RetrogeneDB ID: retro_sscr_254

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 10:78038744..78039200(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF130
• Ensembl ID: ENSSSCG00000014013
• Aliases: None
• Description: ring finger protein 130 [Source:HGNC Symbol;Acc:18280]

Sequence

>retro_sscr_254
ATTATTGCTGTCATGATTACAGAATTGAGGGGTAAAGATATTTTGAGTTATCTGGAGAAAAACATCTTTGTACAAATAAC
AATAGCTGTTGGAACTTGAATGCTGAAGGAGAACTTCAGCCATGGCTCTCTAGTCCTCGTGTCACTATCCTTTACTGCTT
TGATGATTATTTCTTCAGAATGGCTTATATTCTACTTCATTCAGAAGATCAGGTACACAAATGCCTGAGACAGGAACCTG
CATCATCTTGGAGATACAGCCAAGAAAGCCATAAGCAGACTGATGACCAGAATAGTCAAAAAAGGTGATAAGGAAACAGA
TCTAGACTTTGATCACTGTGGAGTCTTCAGACAGAGCTATAAGCAGAATGATGTCTGGATTCTCCCTGCACAGAATTTCC
ACAAATCCTGTGTTGTTCTCTGGCTTAGTGAACATTGTACCAGTCCTATATGCAGA

Alignment

ORF - retro_sscr_254 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.62 %
• Parental protein coverage: 64.71 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IIAVMITELRGKDILSYLEKNISVQMTIAVGTRMPPKNFSRGSLVFVSISFIVLMIISSAWLIFYFIQKI
          IIAVMITELRGKDILSYLEKNI.VQ.TIAVGT.M...NFS.GSLV.VS.SF..LMIISS.WLIFYFIQKI
Retrocopy IIAVMITELRGKDILSYLEKNIFVQITIAVGT*MLKENFSHGSLVLVSLSFTALMIISSEWLIFYFIQKI

Parental  RYTNARDRNQRRLGDAAKKAISKLTTRTVKKGDKETDPDFDHCAVCIESYKQNDVVRILPCKHVFHKSCV
          RYTNA.DRN...LGD.AKKAIS.L.TR.VKKGDKETD.DFDHC.V...SYKQND.V.ILP....FHKSCV
Retrocopy RYTNA*DRNLHHLGDTAKKAISRLMTRIVKKGDKETDLDFDHCGVFRQSYKQND-VWILPAQN-FHKSCV

Parental  DPWLSEHCTCPMCK
          ..WLSEHCT.P.C.
Retrocopy VLWLSEHCTSPICR

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	27.48 RPM
SRP014902_testis	0.00 RPM	61.39 RPM
SRP018288_heart	0.00 RPM	32.77 RPM
SRP018288_kidney	0.00 RPM	47.18 RPM
SRP018288_liver	0.00 RPM	73.88 RPM
SRP018288_lung	0.00 RPM	75.86 RPM
SRP018856_adipose	0.00 RPM	210.28 RPM
SRP035408_brain	0.00 RPM	20.17 RPM
SRP035408_liver	0.00 RPM	40.39 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_254 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_254 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_254 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000008735	3 retrocopies	retro_lafr_628, retro_lafr_876, retro_lafr_969,
Nomascus leucogenys	ENSNLEG00000001941	1 retrocopy	retro_nleu_100,
Sus scrofa	ENSSSCG00000012551	1 retrocopy	retro_sscr_597,
Sus scrofa	ENSSSCG00000014013	3 retrocopies	retro_sscr_150, retro_sscr_253, retro_sscr_254 ,
Sus scrofa	ENSSSCG00000017906	1 retrocopy	retro_sscr_518,