RetrogeneDB ID: retro_sscr_689

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 2:153735474..153735999(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFB10
• Ensembl ID: ENSSSCG00000030328
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 10, 22kDa [Source:HGNC Symbol;Acc:7696]

Sequence

>retro_sscr_689
GATGGCTGGGCCAAGGACGTGCACCCTGAGCCCCCACGCCGCACAACTGGCCTCACTGGCAGACGTTGCCACCCAACCCT
AGGACCTGCTTTACAAAGGCCTTCGACCTCCTCATGGACCAGCTTGTGACCCTCACGACAGAGTCCAGAGCAGCAGCACT
CCGAGAACACCTGTACTACCACCCCCGCGAGGTCTGCCGCGTGGCGGACTTCCCCGGGTGCAAGGAAAAGGACATCCTGT
GGATGTCTGGAGCAGAAACGCCACGGGGGAGAGGCTGCAAAGTCACCACGAGGTCATCGGCATCATCCAGGGAGGCCGAA
GGCTGGTCAGCGGAGGGGAGGCAGAGCTACAGGCAGGACTGTGCCAAGGCGCTGGAGCCACTCGCCCGGGCGGCCTGGGC
CTACCAGCCCCACTGTCATGACCGGGCAGAGGATCATGGAAGCCCACTGGTCTGCTGGGAAGTGCCTGGCAAAACGGAAG
CAGAGGACGCTGGCAGAGAGAAACGCCACCAACACAGCCGCCGCC

Alignment

ORF - retro_sscr_689 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.65 %
• Parental protein coverage: 98.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  DSWDKDVYPEPPRRTPA-PAPQTSLPNPVTYLTKIFDLLVDRPVTLAREFIEQQHAKNRYYYYHREFRRV
          D.W.KDV.PEPPRRT...P..QT..PNP.T..TK.FDLL.D..VTL..E...........YY..RE..RV
Retrocopy DGWAKDVHPEPPRRTTG<PHWQTLPPNPRTCFTKAFDLLMDQLVTLTTE-SRAAALREHLYYHPREVCRV

Parental  PDITECEEKDILCMFEAEMQWRRDYKV-DQEIVNIIQ-ERLKACQQREG-ESYRQNCAKELEQFTQVSKA
          .D...C.EKDIL.M..AE....R..KV...E...IIQ..R.KA.Q.R.G..SYRQ.CAK.LE.......A
Retrocopy ADFPGCKEKDILWMSGAETPRGRGCKV<HHEVIGIIQ<GRPKAGQRRGG<QSYRQDCAKALEPLARAAWA

Parental  FQ----DRYSDLG-AHYSARKCLAKQKQRMLAERKAAKEAAA
          .Q....DR..D.G.AH.SA.KCLAK.KQR.LAER.A...AAA
Retrocopy YQPHCHDRAEDHG>AHWSAGKCLAKRKQRTLAERNATNTAAA

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	0.27 RPM	94.50 RPM
SRP014902_testis	0.42 RPM	39.04 RPM
SRP018288_heart	0.00 RPM	64.36 RPM
SRP018288_kidney	0.00 RPM	38.02 RPM
SRP018288_liver	0.00 RPM	26.70 RPM
SRP018288_lung	0.00 RPM	40.22 RPM
SRP018856_adipose	0.12 RPM	37.59 RPM
SRP035408_brain	0.03 RPM	46.81 RPM
SRP035408_liver	0.00 RPM	41.24 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_689 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_689 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_689 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019476	1 retrocopy	retro_cfam_1861,
Echinops telfairi	ENSETEG00000017154	1 retrocopy	retro_etel_1955,
Felis catus	ENSFCAG00000011738	1 retrocopy	retro_fcat_307,
Homo sapiens	ENSG00000140990	2 retrocopies	retro_hsap_1573, retro_hsap_3801,
Gorilla gorilla	ENSGGOG00000009367	2 retrocopies	retro_ggor_1198, retro_ggor_2555,
Latimeria chalumnae	ENSLACG00000013152	1 retrocopy	retro_lcha_100,
Macaca mulatta	ENSMMUG00000029268	1 retrocopy	retro_mmul_2218,
Mus musculus	ENSMUSG00000040048	1 retrocopy	retro_mmus_2566,
Nomascus leucogenys	ENSNLEG00000008867	1 retrocopy	retro_nleu_1740,
Pongo abelii	ENSPPYG00000006974	2 retrocopies	retro_pabe_1297, retro_pabe_3106,
Pan troglodytes	ENSPTRG00000007618	2 retrocopies	retro_ptro_1060, retro_ptro_2578,
Rattus norvegicus	ENSRNOG00000014568	1 retrocopy	retro_rnor_1056,
Sus scrofa	ENSSSCG00000030328	1 retrocopy	retro_sscr_689 ,