RetrogeneDB ID: retro_rnor_1309

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 17:53603510..53604907(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Noc3l
• Ensembl ID: ENSRNOG00000013965
• Aliases: Noc3l, RGD1560656
• Description: nucleolar complex protein 3 homolog [Source:RefSeq peptide;Acc:NP_001101993]

Sequence

>retro_rnor_1309
ACTATCAAGAAGTATCAAAAAGAGCAGAGGAAATTAAGACAAGTTGTAAAAGATTCTGTGTCTAAAAAACCCATTCCATT
GGAGGACCAGAGAACAAACAACCAGTTAAAAGGATCGAGAGGGAAGAGGAAGAAGCCGTTCCTTTAGTTATGATGGATGA
GGATGACTTACAGTTAATGAAAGATTTAGAGTAAAAAGAATCTTTTCTCAGAAGAGATCTTTCTTCTAGTGAACCAGTTC
ACATCAAGAAACTAAAGCATCAGAGTGTGATAGAGAAATATGAAAAGTGCCAAGAACTCTGCAAACTGCAACAGAGAAGG
AGTTGATGCCCCTGCTTCCTATCAAGGATAAGAGTGGACTGACTCGGGAGAAGCCAGTCATGGGCATCCAGCAAGAAAAA
GAGGATGAAGAAGAGCTGGAAGTTGAGGTCATGGACGACCCCAGGCAAGAGCTGACCGTAGAAGAGCATGTGATCGAGAG
AAAGAAGAAACTGCAGAACAAGAAAATTCAGATTGCAACCTTGGCATCTGCTATTCTGTCACATCCAGAAAGTCATTAAA
AAAAACTGAAAGAGCTGCATGCCAGGCCGATGGAGCAGGTCCCCGATGTGGCTGTCACTGACCAGGAGCTGGTTATCATC
TCACTGATTGAGCTGTTTAAGTACATCACTCCCTTGTATAAAATCCTGCCCCTAACCGAAGCAGAAAAATCTACCAAGAT
CCTTAAAGAAACCCAGAAGTTAAGAGAATCTGAAGAAGGCCTGGTTAGCCAATACAAATTTTATTTGGAAAATCTGGAGC
AATTAATTAAAGGCTGGAAGCAAGAAAAGCTGAAGAAAAGCAACATGGTGTTCTCAAAGGCCTACAAAGGGCCGGCTGAG
GTGGCAATTAGGAGCCTGTGTGAGCTGTTGGAGCCCCTGCCCCATTTTAACTTTCACAACAACATCATTGTACTGATTGT
CCCTCTGATGAATGATGGACCAAATTCAGTACCTGAAATGTGTTGCAAAGCAGTAAAGAAACTCTTTAAATAAGATAAAT
TAGGGCAAGCTTCTCTTAGTGTAACTAAAGTGATCTCCAGTTTTGTAAAGGGCAGAAATTACGAAGTTAGGTCAGAGATG
TTAAAAACATTTTCATACCTGCAAATCAAGGAAGTGGAAGTGAAAAAGAAATACAGAAGACATTAACAAACCAAAAAAAT
TCATGACTTTCGAGGAAAAGAGAAAAACTCTATCAAGAATGCAAAGAAAGTGGAAGAAAGCCGAAGAGAAACTCGAACGG
AAACTTTGGGAGGCTGAAGCTTTGGATAGCACTGAGAGAAAGCTGAAACTGCACACAGAGACTCTGAATATTGTGTTTGT
GACCTACTTCAGAATATTGAAGAAGGCTCAGAGCTCA

Alignment

ORF - retro_rnor_1309 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.29 %
• Parental protein coverage: 59.32 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TIKKYRKEQRKLRQAVKDAVSKKPFPLED-PKSKRPVKRIEREEEDEEEALPLDMLDEDDLQLIKDLGQK
          TIKKY.KEQRKLRQ.VKD.VSKKP.PLED.P..K.PVKRIERE...EEEA.PL.M.DEDDLQL.KDL..K
Retrocopy TIKKYQKEQRKLRQVVKDSVSKKPIPLED<PENKQPVKRIERE---EEEAVPLVMMDEDDLQLMKDLE*K

Parental  ASFLTRDLSSSEPVHIKKRKHESVIEKYEK-VPRTLQTAPEKELIHLLPIKDKSGIIPQTREKPVTAIQQ
          .SFL.RDLSSSEPVHIKK.KH.SVIEKYEK.VPRTLQTA.EKEL..LLPIKDKSG....TREKPV..IQQ
Retrocopy ESFLRRDLSSSEPVHIKKLKHQSVIEKYEK<VPRTLQTATEKELMPLLPIKDKSGL---TREKPVMGIQQ

Parental  EEEEEEEPEVEEEVIEEPRQELTIEEHVIERKKKLQDKKIQIATLASAILSDPESHIKKLKELRAMLMEQ
          E.E.EEE.EVE..V...PRQELT.EEHVIERKKKLQ.KKIQIATLASAILS.PESH...LKEL.A..MEQ
Retrocopy EKEDEEELEVE--VMDDPRQELTVEEHVIERKKKLQNKKIQIATLASAILSHPESHXXXLKELHARPMEQ

Parental  DPDVAVTVRKLAIISLMELFKDITPSYKIRPLTEAEKSAKIRKETQKLREFEEGLVSQYKFYLENLEQIV
          .PDVAVT...L.IISL.ELFK.ITP.YKI.PLTEAEKS.KI.KETQKLRE.EEGLVSQYKFYLENLEQ..
Retrocopy VPDVAVTDQELVIISLIELFKYITPLYKILPLTEAEKSTKILKETQKLRESEEGLVSQYKFYLENLEQLI

Parental  KDWKQRKLKKSNVVSLKAYKGLAEVAVKSLCELLVALPHFNFHNNIIVLIVPLMNDGSKSVSEMCCEAVK
          K.WKQ.KLKKSN.V..KAYKG.AEVA..SLCELL..LPHFNFHNNIIVLIVPLMNDG..SV.EMCC.AVK
Retrocopy KGWKQEKLKKSNMVFSKAYKGPAEVAIRSLCELLEPLPHFNFHNNIIVLIVPLMNDGPNSVPEMCCKAVK

Parental  KLFKQDKLGQASLGVIKVISGFVKGRNYEVRPEMLKTFLCLRIKEVEVKK-DTEDINKPKRFMTFKEKRK
          KLFK.DKLGQASL.V.KVIS.FVKGRNYEVR.EMLKTF..L.IKEVEVKK..TEDINKPK.FMTF.EKRK
Retrocopy KLFK*DKLGQASLSVTKVISSFVKGRNYEVRSEMLKTFSYLQIKEVEVKK>NTEDINKPKKFMTFEEKRK

Parental  TLSRMQRKWKKAEEKLERELREAEASESTEKKLKLHTETLNIVFVTYFRILKKAQKS
          TLSRMQRKWKKAEEKLER.L.EAEA..STE.KLKLHTETLNIVFVTYFRILKKAQ.S
Retrocopy TLSRMQRKWKKAEEKLERKLWEAEALDSTERKLKLHTETLNIVFVTYFRILKKAQSS

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	7.84 RPM
SRP017611_kidney	0.00 RPM	13.61 RPM
SRP017611_liver	0.00 RPM	7.19 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1309 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1309 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1309 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000008033	1 retrocopy	retro_cfam_1008,
Rattus norvegicus	ENSRNOG00000013965	1 retrocopy	retro_rnor_1309 ,