RetrogeneDB ID: retro_rnor_1271

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 17:56302314..56302813(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Psmd14
• Ensembl ID: ENSRNOG00000004911
• Aliases: None
• Description: 26S proteasome non-ATPase regulatory subunit 14 [Source:RefSeq peptide;Acc:NP_001020860]

Sequence

>retro_rnor_1271
ATGGGGAGAGTCCTTAGATGTGGAGAAAGTATGTCTGCCTTGGACAGGGTCATTGACAGAGTGTCCTGCCATGGTCACAG
CAGAGTAAGTTTATATCTCCTCCTTGATGTTGCTAAAGACATCAAAATATGGCCATGCTAGGGTTCCAATAGAAGTTATG
GGTCTAACTCTGGGGATTTTGTTGGTGAGTGTACCATCAGAGTGATGGATCACTCTGATTACATCACAGTCAGACACAGG
TATCAGTGTAGAAGCTGTTGATCCAATGTTCCAAACAAAAACATCAGAAATGCTAAGAGAAACAGGGATTCTGACATGAC
TGTCAGCTGGTATGCAGTCACCATGGCTTGGTGGTTGGCATTCTGCTGCTGATATCAACACACGGCAGAACTCTGATGCT
TTCCCAGATACAGCAGTGGCCTTGGCTGTGGCTCCCACTCAGGGTGTAAAGAGACCAAGTGTTATTAATGCCTTCATACT
GACTTGTTCCAATATGATG

Alignment

ORF - retro_rnor_1271 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.14 %
• Parental protein coverage: 54.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MDRLLRLGGGMPGL-GQG-PPTDAPAVDTAEQVYISSLALLKMLKHGRAGVPMEVMGLML-GEFVDDYTV
          M.R.LR.G..M..L.GQG...T..PA..TAE.VYISSL.LLK..K.G.A.VP.EVMGL.L.G.FV...T.
Retrocopy MGRVLRCGESMSAL<GQG<SLTECPAMVTAE*VYISSLMLLKTSKYGHARVPIEVMGLTL<GDFVGECTI

Parental  RVID-VFAMPQSGTGVSVEAVDPVFQAKMLDMLKQTG-RPEMVVGWYH-SH-PGFGCWLSGVDINTQQSF
          RV.D......QS.TG.SVEAVDP.FQ.K...ML..TG....M.V.WY..SH.P..G.W.S..DINT.Q..
Retrocopy RVMD>TLITSQSDTGISVEAVDPMFQTKTSEMLRETG<DSDMTVSWYA<SH<PWLGGWHSAADINTRQNS

Parental  EALSERAVAVVVDPIQSVKGKVVIDAFRLINANMM
          .A....AVA..V.P.Q.VK...VI.AF.L...NMM
Retrocopy DAFPDTAVALAVAPTQGVKRPSVINAFILTCSNMM

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	34.51 RPM
SRP017611_kidney	0.00 RPM	31.12 RPM
SRP017611_liver	0.00 RPM	20.37 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1271 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1271 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1271 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002556	1 retrocopy	retro_chof_2387,
Callithrix jacchus	ENSCJAG00000005572	1 retrocopy	retro_cjac_1434,
Gorilla gorilla	ENSGGOG00000015747	1 retrocopy	retro_ggor_1710,
Mus musculus	ENSMUSG00000026914	1 retrocopy	retro_mmus_701,
Otolemur garnettii	ENSOGAG00000004933	2 retrocopies	retro_ogar_2955, retro_ogar_3213,
Pongo abelii	ENSPPYG00000012881	1 retrocopy	retro_pabe_2100,
Pan troglodytes	ENSPTRG00000012575	1 retrocopy	retro_ptro_1636,
Rattus norvegicus	ENSRNOG00000004911	1 retrocopy	retro_rnor_1271 ,
Tupaia belangeri	ENSTBEG00000014118	1 retrocopy	retro_tbel_3917,