RetrogeneDB ID: retro_rnor_603

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:124740723..124741991(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Btrc
• Ensembl ID: ENSRNOG00000016280
• Aliases: Btrc, beta-TrCP1
• Description: beta-transducin repeat containing protein [Source:RefSeq peptide;Acc:NP_001007149]

Sequence

>retro_rnor_603
TATTATCAGCATAGCCATATTAACTCTTAACTGAAGCCCATGTTGTAGCAGGACTTTAATCACTGCTTTGCCAGAGCAAG
ATTTAGATCACATAACAGAAAACATTATTTCCTACCTGGATGCCAGGTCTCTGTGTGCAGCAGAGCTGCTGTGTAAAGAA
TAGTAGTGAGTAAGCTCCAAAGGGAATCTTTGGAAGAAGCTGATTGAGAGCATGGTGCGCACAGACACTTTCTGGAAGGA
CTCTCAGAAGGAAGAGGCTGGGATCAGTACCTCTTTAAAAAATGAACTATAGATGGACCTTCCAGCTCATTTTATAGATC
ATTATGCCCAAAGGTTATCCAAGGCACAGAAACCATAGAACCCAACTGGCAATGTGGATGACACAACTCGCAGAGGATCC
AGTGCCATTCTGAAAATACTAAGGGTGTCTACTCTTTGCAATATGATGATGACAAAATTATCAGTGGCCTCTGAGACAAC
TCTGTAAAGATCTGAGATAAAAGCAGCTTGGGATGTTTAAAAGTGCTAATGGGACACACAGGATTTGTCCTCTGCCTCCA
ATATAATGAGCGAGTCATTGTAACTGGTTCTTCAGACTCCACGGTGAGAGCCTGGGATGTGAACACTGGTGAAGTTCTCA
ACACACTCATCCACCACAAATAAGCTGTACTGCACTTATGCTTAGGCAATGGACTGATAGTCACTTGTTCCAAGGATGGT
TCCATCACTGTGTGGGATGTGGTTTCTGCCACTAATACCACTTTACACCGTGTCCTGGTTGGCCACCATGCTGCTGTCAA
TATAGTAGACTTTGATGATAAGTACATCATGTCTACCTCTGGAGACAGGACCATTAAAGTGTGGAGCATGAGCACCTGTG
AGTTTGTCCACACTCTGAATGGGCATAAACAAGGCATCATCTGCCTGCAGTACTGGGACTGGCTTGTTGTTAGTGGATCA
TCAGATAATACCATCCGGTTATGGGATTTTGAATTGGCACCTGCCTAAGAGTCCTAGAGGGGCATGAAGAACTGTTCCGG
TGCATCCATTTTGATAACAAGAGGATTGTCAGTGGCACTTATGATGGGAAGATTAAAGCCTGGGACTTGCAGGCTGCTGT
TGACCCTCAGGCCCCAGCAAGCACATTGTGTCTGCGCACCTTGGTGGAACATTCTGGACATATGTTTTGGCTGCAGCTTG
ATGAATTTCAGATCAGCATCAGCTCCCATTATAACACTATTTTTATTTGTGATTTTTTAAATGTGCCT

Alignment

ORF - retro_rnor_603 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.66 %
• Parental protein coverage: 70.25 %
• Number of stop codons detected: 10
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  HYQHGHINSYLKPMLQRDF-ITALPARGLDHIAENILSYLDARSLCAAELVCKEWYRVTSDGMLWKKLIE
          .YQH.HINS.LKPML..DF.ITALP...LDHI.ENI.SYLDARSLCAAEL.CKE...V.S.G.LWKKLIE
Retrocopy YYQHSHINS*LKPML*QDF>ITALPEQDLDHITENIISYLDARSLCAAELLCKE***VSSKGNLWKKLIE

Parental  RMVRTDSLWR-GLAERRGWGQYLFKNKPPDENAPPNSFYRALYPKIIQDIETIESNWRCGRHSLQRIHCR
          .MVRTD..W..GL.E.RGW.QYLFK....D...P..SFYR.L.PK.IQ..ETIE.NW.CG.H..QRI.C.
Retrocopy SMVRTDTFWK<GLSEGRGWDQYLFKK*TID--GPSSSFYRSLCPKVIQGTETIEPNWQCG*HNSQRIQCH

Parental  SETSKGVYCLQYDDQKIVSGLRDNTIKIWDKSTLECKRILTGHTGSVLCLQYDERVIITGSSDSTVRVWD
          SE..KGVY.LQYDD.KI.SGL.DN..KI.DKS.L.C...L.GHTG.VLCLQY.ERVI.TGSSDSTVR.WD
Retrocopy SENTKGVYSLQYDDDKIISGL*DNSVKI*DKSSLGCLKVLMGHTGFVLCLQYNERVIVTGSSDSTVRAWD

Parental  VNAGEMLNTLIHHCEAVLHLRFNNGMMVTCSKDRSIAVWDMASPTDITLRRVLVGHRAAVNVVDFDDKYI
          VN.GE.LNTLIHH..AVLHL...NG..VTCSKD.SI.VWD..S.T..TL.RVLVGH.AAVN.VDFDDKYI
Retrocopy VNTGEVLNTLIHHK*AVLHLCLGNGLIVTCSKDGSITVWDVVSATNTTLHRVLVGHHAAVNIVDFDDKYI

Parental  VSASGDRTIKVWNTSTCEFVRTLNGHKRGIACLQYRDRLVVSGSSDNTIRLWDIE-CGACLRVLEGHEEL
          .S.SGDRTIKVW..STCEFV.TLNGHK.GI.CLQY.D.LVVSGSSDNTIRLWD.E..G.CLRVLEGHEEL
Retrocopy MSTSGDRTIKVWSMSTCEFVHTLNGHKQGIICLQYWDWLVVSGSSDNTIRLWDFE<IGTCLRVLEGHEEL

Parental  VRCIRFDNKRIVSGAYDGKIKVWDLMAALDPRAPAGTLCLRTLVEHSGRVFRLQFDEFQIVSSSHDDTIL
          .RCI.FDNKRIVSG.YDGKIK.WDL.AA.DP.APA.TLCLRTLVEHSG..F.LQ.DEFQI..SSH..TI.
Retrocopy FRCIHFDNKRIVSGTYDGKIKAWDLQAAVDPQAPASTLCLRTLVEHSGHMFWLQLDEFQISISSHYNTIF

Parental  IWDFLNDP
          I.DFLN.P
Retrocopy ICDFLNVP

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	47.09 RPM
SRP017611_kidney	0.00 RPM	11.03 RPM
SRP017611_liver	0.00 RPM	6.86 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_603 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_603 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_603 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000013579	1 retrocopy	retro_meug_1243,
Pongo abelii	ENSPPYG00000002583	1 retrocopy	retro_pabe_1856,
Rattus norvegicus	ENSRNOG00000016280	1 retrocopy	retro_rnor_603 ,
Rattus norvegicus	ENSRNOG00000018687	1 retrocopy	retro_rnor_2358,