RetrogeneDB ID: retro_rnor_1230

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 16:47292056..47292485(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Psma5
• Ensembl ID: ENSRNOG00000019868
• Aliases: None
• Description: proteasome subunit alpha type-5 [Source:RefSeq peptide;Acc:NP_058978]

Sequence

>retro_rnor_1230
ATCCAGGCGTCAGAGGGTGCATATCTAACTGTGGAGAAGAGAATTACCTCCCCACTAATGGAGCCTAGCGGCATTGAGAA
AATTGTAGCAATTGGCGCTCATATAGGTTGTGCCGTGAGTGGGCTCACTGTTGATGCTGAAACTTTAATTGATAAAACCA
GAGTGGAGACACAGAACCACTAGTTCACCTATAAGGAAACAATGACAGTTGAGAGTGTGACCCAGGCTGTGTCCGATCTG
GCTTTGCAGTTTGGAGAAGATGCAGATCCAGGTGCCACATCTCGTCCCTGTGGAGTAGCATTGTTTTAAGGAGATGAGGA
GGAGTTTCGCATGGACCCATCTGGGACCTTTGTACAGTGAGATGCTCGAGCAACTGGCTCTGCCACAGGGAGACCAGAGC
TCCTTGCAAGAAGTTTACCACAAGTCTAT

Alignment

ORF - retro_rnor_1230 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.15 %
• Parental protein coverage: 60.58 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IQTSEGVCLAVEKRITSPLMEPSSIEKIVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTV
          IQ.SEG..L.VEKRITSPLMEPS.IEKIV.I.AHIGCA.SGL..DA.TLIDK.RVETQNH.FTY.ETMTV
Retrocopy IQASEGAYLTVEKRITSPLMEPSGIEKIVAIGAHIGCAVSGLTVDAETLIDKTRVETQNH*FTYKETMTV

Parental  ESVTQAVSNLALQFGEEDADPGAMSRPFGVALLFGGVDEKGPQLFHMDPSGTFVQCDARAIGSAS---EG
          ESVTQAVS.LALQFGE.DADPGA.SRP.GVAL.F.G..E.....F.MDPSGTFVQ.DARA.GSA....E.
Retrocopy ESVTQAVSDLALQFGE-DADPGATSRPCGVAL-F*GDEEE----FRMDPSGTFVQ*DARATGSATGRPEL

Parental  AQSSLQEVY
          ...SL..VY
Retrocopy LARSLPQVY

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
SRP017611_brain	0.00 RPM	36.24 RPM
SRP017611_kidney	0.00 RPM	35.31 RPM
SRP017611_liver	0.00 RPM	33.48 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1230 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1230 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1230 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 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,
Mus musculus	ENSMUSG00000068749	1 retrocopy	retro_mmus_52,
Ochotona princeps	ENSOPRG00000008863	1 retrocopy	retro_opri_449,
Rattus norvegicus	ENSRNOG00000019868	2 retrocopies	retro_rnor_1230 , retro_rnor_658,
Sus scrofa	ENSSSCG00000006830	2 retrocopies	retro_sscr_1156, retro_sscr_1194,