM
SRP018288_liver	0.00 RPM	31.98 RPM
SRP018288_lung	0.51 RPM	25.86 RPM
SRP018856_adipose	0.35 RPM	18.57 RPM
SRP035408_brain	0.00 RPM	23.88 RPM
SRP035408_liver	0.06 RPM	42.30 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_542 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_542 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_542 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 24 parental genes, and 59 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008551	1 retrocopy	retro_amel_572,
Bos taurus	ENSBTAG00000026114	2 retrocopies	retro_btau_1698, retro_btau_948,
Canis familiaris	ENSCAFG00000012363	1 retrocopy	retro_cfam_1275,
Callithrix jacchus	ENSCJAG00000000476	3 retrocopies	retro_cjac_2378, retro_cjac_2980, retro_cjac_3219,
Cavia porcellus	ENSCPOG00000006368	1 retrocopy	retro_cpor_1122,
Dasypus novemcinctus	ENSDNOG00000000506	2 retrocopies	retro_dnov_1301, retro_dnov_132,
Equus caballus	ENSECAG00000011687	1 retrocopy	retro_ecab_158,
Echinops telfairi	ENSETEG00000009230	1 retrocopy	retro_etel_1534,
Homo sapiens	ENSG00000184182	2 retrocopies	retro_hsap_2439, retro_hsap_2773,
Gorilla gorilla	ENSGGOG00000010709	3 retrocopies	retro_ggor_1518, retro_ggor_1519, retro_ggor_1930,
Microcebus murinus	ENSMICG00000012075	5 retrocopies	retro_mmur_1014, retro_mmur_114, retro_mmur_1365, retro_mmur_584, retro_mmur_815,
Myotis lucifugus	ENSMLUG00000001286	5 retrocopies	retro_mluc_1237, retro_mluc_1674, retro_mluc_1747, retro_mluc_1789, retro_mluc_2627,
Macaca mulatta	ENSMMUG00000018482	4 retrocopies	retro_mmul_1450, retro_mmul_1585, retro_mmul_254, retro_mmul_628,
Mustela putorius furo	ENSMPUG00000000101	1 retrocopy	retro_mputfur_782,
Mus musculus	ENSMUSG00000034343	3 retrocopies	retro_mmus_2161, retro_mmus_255, retro_mmus_845,
Nomascus leucogenys	ENSNLEG00000011152	2 retrocopies	retro_nleu_1340, retro_nleu_677,
Otolemur garnettii	ENSOGAG00000005308	7 retrocopies	retro_ogar_1109, retro_ogar_1995, retro_ogar_2491, retro_ogar_2551, retro_ogar_2715, retro_ogar_639, retro_ogar_761,
Pongo abelii	ENSPPYG00000013315	3 retrocopies	retro_pabe_1395, retro_pabe_1785, retro_pabe_2242,
Pan troglodytes	ENSPTRG00000013081	2 retrocopies	retro_ptro_1410, retro_ptro_1876,
Rattus norvegicus	ENSRNOG00000019953	1 retrocopy	retro_rnor_2696,
Sus scrofa	ENSSSCG00000027723	3 retrocopies	retro_sscr_291, retro_sscr_423, retro_sscr_542 ,
Tarsius syrichta	ENSTSYG00000011510	3 retrocopies	retro_tsyr_1718, retro_tsyr_1944, retro_tsyr_2133,
Tursiops truncatus	ENSTTRG00000011528	2 retrocopies	retro_ttru_1297, retro_ttru_1455,
Vicugna pacos	ENSVPAG00000010485	1 retrocopy	retro_vpac_361,