RetrogeneDB ID: retro_sscr_260

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 11:26295005..26295265(+)
• Located in intron of: ENSSSCG00000009435

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFB6
• Ensembl ID: ENSSSCG00000011003
• Aliases: None
• Description: Sus scrofa NADH dehydrogenase 1 beta subcomplex 6 (LOC733605), mRNA. [Source:RefSeq mRNA;Acc:NM_001044554]

Sequence

>retro_sscr_260
TGGCCTATGGAGCAATTCTGGAGTAAGTTTTTGCAGGATGGTGTCCCCTGGAAGAACGTGATCTATAAGACATACCAACA
CAGTGTCTTTGCCTTTACTCATGTACTTATCCCTGAATGAATCGTTATTATCTTAAATATCACGTGACTGCAAAACCATA
TACCACTGCTGAAAGGAAGTCCAGAATATTCGCAGGTGATACAATCCTGGCAACTGGAGAAGTAATCCCACTAATGCAAG
AATTTCGTGATCAACATCAC

Alignment

ORF - retro_sscr_260 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.78 %
• Parental protein coverage: 68.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  WPMEQFWNKFLQDGAPWKNVIYKTYRHSIFAVTHVLIPVWII-HYYLKYHVTAKPYTVVERKPRIFPGDT
          WPMEQFW.KFLQDG.PWKNVIYKTY.HS.FA.THVLIP..I...Y.LKYHVTAKPYT..ERK.RIF.GDT
Retrocopy WPMEQFWSKFLQDGVPWKNVIYKTYQHSVFAFTHVLIPE*IV<YY-LKYHVTAKPYTTAERKSRIFAGDT

Parental  ILETGEVIPLMKEFPDQHH
          IL.TGEVIPLM.EF.DQHH
Retrocopy ILATGEVIPLMQEFRDQHH

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	8.49 RPM
SRP014902_testis	0.00 RPM	20.37 RPM
SRP018288_heart	0.05 RPM	100.32 RPM
SRP018288_kidney	0.00 RPM	71.81 RPM
SRP018288_liver	0.00 RPM	27.66 RPM
SRP018288_lung	0.00 RPM	14.26 RPM
SRP018856_adipose	0.00 RPM	16.81 RPM
SRP035408_brain	0.00 RPM	71.37 RPM
SRP035408_liver	0.00 RPM	47.79 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_260 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_260 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_260 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000001263	3 retrocopies	retro_acar_110, retro_acar_116, retro_acar_117,
Callithrix jacchus	ENSCJAG00000007852	3 retrocopies	retro_cjac_1287, retro_cjac_255, retro_cjac_303,
Dasypus novemcinctus	ENSDNOG00000019864	2 retrocopies	retro_dnov_2281, retro_dnov_920,
Ochotona princeps	ENSOPRG00000007428	5 retrocopies	retro_opri_148, retro_opri_525, retro_opri_591, retro_opri_614, retro_opri_722,
Sus scrofa	ENSSSCG00000011003	1 retrocopy	retro_sscr_260 ,
Tupaia belangeri	ENSTBEG00000013268	2 retrocopies	retro_tbel_195, retro_tbel_197,
Tarsius syrichta	ENSTSYG00000002785	1 retrocopy	retro_tsyr_382,
Tursiops truncatus	ENSTTRG00000012172	1 retrocopy	retro_ttru_1505,