RetrogeneDB ID: retro_sscr_1017

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 8:143079756..143080085(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFAB1
• Ensembl ID: ENSSSCG00000010795
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex, 1, 8kDa [Source:HGNC Symbol;Acc:7694]

Sequence

>retro_sscr_1017
GCTCTGCAGCCGGGCCCGGTGCTCGCGCAGGTTCCAGGCGGAGTTACACAGCTGTGTAGCCAGCACAGCGACGCGCCCAC
TTGGACATCAGAGAGCATCGCGGACCGAGCTCTTTACGTCCTGAAACGCTGGGACAAGATGCACCCAGAAAAGCTCTCGG
TAAATTCTCGTTTTATGAAAGACCTGGGCTGAGGCAGTTTGGACCAAGGGAAGACGATCATGGCCACAGAGGACGAACTC
GGGTTTGAAAGTCCTGACATGAATGCGGAGAAGTTAATGTGCCCACAAGAAATTTGCGTTACACTGCAGATAAGAAGGAG
GTATATGAA

Alignment

ORF - retro_sscr_1017 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.27 %
• Parental protein coverage: 70.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ALQPALVLAQAPGGVTQMCRRYSDAPPLTLEAIKDRVLYVLKLYDKIDPEKLSVNSHFMKDLGLDSLDQV
          ALQP..VLAQ.PGGVTQ.C...SDAP..T.E.I.DR.LYVLK..DK..PEKLSVNS.FMKDLG..SLDQ.
Retrocopy ALQPGPVLAQVPGGVTQLCSQHSDAPTWTSESIADRALYVLKRWDKMHPEKLSVNSRFMKDLG*GSLDQG

Parental  EIIMAMEDEFGFEIPDIDAEKLMCPQEI-VDYIADKKDVYE
          ..IMA.EDE.GFE.PD..AEKLMCPQEI...Y.ADKK.VYE
Retrocopy KTIMATEDELGFESPDMNAEKLMCPQEI<LRYTADKKEVYE

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	21.10 RPM
SRP014902_testis	0.00 RPM	31.68 RPM
SRP018288_heart	0.00 RPM	159.34 RPM
SRP018288_kidney	0.00 RPM	106.39 RPM
SRP018288_liver	0.00 RPM	55.97 RPM
SRP018288_lung	0.00 RPM	36.45 RPM
SRP018856_adipose	0.00 RPM	24.65 RPM
SRP035408_brain	0.00 RPM	136.70 RPM
SRP035408_liver	0.00 RPM	105.01 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1017 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1017 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1017 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014304	1 retrocopy	retro_amel_1692,
Canis familiaris	ENSCAFG00000017667	3 retrocopies	retro_cfam_1738, retro_cfam_1821, retro_cfam_450,
Choloepus hoffmanni	ENSCHOG00000003558	2 retrocopies	retro_chof_1517, retro_chof_2498,
Callithrix jacchus	ENSCJAG00000020616	2 retrocopies	retro_cjac_2635, retro_cjac_3099,
Cavia porcellus	ENSCPOG00000012038	2 retrocopies	retro_cpor_728, retro_cpor_767,
Dasypus novemcinctus	ENSDNOG00000017122	5 retrocopies	retro_dnov_1450, retro_dnov_1733, retro_dnov_2024, retro_dnov_89, retro_dnov_911,
Felis catus	ENSFCAG00000013241	3 retrocopies	retro_fcat_1104, retro_fcat_1181, retro_fcat_2012,
Loxodonta africana	ENSLAFG00000001032	1 retrocopy	retro_lafr_330,
Macropus eugenii	ENSMEUG00000012681	3 retrocopies	retro_meug_1780, retro_meug_303, retro_meug_830,
Macaca mulatta	ENSMMUG00000020522	1 retrocopy	retro_mmul_101,
Monodelphis domestica	ENSMODG00000016352	1 retrocopy	retro_mdom_389,
Mus musculus	ENSMUSG00000030869	6 retrocopies	retro_mmus_1724, retro_mmus_2073, retro_mmus_2188, retro_mmus_2947, retro_mmus_3094, retro_mmus_3332,
Otolemur garnettii	ENSOGAG00000005562	2 retrocopies	retro_ogar_2916, retro_ogar_325,
Rattus norvegicus	ENSRNOG00000018129	2 retrocopies	retro_rnor_1353, retro_rnor_2058,
Sus scrofa	ENSSSCG00000010795	1 retrocopy	retro_sscr_1017 ,