RetrogeneDB ID: retro_rnor_2229

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:90957560..90957971(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000047928
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rgcc
• Ensembl ID: ENSRNOG00000042960
• Aliases: Rgcc, Rgc32
• Description: Regulator of cell cycle RGCC [Source:UniProtKB/Swiss-Prot;Acc:Q9Z2P4]

Sequence

>retro_rnor_2229
ATGAAGCCGCCCTCCACGCAGAGCAGCCCCGCGGCCGTGGCGGCCGCAGCCCCGGCCATGGACTCCGCGGCCGCTGCAGA
CCTGACGGACATGCTGTGCGAGTTCGACGCGGTGCTGGCCGACTTCGCGTCGCCCTTCCACGAGCGCCACTTCCACTATG
AGGAGCACCTGGAGTGCATGAAGCGGCGCAGCAGCGCCAGCGTCAGTGACAGCAGCGGCTTCAGCGACTCCGAGAGTGCA
GACTCGTTGTACAGGGACAGCTTCACCTTCAGTGATGAGAAGCTGAATTCTCCGACGGACTCCACTCCAGCCCTCTTGTC
CTCCGCTGTCACTCCTCGGAAAGCCAAATTAGGTGACACTAAAAAGCTCGAAGACTTCATCGCTGATCTGGACAGAACCT
TAGCAAGTATG

Alignment

ORF - retro_rnor_2229 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.81 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKPPSTQSSPAAVAAAAPAMDSAAAADLTDVLCEFDAVLADFASPFHERHFHYEEHLERMKRRSSASVSD
          MKPPSTQSSPAAVAAAAPAMDSAAAADLTD.LCEFDAVLADFASPFHERHFHYEEHLE.MKRRSSASVSD
Retrocopy MKPPSTQSSPAAVAAAAPAMDSAAAADLTDMLCEFDAVLADFASPFHERHFHYEEHLECMKRRSSASVSD

Parental  SSGFSDSESADSLYRDSFTFSDEKLNSPTDSTPALLSSAVTPRKAKLGDTKELEDFIADLDRTLASM
          SSGFSDSESADSLYRDSFTFSDEKLNSPTDSTPALLSSAVTPRKAKLGDTK.LEDFIADLDRTLASM
Retrocopy SSGFSDSESADSLYRDSFTFSDEKLNSPTDSTPALLSSAVTPRKAKLGDTKKLEDFIADLDRTLASM

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	0.14 RPM	17.83 RPM
SRP017611_kidney	0.00 RPM	9.77 RPM
SRP017611_liver	0.00 RPM	0.13 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2229 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2229 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2229 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000042960	1 retrocopy	retro_rnor_2229 ,