RetrogeneDB ID: retro_sscr_1156

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: X:54309991..54310357(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000030964
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000006830
• Aliases: None
• Description: Sus scrofa proteasome (prosome, macropain) subunit, alpha type, 5 (PSMA5), mRNA. [Source:RefSeq mRNA;Acc:NM_001144901]

Sequence

>retro_sscr_1156
GGAAAGAATCTTCTCTCATTATTTCCAAGATTATTTCATATGCAATATGAGACACTCAAACTTGGTTCCATAGCCACTGG
GATACAGACTTCAGAGGTGTGTATGCCTAGCAATAGAGAAGAAAATTACCTCCTACTGTCCTTCAGCTATTAGAAAGTTG
CATATATTGATGCTCATACAAGCTGTACTGGAAGTATGCTACTCACTGAAGCTAAGACTTTACTTAATAAAGCCAGAATG
GAGACACAGAATCACTTGTTCACTTACAAAAAGATAATGACACTGGAGAATATAGCCTAGTTTGAGTCAAGCCTGCATGT
CAAATTTGGAGAAGATGCAGATCCAGATGCCGTATTTCATTCCTTT

Alignment

ORF - retro_sscr_1156 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.71 %
• Parental protein coverage: 52.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GVNTFSPEGRLFQVEYAIEAIKLGSTAIGIQTSEG-VCLAVEKRITSPLMEPSSIEK-IVEIDAHIGCAM
          G.N..S...RLF...Y..E..KLGS.A.GIQTSE..VCLA.EK.ITS....PS.I.K....IDAH..C..
Retrocopy GKNLLSLFPRLFHMQY--ETLKLGSIATGIQTSEV>VCLAIEKKITSYC--PSAIRK<VAYIDAHTSCTG

Parental  SGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLALQFGEEDADPGAMSRPF
          S.L...AKTL..KAR.ETQNH.FTY...MT.E......S.L...FG.EDADP.A....F
Retrocopy SMLLTEAKTLLNKARMETQNHLFTYKKIMTLENIA*FESSLHVKFG-EDADPDAVFHSF

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	23.23 RPM
SRP014902_testis	0.00 RPM	24.89 RPM
SRP018288_heart	0.00 RPM	32.01 RPM
SRP018288_kidney	0.00 RPM	45.31 RPM
SRP018288_liver	0.00 RPM	46.21 RPM
SRP018288_lung	0.00 RPM	22.71 RPM
SRP018856_adipose	0.00 RPM	57.25 RPM
SRP035408_brain	0.00 RPM	49.83 RPM
SRP035408_liver	0.00 RPM	51.78 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1156 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1156 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1156 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013670	1 retrocopy	retro_cpor_1063,
Equus caballus	ENSECAG00000011835	1 retrocopy	retro_ecab_1106,
Echinops telfairi	ENSETEG00000012916	1 retrocopy	retro_etel_1053,
Myotis lucifugus	ENSMLUG00000008497	2 retrocopies	retro_mluc_1002, retro_mluc_926,
Mustela putorius furo	ENSMPUG00000003189	1 retrocopy	retro_mputfur_1295,
Mus musculus	ENSMUSG00000068749	1 retrocopy	retro_mmus_52,
Otolemur garnettii	ENSOGAG00000013560	1 retrocopy	retro_ogar_3137,
Ochotona princeps	ENSOPRG00000008863	1 retrocopy	retro_opri_449,
Pteropus vampyrus	ENSPVAG00000008908	1 retrocopy	retro_pvam_222,
Rattus norvegicus	ENSRNOG00000019868	2 retrocopies	retro_rnor_1230, retro_rnor_658,
Sus scrofa	ENSSSCG00000006830	2 retrocopies	retro_sscr_1156 , retro_sscr_1194,