RetrogeneDB ID: retro_sscr_193

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:242951635..242952182(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFB5
• Ensembl ID: ENSSSCG00000011764
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 5, 16kDa [Source:HGNC Symbol;Acc:7700]

Sequence

>retro_sscr_193
GCTTTGGTCACTGCTATGGCGGCTCTGTCCCGCAGGCACTTTGGCACTCGATTAGATTTGGGGTGGGGTGTTCCTCACCC
ATGGCTTTCCTAAGATTGCCACTCCTTTGAGACACAGTGGAGACCATGGGAAAAGACTGTTTATCATCAAGCCTTCTGGA
TTATATGGCAGTTGTTTTTTGAAATTAATGAGATTCTATATTTTGTTGACTGGGATTCCAGCAGCAATTGGCATAACTTT
ACTGGTGAATGTATTCACTGGTAAAGCTGAGTTAGCAGAAATTCCAGAAGACTATATCCCAGAACACTGGGAATGTTTCA
AGCATCCTGTACCAAGATGGATTGCCCGAACTTTCTTTGATGGTCATGAAAAGAATTGTGAAAAATCAATGGCTATCCTT
CAAATGGAAGCTAAAAAGGCTGAATTACGGTTAAAGGAGTTGGAAGTGTGAAGATTAATGTGTGCAAGAGGTGATGGTCC
CTGATATCAGTATCCAACCATTGACAAAGGACTTACTGATCATTCTCCAAAAGCAACTCCTGACAAT

Alignment

ORF - retro_sscr_193 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.6 %
• Parental protein coverage: 95.24 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ASVTAVATLSRSRLGTRFG-FGG-FLTHGFPKTGAPVRHSGDHGKRLFIIKPSGFYDRRFLKLMRFYILL
          A.VTA.A.LSR...GTR....GG.FLTHGFPK...P.RHSGDHGKRLFIIKPSG.Y...FLKLMRFYILL
Retrocopy ALVTAMAALSRRHFGTRLD>WGGVFLTHGFPKIATPLRHSGDHGKRLFIIKPSGLYGSCFLKLMRFYILL

Parental  TGIPVAIGITL-VNVFIGEAELADIPEGYVPEHWEYFKHPISRWIARTFYDGPEKNYEKTMAILQIEAEK
          TGIP.AIGITL.VNVF.G.AELA.IPE.Y.PEHWE.FKHP..RWIARTF.DG.EKN.EK.MAILQ.EA.K
Retrocopy TGIPAAIGITLLVNVFTGKAELAEIPEDYIPEHWECFKHPVPRWIARTFFDGHEKNCEKSMAILQMEAKK

Parental  AELRLKELEVRRLMRARGDGPWYQYPTIDKALIDHSPKTTPDN
          AELRLKELEV.RLM.ARGDGP.YQYPTIDK.L.DHSPK.TPDN
Retrocopy AELRLKELEV*RLMCARGDGP*YQYPTIDKGLTDHSPKATPDN

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	5.31 RPM
SRP014902_testis	0.00 RPM	9.90 RPM
SRP018288_heart	0.00 RPM	131.36 RPM
SRP018288_kidney	0.00 RPM	66.49 RPM
SRP018288_liver	0.00 RPM	28.62 RPM
SRP018288_lung	0.00 RPM	12.22 RPM
SRP018856_adipose	0.00 RPM	13.92 RPM
SRP035408_brain	0.00 RPM	23.60 RPM
SRP035408_liver	0.06 RPM	17.53 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_193 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_193 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_193 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002684	1 retrocopy	retro_chof_1511,
Equus caballus	ENSECAG00000000682	1 retrocopy	retro_ecab_235,
Echinops telfairi	ENSETEG00000019363	1 retrocopy	retro_etel_1110,
Homo sapiens	ENSG00000136521	2 retrocopies	retro_hsap_3127, retro_hsap_4879,
Macropus eugenii	ENSMEUG00000014166	1 retrocopy	retro_meug_1852,
Myotis lucifugus	ENSMLUG00000000999	1 retrocopy	retro_mluc_2181,
Macaca mulatta	ENSMMUG00000009746	1 retrocopy	retro_mmul_2619,
Monodelphis domestica	ENSMODG00000021300	1 retrocopy	retro_mdom_1105,
Nomascus leucogenys	ENSNLEG00000005842	2 retrocopies	retro_nleu_2247, retro_nleu_2558,
Pongo abelii	ENSPPYG00000014493	2 retrocopies	retro_pabe_3018, retro_pabe_3796,
Pan troglodytes	ENSPTRG00000015649	1 retrocopy	retro_ptro_3252,
Pteropus vampyrus	ENSPVAG00000004286	1 retrocopy	retro_pvam_81,
Sorex araneus	ENSSARG00000006918	1 retrocopy	retro_sara_200,
Sus scrofa	ENSSSCG00000011764	1 retrocopy	retro_sscr_193 ,
Ictidomys tridecemlineatus	ENSSTOG00000010557	1 retrocopy	retro_itri_1810,
Tursiops truncatus	ENSTTRG00000008910	3 retrocopies	retro_ttru_1445, retro_ttru_1719, retro_ttru_1755,