RetrogeneDB ID: retro_rnor_1069

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 14:83070416..83070896(-)
• Located in intron of: ENSRNOG00000017548

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cenpo
• Ensembl ID: ENSRNOG00000050111
• Aliases: None
• Description: centromere protein O [Source:MGI Symbol;Acc:MGI:1923800]

Sequence

>retro_rnor_1069
ATGGAGTCTGCAAATACTTTGTGTCCAGGCAGGAAGTGCAAAGGAGGTGTTTTAGCTCACCTGGAAAGACTAGAGGCTCA
AACGAACGTATCGAATAGAAAGTCTGAAGAACCAACAGTTCGTAAAAAGGAAAGTTCTCTTAGAACCAAGATTCGCGAAC
TGCGGCAACAACGAGATAAGCTGAGGGCAGAAGTGAAGCAGTGGGGAGCCAGAGTTAAAGAACCTCCTGCCAAAGAAGAC
CCAAGCAGAACCGTGATCAGTGAACAGGAAGTTCTGGAAAGGGAGTGGAGAAATGTGGACGCCATTCTGGAGGCATATCG
CTTTACGGGGCTCAGCGGGAAGTTGACCAGTCGTGGCGTCTGCATGTGCATCAGCACAGCCTTTGAGGGGAACCTACTAG
ATTCCTACTTTGTGGACCTTGTCATAGAGAAACCACTCCGGATTCATCACCATTCCGTCCCAGTCTTCATCCCTCTGGAA

Alignment

ORF - retro_rnor_1069 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.5 %
• Parental protein coverage: 53.51 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MESANSLCPGTECKGGVLAHLERLEAQMNRSNRKSEEPTVREKESSLRTKIRELQQQRDRLRVEVKQWRA
          MESAN.LCPG..CKGGVLAHLERLEAQ.N.SNRKSEEPTVR.KESSLRTKIREL.QQRD.LR.EVKQW.A
Retrocopy MESANTLCPGRKCKGGVLAHLERLEAQTNVSNRKSEEPTVRKKESSLRTKIRELRQQRDKLRAEVKQWGA

Parental  RVKESSAKEDSSKTTLSEQEVLEKQWRNLKAILQAYRFTGLSGKLTNRRVCVYISTAFEGNLLDSYFVDL
          RVKE..AKED.S.T..SEQEVLE..WRN..AIL.AYRFTGLSGKLT.R.VC..ISTAFEGNLLDSYFVDL
Retrocopy RVKEPPAKEDPSRTVISEQEVLEREWRNVDAILEAYRFTGLSGKLTSRGVCMCISTAFEGNLLDSYFVDL

Parental  AIEKPLRIHHHSIPAFIPLE
          .IEKPLRIHHHS.P.FIPLE
Retrocopy VIEKPLRIHHHSVPVFIPLE

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	0.72 RPM
SRP017611_kidney	0.00 RPM	1.33 RPM
SRP017611_liver	0.00 RPM	0.47 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1069 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1069 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1069 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000010491	1 retrocopy	retro_meug_568,
Pongo abelii	ENSPPYG00000012596	1 retrocopy	retro_pabe_2764,
Rattus norvegicus	ENSRNOG00000050111	1 retrocopy	retro_rnor_1069 ,
Sarcophilus harrisii	ENSSHAG00000005861	1 retrocopy	retro_shar_388,