RetrogeneDB ID: retro_rnor_2358

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:48421265..48422005(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Fbxw2
• Ensembl ID: ENSRNOG00000018687
• Aliases: None
• Description: F-box/WD repeat-containing protein 2 [Source:UniProtKB/Swiss-Prot;Acc:B2RZ17]

Sequence

>retro_rnor_2358
GTGACAGGCTCCTTTGATAGCACTATGGCCTGCTGGGAATGGAGTTCCGGAGCCAGGACCCAGCACTTCCGGGGTCATAT
GGGTGCGGTGTTCAGTGCGGACTACAGTGATGAACTGGATATTTTGGTAAGTGGTTCTGCAGACTTCGTTATGAAAGTAT
GGGCTTTGACTGATGGGACATACCTGAACACACTCCTTGGGCATACTGAATGAGTTACCAAGGTGGTCTTGCAGAAGTGC
CAAGTCAAGTCTCCTTGCACAGCCGTGGAGACTACATCCTCATAAGTGCAGACAAATATGAGATTGAGATTTGGCCAATT
GGGAGAGAAGTCAACTGTAAGTGCTTAACGGGACTGTCTATCTCCAAGGATAGAAGTATCTGCTTACAGTCAAGACTTCA
CTTTGATGGAAAATACATTGTATGTAGTTCAGCCCTGGGTTTGTATCAGTGGGACTTTGCTAGTTATGATATTCTCGGGG
TCATCAAGACACCCAAGGTAGCAAACTTGGCCTTCCTTGGCTTTGGAGATGTCTTCACTCTACTTCGCCACTGCCTATAC
ATCATGGACTTGAGGACAGGGAGCTCATTAACCACTGGCCACTGCCAGAGGACAGAAAATCAGAGAAGCTCCAGCTTCCT
GGCAGGAGAAGCATCCTGGCTGAATGGACTGGATGAACGCAATGACATGGGCTTGGTGTTTGCCACCAGCATGCTTGACC
ACAGTGTTCACCTGGTCTTA

Alignment

ORF - retro_rnor_2358 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.88 %
• Parental protein coverage: 55.07 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VTGSFDNTVACWEWSSGARTQHFRGHTGAVFSVDYSDELDILVSGSADFAVKVWALSAGTCLNTLTGHTE
          VTGSFD.T.ACWEWSSGARTQHFRGH.GAVFS.DYSDELDILVSGSADF..KVWAL..GT.LNTL.GHTE
Retrocopy VTGSFDSTMACWEWSSGARTQHFRGHMGAVFSADYSDELDILVSGSADFVMKVWALTDGTYLNTLLGHTE

Parental  WVTKVVLQQCKVKS-LLHSPGDYILLSADKYEIKIWPIGREINCKCLKTLSVSEDRSICLQPRLHFDGKY
          .VTKVVLQ.C.VKS..LHS.GDYIL.SADKYEI.IWPIGRE.NCKCL..LS.S.DRSICLQ.RLHFDGKY
Retrocopy *VTKVVLQKCQVKS<SLHSRGDYILISADKYEIEIWPIGREVNCKCLTGLSISKDRSICLQSRLHFDGKY

Parental  IVCSSALGLYQWDFASYDILRVIKTPEVANLALLGFGDVFALLFDNHYLYIMDLRTESLISRWPLPEYRK
          IVCSSALGLYQWDFASYDIL.VIKTP.VANLA.LGFGDVF.LL...H.LYIMDLRT.S............
Retrocopy IVCSSALGLYQWDFASYDILGVIKTPKVANLAFLGFGDVFTLL--RHCLYIMDLRTGSSLTTGHC-QRTE

Parental  SKRGSSFLAGEASWLNGLDGHNDTGLVFATSMPDHSIHLVL
          ..R.SSFLAGEASWLNGLD..ND.GLVFATSM.DHS.HLVL
Retrocopy NQRSSSFLAGEASWLNGLDERNDMGLVFATSMLDHSVHLVL

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	63.70 RPM
SRP017611_kidney	0.00 RPM	31.82 RPM
SRP017611_liver	0.00 RPM	34.49 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2358 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2358 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2358 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000016280	1 retrocopy	retro_rnor_603,
Rattus norvegicus	ENSRNOG00000018687	1 retrocopy	retro_rnor_2358 ,
Tarsius syrichta	ENSTSYG00000008021	1 retrocopy	retro_tsyr_1373,