RetrogeneDB ID: retro_rnor_658

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:260594259..260594978(-)
• 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_658
ATGTTCCTCACTCCATTGGAATATGACAGGGGTGTGACTACTTTTTCTCCTGAAGGAAGATCATTTCAAGTAGAATATGT
CATTGAGGCTATTAAGCTTGGTTCTATGGCCATTGGCATGCAGACATCAGAAGGTGTACATCCAACTGTGGAGAAGAGAA
TTACATCCCCACTAATGGAGCCTAGCGGCATTGAGAAAATTGTAGAGATCAATGCTCATGTAGGTTGTGCCATGAATGGG
CTCATTGATGATGCTAAAACTTTAATGACTAAAACCAGAGTGAAGACACAAAAACACTGGTTCACCTATAATGAGACAAT
GGCAGTTGAGAGTGTGACCTAGGCTATGTTCAATCAGACTTTGCAGTTTGGAGAAGAGGATGCAGATCTCGGGGTCACAT
CTTGTTCCTTTGGAGTAGCATTGTTGTTTGGAGGAGTTGATGAGAAAGGATCCCAATTGTTTCACATGGACCAATCTGGG
ACCTTTGTATAGTGATGCTCGTGCAATTAACTCTGCTTCAGAAGTTCCCAGACCTCCTTGCAAGAAGTTTACCACAAGTC
TATGACTCTGATGGAGGCCATCAAGTCTTCACTCATCATCCTCAAGTGTGTCATAGAGGAGTAGTTAACACAACTAACAT
TGAGCTAGTCACAGTGCAGCCTGGTCAGATTTTCCACATGTTCACAAAGGAAGAACTGGAGAAAGTAATGAAGGATATT

Alignment

ORF - retro_rnor_658 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.82 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MFLTRSEYDRGVNTFSPEGRLFQVEYAIEAIKLGSTAIGIQTSEGVCLAVEKRITSPLMEPSSIEKIVEI
          MFLT..EYDRGV.TFSPEGR.FQVEY.IEAIKLGS.AIG.QTSEGV...VEKRITSPLMEPS.IEKIVEI
Retrocopy MFLTPLEYDRGVTTFSPEGRSFQVEYVIEAIKLGSMAIGMQTSEGVHPTVEKRITSPLMEPSGIEKIVEI

Parental  DAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLALQFGEEDADPGAMSRPFGVA
          .AH.GCAM.GLI.DAKTL..K.RV.TQ.HWFTYNETM.VESVT.A..N..LQFGEEDAD.G..S..FGVA
Retrocopy NAHVGCAMNGLIDDAKTLMTKTRVKTQKHWFTYNETMAVESVT*AMFNQTLQFGEEDADLGVTSCSFGVA

Parental  LLFGGVDEKG-PQLFHMDPSGTFVQCDARAIGSASE-GAQSSLQEVYHKSMTLKEAIKSSLIILKQVMEE
          LLFGGVDEKG.P..F.....G.....DARAI.SASE...Q.SLQEVYHKSMTL.EAIKSSLIILK.V.EE
Retrocopy LLFGGVDEKG>PNCFTWTNLGPLYS-DARAINSASE<SSQTSLQEVYHKSMTLMEAIKSSLIILKCVIEE

Parental  KL-NATNIELATVQPGQNFHMFTKEELEEVIKDI
          .L.N.TNIEL.TVQPGQ.FHMFTKEELE.V.KDI
Retrocopy *L<NTTNIELVTVQPGQIFHMFTKEELEKVMKDI

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_658 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_658 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_658 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,