RetrogeneDB ID: retro_rnor_533

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:232986592..232987190(+)
• Located in intron of: ENSRNOG00000020440

Retrocopy information

• Ensembl ID: ENSRNOG00000036633
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RGD1359508
• Ensembl ID: ENSRNOG00000038330
• Aliases: None
• Description: UPF0462 protein C4orf33 homolog [Source:UniProtKB/Swiss-Prot;Acc:Q5M845]

Sequence

>retro_rnor_533
GTGGATTGTAAAATTGAATACACTTGGGATAGTTTTCCAGTAAGTCAGGAGCCAGTGCGTGCCAGGCTGAATCCATGTGA
CAAGGGATTGAAGATGGAGGTTACTGCTCCATATTTCAGTGATCCTCTAGCCCCTCTTGGAGAACCAGGAAAGCCTTTCA
GTGAACTGTGGAATTATGAAGTTGTGGAAGCATTCTTCTTGAATGATACCACTGAGCAGTATTTAGAAGTTGAACTTTGT
CCACATGGACAACATTTAGTTCTTTTACTTCCTGGAAGAAAAAATGTTTGGGAAAAAAGAGCTTGCATTATCATTCAAAG
TGTCCAGAGGAGAGACTCATTGGGAAGGTGAAGCTTATCTTCCTTGGGGTTATTTTCCATCTAATGTGACACGATTCAAC
TCATTTGCAATCCATGGATCAAATGATAGAAGAGTTTATGAAGCGCTTTACCCTGCGCCACAACCTGAGCTGCAACAAGG
ACAAAATCCTGACTTCCATCGTCTAAAATATTTCAAGCCTTTCAGTTTTAACACACTGCTTGGAGAAGAGTGGAAGCAGC
CAGAATCAGACCTGTGGCTGATAGAGAAATCCGATGTA

Alignment

ORF - retro_rnor_533 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.5 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDFKIEYTWDSFPVSHEPVRIRLNPCDKGLKMEVSAPFFNDPPAPLGEPGKPFSELWNYEVVEAFFLNNT
          .D.KIEYTWDSFPVS.EPVR.RLNPCDKGLKMEV.AP.F.DP.APLGEPGKPFSELWNYEVVEAFFLN.T
Retrocopy VDCKIEYTWDSFPVSQEPVRARLNPCDKGLKMEVTAPYFSDPLAPLGEPGKPFSELWNYEVVEAFFLNDT

Parental  TEQYLEVELCPHGQHLVLLLSGRRNVW-KKELALSFKVSRGETHWEGEAFLPWSYFPSKVTRFNSFAIHG
          TEQYLEVELCPHGQHLVLLL.GR.NVW.KKELALSFKVSRGETHWEGEA.LPW.YFPS.VTRFNSFAIHG
Retrocopy TEQYLEVELCPHGQHLVLLLPGRKNVW>KKELALSFKVSRGETHWEGEAYLPWGYFPSNVTRFNSFAIHG

Parental  SNDKRVYEALYPVPQPELQQGQNPDFHRLEYFKPFSFNTLLGEEWKQPESDLWLIEKSDI
          SND.RVYEALYP.PQPELQQGQNPDFHRL.YFKPFSFNTLLGEEWKQPESDLWLIEKSD.
Retrocopy SNDRRVYEALYPAPQPELQQGQNPDFHRLKYFKPFSFNTLLGEEWKQPESDLWLIEKSDV

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	2.37 RPM
SRP017611_kidney	0.00 RPM	4.88 RPM
SRP017611_liver	0.00 RPM	3.43 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_533 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_533 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_533 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
Mus musculus	ENSMUSG00000025766	1 retrocopy	retro_mmus_1879,
Otolemur garnettii	ENSOGAG00000010368	1 retrocopy	retro_ogar_2045,
Rattus norvegicus	ENSRNOG00000038330	1 retrocopy	retro_rnor_533 ,
Tupaia belangeri	ENSTBEG00000014766	1 retrocopy	retro_tbel_4617,