RetrogeneDB ID: retro_rnor_1371

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 18:80668857..80669802(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Pramef17
• Ensembl ID: ENSRNOG00000042820
• Aliases: None
• Description: Protein Pramef17 [Source:UniProtKB/TrEMBL;Acc:F1LYT8]

Sequence

>retro_rnor_1371
CCTACTCTTCATGTTGGGTTGCTGATTAATAACCCCAACTCGGAGACCTTCCAGGCTATACTGGATGGAGAAGACACATG
ACTGAAACGGAAGTATTGCCCCAGGACGTGTAGGTTTCAAGTGGCTGACTTGAGGGATGGACACCATGCCTCCTTGGATA
TGCAGGATGCAAGAGAGGGTAGAAACCACTTAGTAGAAACTATGCTTGAGGAGTAAATAGTGGAGGGCCACTCAAGGTAC
ACGAGGAAGCAGCATTTAGGGGTGTTCAATGACCTTTCCTTCATGTCTTCTCTGCATGAAGATAAACACCAAATACAGTT
GTGGCAGTGGACAAAGGAGAGGAAGGATTTCCTGCATCTGGGCTTTGAGAAGTTGGAGATTGGAATAACACAAGTGTCCA
AGATCAGGATTGTGCTAAAATTTTTGCAGCTAGAGTTCATCAAGGAGTTGGAACTGAATGCAGTGGGAAATCTGTCCAAA
CTGGCAAAGTTTGTACCTTGCATCAGCAAGATGAGAAATCTTCAGAAACTCACGCTAGTATGCATTGGAACAAGTACTCA
CACACTTGAGGAGGAGGGGAATGTCACCAAGATCATTTCTTTGTTCCCCAAACTCGGCCGTCTTCAGCATCTCACTATTG
ATGATGTCGATTTTCTCACAGACCACATGAAAGAGTTGTCCAGGTGTCTGGAGGCCCCACTGCTGTCCCTCAAGATCACT
CTGTGCTGGCTCCCTCAGTCAGACTTGGAGTCACTTGCTCAGCGTTGGAACTACAGTCAGCTTAAACATCTGTGCTTGAG
AGGTGTCGCTTTAACTCATTTGAATGTCATGCCTGTAAACGTTTTCTCAGAGAGTGCTGTAGATACACTGCAGATTCTGG
AATTAGAAGACTGTAGGAAGAATGACTTTCACCTCAGTATCTTTCTGCTTTCCCTGACCCAATGC

Alignment

ORF - retro_rnor_1371 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.49 %
• Parental protein coverage: 66.03 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PCLLVRLLIDKPNLEIFQAILDGVGTWLKRKYRPRMGKLEVVDLRNGHLDSWDLQAGREGGGAQSETVPE
          P.L.V.LLI..PN.E.FQAILDG..T.LKRKY.PR.....V.DLR.GH..S.D.Q..REG.....ET..E
Retrocopy PTLHVGLLINNPNSETFQAILDGEDT*LKRKYCPRTCRFQVADLRDGHHASLDMQDAREGRNHLVETMLE

Parental  KQVMEGHSN---RRRLRVFCDLSFKSSKHEDKHQTHLLRWAKDREDFLHLCCKKLEIGALEVSKVKKELK
          ....EGHS.......L.VF.DLSF.SS.HEDKHQ..L..W.K.R.DFLHL...KLEIG...VSK....LK
Retrocopy E*IVEGHSRYTRKQHLGVFNDLSFMSSLHEDKHQIQLWQWTKERKDFLHLGFEKLEIGITQVSKIRIVLK

Parental  FLQPEFIKELELNTVGNLSKLAKLVPCISKMRNLHKLMLVRIFERTYTPSEK-NVSKIISLFPELRYLQN
          FLQ.EFIKELELN.VGNLSKLAK.VPCISKMRNL.KL.LV.I...T.T..E..NV.KIISLFP.L..LQ.
Retrocopy FLQLEFIKELELNAVGNLSKLAKFVPCISKMRNLQKLTLVCIGTSTHTLEEEGNVTKIISLFPKLGRLQH

Parental  LTIGDVYFLKDHMNELLRCLVAPLVSLTITLCQISQSDLESFAQRWNYGQLKHLCLKGVSLTALNVTPLK
          LTI.DV.FL.DHM.EL.RCL.APL.SL.ITLC...QSDLES.AQRWNY.QLKHLCL.GV.LT.LNV.P..
Retrocopy LTIDDVDFLTDHMKELSRCLEAPLLSLKITLCWLPQSDLESLAQRWNYSQLKHLCLRGVALTHLNVMPVN

Parental  FFLESVANTLQTLELEGCRMSDSHLSILQPALTQC
          .F.ES...TLQ.LELE.CR..D.HLSI....LTQC
Retrocopy VFSESAVDTLQILELEDCRKNDFHLSIFLLSLTQC

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_1371 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1371 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1371 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000013324	1 retrocopy	retro_dord_231,
Homo sapiens	ENSG00000187545	1 retrocopy	retro_hsap_220,
Otolemur garnettii	ENSOGAG00000000273	2 retrocopies	retro_ogar_1100, retro_ogar_1238,
Ochotona princeps	ENSOPRG00000009716	1 retrocopy	retro_opri_661,
Pan troglodytes	ENSPTRG00000029629	1 retrocopy	retro_ptro_330,
Rattus norvegicus	ENSRNOG00000042820	1 retrocopy	retro_rnor_1371 ,
Rattus norvegicus	ENSRNOG00000048835	1 retrocopy	retro_rnor_396,