RetrogeneDB ID: retro_rnor_1992

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:152972250..152973146(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Vom1r71
• Ensembl ID: ENSRNOG00000047851
• Aliases: None
• Description: vomeronasal 1 receptor 71 [Source:RefSeq peptide;Acc:NP_001009523]

Sequence

>retro_rnor_1992
ATGTCCTCATTAAAGAATATACTTTATTGCCAAGCTGGACTTGGAGTTCTAGCCAATATGTTTCTCCTTGCTTCTATACT
TCCATAATCCTAGGTCACAGTCCGAAGCCCATGGATATGATTTCCTGCCAAATGACCTTCATTCACATAACGTTTTTGCT
CACTGGAGCGGATATTTGGCTTACAGACATACTTGAGTCACTGAACATTGAAAATGATTTGAAGTGTAAGACAATTTTTT
ACACAAGTAGGGTGATGAGAGGCCTCTCTATCTGCATCACCTGCCTCCTGAGTGTGTTCCAAGCTGTCATTATCAGTCCT
CACACCTCACTGCTGGCAAAATTTAAACAGAAAATAAAAATATACATGATCAATGCTTTTTTCTATATTTGGTTTTTCAA
TTTTTCAACCAATAGTCACATGATCTTCTATATTAGTGGTTTTAACAATGTGAGTGAAACCAACCAGTTGAAAGTCACTA
AATCCTGCTCACTACTCCCCATGAACTACATCATCAGGGGATTGATTTTAACACTGACAACCTCCAGAGATGTGTTTCTT
GTAGGAGTCATGCTGATCACAAATGCATATACAGTGATTATCTTGTTCAGACACCAGAAACATTGCAAGTATCTTCATAG
CGACAACCACCTGACAGCATCTCCTGAGAAAAGAGCCACCCAGACCATCTTGCTACTGGTGATTTTCTTTATGGTCATTT
ACTGGGTGGACTTCATCATCTCATCCACCTCACTCTTGTTATGGCTGTATGACACAGTTATCCTGACTGTTCAGAAGTTT
GTGATGAATGCCTATCTCACAATTATTCCTTTGGTACAAATCAATTCTGATAAAAGAATAATCAATGTGTTGAAAAATTT
GCAGTCAAAGTGCCAC

Alignment

ORF - retro_rnor_1992 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.67 %
• Parental protein coverage: 96.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MFSLKNVLYFQTGLGVLANMFLV-CFYIYVILGHRPKPTDLISCQLTFIHIMMFLTGGDIWLTDLFELLN
          M.SLKN.LY.Q.GLGVLANMFL..CFY...ILGH.PKP.D.ISCQ.TFIHI...LTG.DIWLTD..E.LN
Retrocopy MSSLKNILYCQAGLGVLANMFLL<CFYTSIILGHSPKPMDMISCQMTFIHITFLLTGADIWLTDILESLN

Parental  IENDFKCKTIFYTSRVMRGLSICTTCLLSVFQAVTISPNTSFLAKFKQKLKKYMVYVFLCIWSFNLSFST
          IEND.KCKTIFYTSRVMRGLSIC.TCLLSVFQAV.ISP.TS.LAKFKQK.K.YM...F..IW.FN.S...
Retrocopy IENDLKCKTIFYTSRVMRGLSICITCLLSVFQAVIISPHTSLLAKFKQKIKIYMINAFFYIWFFNFSTNS

Parental  NRIFYVGGFINVSETNQMKITKSCSLFPMNYIIRGMIVTVTTSRDVFLVGIMLITSTYMVIILCRHQRQC
          ..IFY..GF.NVSETNQ.K.TKSCSL.PMNYIIRG.I.T.TTSRDVFLVG.MLIT..Y.VIIL.RHQ..C
Retrocopy HMIFYISGFNNVSETNQLKVTKSCSLLPMNYIIRGLILTLTTSRDVFLVGVMLITNAYTVIILFRHQKHC

Parental  KHLHRISHLSASPEKRATQTILLLVVFFVVIYWEDFIISFTSILLWMYDPVVLRVQKFVIYAYPTITPLV
          K.LH...HL.ASPEKRATQTILLLV.FF.VIYW.DFIIS.TS.LLW.YD.V.L.VQKFV..AY.TI.PLV
Retrocopy KYLHSDNHLTASPEKRATQTILLLVIFFMVIYWVDFIISSTSLLLWLYDTVILTVQKFVMNAYLTIIPLV

Parental  QISSDKRIISVLKNLHSKCH
          QI.SDKRII.VLKNL.SKCH
Retrocopy QINSDKRIINVLKNLQSKCH

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	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1992 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1992 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1992 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000047851	3 retrocopies	retro_rnor_1989, retro_rnor_1992 , retro_rnor_248,