RetrogeneDB ID: retro_rnor_455

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:82247639..82248129(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rab12
• Ensembl ID: ENSRNOG00000019295
• Aliases: None
• Description: ras-related protein Rab-12 [Source:RefSeq peptide;Acc:NP_037149]

Sequence

>retro_rnor_455
GGCGCACTGCACCGCTGCCGGAAGCAGCCCCGCGGGCCGGCGGACTTCAAGCTGCGGGTCATCATCAACGGCTCCCACGG
AGTGGGCAAGACCAGCCTGATGGAGTGCTTCACCGAGGACACCTTCTGCGAGAGACCTGCAAGTCCACCGTGGGTGTTGA
CTTTAAAATCAAGACTGTAGAACTAAGAGGGAAGAAAATTAGATTACAGATCTGGGACACAGCAGGGCAGAGCAATTTAA
CAGCATTACCTCAGCCTATTACAGAAGTGCCAAGGGCATCATACTCGTGTATGACATCACCAAGAAAGAGCCGTTCGATG
ACTTGACAAAGTGGATGGCGATGATCGGTAAGTATGCTTCAGAAGACGCTGAGCTTCTCCTGGTCGGAAATAAACTGGAC
TGTGAAACAGACAGAGAAAGCTCCAGGCAGCAAGGAGAAAAGCTTGCACAGCAGATAACCGGGATGCGGTTCTGCGAAGC
CAGTGCCAAG

Alignment

ORF - retro_rnor_455 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.11 %
• Parental protein coverage: 87.17 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GGQARRRKQPPRPADFKLQVIIIGSRGVGKTSLMERFTDDTFCEACKSTVGV-DFKIKTVELRGKKI-RL
          G...R.RKQP..PADFKL.VII.GS.GVGKTSLME.FT.DTFCE...S...V...K.......G.K..RL
Retrocopy GALHRCRKQPRGPADFKLRVIINGSHGVGKTSLMECFTEDTFCERPASPPWVLTLKSRL*N*EGRKL<RL

Parental  QIWDTAGQ-ERFNSITSAYYRSAKGIILVYDITKKETFDDLPKWMKMIDKYASEDAELLLVGNKLDCETD
          QIWDTAGQ.E.FNSITSAYYRSAKGIILVYDITKKE.FDDL.KWM.MI.KYASEDAELLLVGNKLDCETD
Retrocopy QIWDTAGQ<EQFNSITSAYYRSAKGIILVYDITKKEPFDDLTKWMAMIGKYASEDAELLLVGNKLDCETD

Parental  REISRQQGEKFAQQITGMRFCEASAK
          RE.SRQQGEK.AQQITGMRFCEASAK
Retrocopy RESSRQQGEKLAQQITGMRFCEASAK

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	3.38 RPM	14.38 RPM
SRP017611_kidney	0.91 RPM	6.28 RPM
SRP017611_liver	0.07 RPM	2.22 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_455 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_455 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_455 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
Rattus norvegicus	ENSRNOG00000004992	1 retrocopy	retro_rnor_110,
Rattus norvegicus	ENSRNOG00000019295	1 retrocopy	retro_rnor_455 ,