RetrogeneDB ID: retro_rnor_2219

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:69742333..69742982(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ola1
• Ensembl ID: ENSRNOG00000019047
• Aliases: Ola1, PTD004, RGD1307982
• Description: Obg-like ATPase 1 [Source:UniProtKB/Swiss-Prot;Acc:A0JPJ7]

Sequence

>retro_rnor_2219
CCCAAAAAGGGAGGACATGGAATTAAACCACCTGCAATTGTGGGAAGACTTGGAACCTCACAGAAAATTGATATTGTTAG
TATGTGAAATCTTGGTTAGTCTACCTTCTTCAGTGTATTAACCAATAGTTAGGCTCAAGGAGAAAACTTCCTATTCTGCC
TTGTTAATCCTATTGAGAGTAGATTTCCTGTGTCAGATGAGAGGTTTGAGTTCCTTTGCTAATATCACAAACCAGGAAGC
AAAATTCCTCCTTCTTAAATGTAGTGGATATTGCTGGCCATATGAAAGAGGCCCATAATGGGTGGGGCTTGGGGAATACC
TTTTGATCTCACAGCAGTGATTATGATGGGATTTTTTCATCTAAAACATGCCTTTGAAGACGATGATATCACACATGCTG
AAGGAAGTATAGATTCCAGTCGAGATATACAAGTAATTCATGAAAAGCTTCAGTTGAAAGATGAGAAAATGATTGAACCT
GTTATAAATAAACTAGGGACGGTGGCTGTGAGAAAAAGTGATAAGAAATTAAAGCCCAAGTCCAAACATGACATAATATT
GCAAAGTCAAATCTAGGGCTACAGATCATTAAAAACCTATTGACTTCTATCATGACTAGAATGACAAAGAGATTAAAGTG
TTGAATAAA

Alignment

ORF - retro_rnor_2219 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.58 %
• Parental protein coverage: 54.04 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PKKGGDGLKPPPIIGRFGTSLKIGIVGLPNVGKSTFFNVLTNSQASAENFPFCTIDPNESRVPVPDERFD
          PKKGG.G.KPP.I.GR.GTS.KI.IV...N.G.STFF.VLTNS.A..ENF.FC...P.ESR.PV.DERF.
Retrocopy PKKGGHGIKPPAIVGRLGTSQKIDIVSM*NLG*STFFSVLTNS*AQGENFLFCLVNPIESRFPVSDERFE

Parental  FLCQCHKPASKIP-AFLNVVDIAGLVKGAHNGQGLGNAFLSHISACDGI-FHLTRAFEDDDITHVEGSVD
          FLC..HKP.SKIP..FLNVVDIAG..K.AHNG.GLGN.F.SH.S..DGI.FHL..AFEDDDITH.EGS.D
Retrocopy FLC*YHKPGSKIP<SFLNVVDIAGHMKEAHNGWGLGNTF*SHSSDYDGI>FHLKHAFEDDDITHAEGSID

Parental  PIRDIEIIHEELQLKDEEMIGPIIDKLEKVAVRGGDKKLKP--EYDIM-CKVKSWVIDQKKPVRFYHDWN
          ..RDI..IHE.LQLKDE.MI.P.I.KL..VAVR..DKKLKP....DI..CKVKS...D..KP..FYHD.N
Retrocopy SSRDIQVIHEKLQLKDEKMIEPVINKLGTVAVRKSDKKLKPKSKHDII>CKVKSRATDH*KPIDFYHD*N

Parental  DKEIEVLNK
          DKEI.VLNK
Retrocopy DKEIKVLNK

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	75.35 RPM
SRP017611_kidney	0.00 RPM	33.22 RPM
SRP017611_liver	0.00 RPM	14.93 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2219 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2219 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2219 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000025196	1 retrocopy	retro_mluc_626,
Monodelphis domestica	ENSMODG00000009296	1 retrocopy	retro_mdom_1428,
Rattus norvegicus	ENSRNOG00000019047	1 retrocopy	retro_rnor_2219 ,
Tupaia belangeri	ENSTBEG00000007574	8 retrocopies	retro_tbel_1749, retro_tbel_2506, retro_tbel_3217, retro_tbel_3581, retro_tbel_418, retro_tbel_4356, retro_tbel_4475, retro_tbel_88,