RetrogeneDB ID: retro_sscr_566

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 17:42098306..42098799(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5O
• Ensembl ID: ENSSSCG00000012042
• Aliases: LOC733678, ATP5O, OSCP
• Description: Sus scrofa ATP synthase H+-transporting mitochondrial F1 complex O subunit (LOC733678), nuclear gene encoding mitochondrial protein, mRNA. [Source:RefSeq mRNA;Acc:NM_001044606]

Sequence

>retro_sscr_566
GTGGTCAGGCCACCTGTTCACATATGTGGTATCGAAGGTCACTATGTCACTGCTCTTTAATCTGCTGTTTCTAATCAGAA
TAAACTGGAACAAGTAGCAAAGGAATTGTTGGGAGTAGCACAAATCTTGAAGGAAAACTTGGTTGCTCCTATTATGAATC
CCTATGTAAAGCATTGCATTAAAGTGAAAAGCCTATATGACATGATAGCAAAAGAGAGGTTTTCTCCCCTCACAGCCAAC
CTGATCAATTTGCTTGCTGAAAATGGTCGCTTGAGCAATAACCCTGGAGTCATTTCTGCTTTTTCTACCATGATGTCTGT
CCACACTGGAGAAGTACCTTGCAGTTATCACTACATCTCCTTTCGATGAAGCCACTCTTACTGGATTAAAAACAGTCCTG
AAGAGCTTCCTAAGTAAAGGGCAAGTATTGGAAGTTAAGATTGATGCGACAATCGTGAGTAGAATGATTGTCCATATTGG
AGAGAAATATGTC

Alignment

ORF - retro_sscr_566 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.33 %
• Parental protein coverage: 78.87 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LVRPPVQIYGIEGRYATALYSAASKQNKLEQVEKELLRVAQILKEPKVAASIMNPYVKRSVKVKSLSDMT
          .VRPPV.I.GIEG.Y.TAL.SA.S.QNKLEQV.KELL.VAQILKE....A.IMNPYVK...KVKSL.DM.
Retrocopy VVRPPVHICGIEGHYVTAL*SAVSNQNKLEQVAKELLGVAQILKE-NLVAPIMNPYVKHCIKVKSLYDMI

Parental  AKEKFSPLTSNLINLLAENGRLSSTPGVISAFSTMMSVHRGEVPCS-VTTASPLDEATLTELKTVLKSFL
          AKE.FSPLT.NLINLLAENGRLS..PGVISAFSTMMSVH.GEVPCS..TT.SP.DEATLT.LKTVLKSFL
Retrocopy AKERFSPLTANLINLLAENGRLSNNPGVISAFSTMMSVHTGEVPCS>ITT-SPFDEATLTGLKTVLKSFL

Parental  SKGQILKLEVKVDPSIMGGMIVRIGEKYV
          SKGQ...LEVK.D..I...MIV.IGEKYV
Retrocopy SKGQV--LEVKIDATIVSRMIVHIGEKYV

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	0.13 RPM	43.67 RPM
SRP014902_testis	0.00 RPM	51.63 RPM
SRP018288_heart	0.03 RPM	581.65 RPM
SRP018288_kidney	0.00 RPM	229.52 RPM
SRP018288_liver	0.00 RPM	101.86 RPM
SRP018288_lung	0.00 RPM	101.52 RPM
SRP018856_adipose	0.00 RPM	70.25 RPM
SRP035408_brain	0.44 RPM	360.32 RPM
SRP035408_liver	0.00 RPM	339.56 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_566 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_566 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_566 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014708	1 retrocopy	retro_amel_1914,
Canis familiaris	ENSCAFG00000009541	3 retrocopies	retro_cfam_1277, retro_cfam_2198, retro_cfam_235,
Choloepus hoffmanni	ENSCHOG00000011242	1 retrocopy	retro_chof_638,
Callithrix jacchus	ENSCJAG00000002873	1 retrocopy	retro_cjac_1567,
Equus caballus	ENSECAG00000009059	1 retrocopy	retro_ecab_633,
Echinops telfairi	ENSETEG00000000807	5 retrocopies	retro_etel_1412, retro_etel_1906, retro_etel_507, retro_etel_839, retro_etel_841,
Felis catus	ENSFCAG00000028656	1 retrocopy	retro_fcat_1511,
Homo sapiens	ENSG00000241837	1 retrocopy	retro_hsap_2377,
Gorilla gorilla	ENSGGOG00000012611	1 retrocopy	retro_ggor_1803,
Macropus eugenii	ENSMEUG00000006613	4 retrocopies	retro_meug_122, retro_meug_1552, retro_meug_381, retro_meug_805,
Myotis lucifugus	ENSMLUG00000008224	3 retrocopies	retro_mluc_1833, retro_mluc_826, retro_mluc_856,
Macaca mulatta	ENSMMUG00000015504	1 retrocopy	retro_mmul_253,
Monodelphis domestica	ENSMODG00000021057	2 retrocopies	retro_mdom_280, retro_mdom_95,
Mustela putorius furo	ENSMPUG00000001319	5 retrocopies	retro_mputfur_1593, retro_mputfur_1628, retro_mputfur_1639, retro_mputfur_581, retro_mputfur_918,
Mus musculus	ENSMUSG00000022956	2 retrocopies	retro_mmus_2196, retro_mmus_955,
Otolemur garnettii	ENSOGAG00000015850	4 retrocopies	retro_ogar_3518, retro_ogar_418, retro_ogar_559, retro_ogar_944,
Pongo abelii	ENSPPYG00000011384	1 retrocopy	retro_pabe_2247,
Pan troglodytes	ENSPTRG00000013876	1 retrocopy	retro_ptro_1739,
Rattus norvegicus	ENSRNOG00000001991	1 retrocopy	retro_rnor_2210,
Sarcophilus harrisii	ENSSHAG00000000409	3 retrocopies	retro_shar_369, retro_shar_389, retro_shar_668,
Sus scrofa	ENSSSCG00000012042	2 retrocopies	retro_sscr_226, retro_sscr_566 ,
Ictidomys tridecemlineatus	ENSSTOG00000008658	3 retrocopies	retro_itri_1030, retro_itri_565, retro_itri_794,