RetrogeneDB ID: retro_rnor_562

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:6889415..6889973(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000014431
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Dctn3
• Ensembl ID: ENSRNOG00000014208
• Aliases: None
• Description: dynactin 3 [Source:RefSeq peptide;Acc:NP_001102129]

Sequence

>retro_rnor_562
ATGGCGGCTCTGACCGATGTGCAGCGGCTACAGTCCCGAGTGGAGGAGCTGGAGCGCTGGGTGTATGGGCCAGGCGGGAC
CCGAGGCTCTAGGAAGGTAGCTGATGGTCTAGTCAAGGTGCAGGTGGCTTTAGGGAACATTGCCAGTAAGAGGGAGAGGG
TGAAGATTCTCTACAAAAAGATTGAAGTCCTGATCAAATACCTGGATCCTGAGTACATTGATCGCATTGCTATACCTGAG
GCCTCGAAGTTGCAGTTCATCTTGGCAGAGGAACAGTTCATCCTCTCCCAGGTGGCGCTCTTGGAACAAGTGAACACCTT
GGTGCCGGTGCTGGACAGCGCTTCTATCAAAGCCGTTCCTGAGCATGCTGCCCGCCTGCAGCGCTTGGCGCAGATCCACA
TCCAACAGCAGGACCAGTGTGTGGAGATCACTGAGGAGTCCAAGGCTCTCCTGGAGGAGTATAACAAGACTACAATGCTT
CTCTCCAAGCAGCTTGTGCAGTGGGACGAGCTACTCTGCCAGCTAGAGGCTGCCAAGCAAGTGAAGCCAGCAGCAGAA

Alignment

ORF - retro_rnor_562 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.39 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAALTDVQRLQSRVEELERWVYGPGGTRGSRKVADGLVKVQVALGNIASKRERVKILYKKIEDLIKYLDP
          MAALTDVQRLQSRVEELERWVYGPGGTRGSRKVADGLVKVQVALGNIASKRERVKILYKKIE.LIKYLDP
Retrocopy MAALTDVQRLQSRVEELERWVYGPGGTRGSRKVADGLVKVQVALGNIASKRERVKILYKKIEVLIKYLDP

Parental  EYIDRIAIPEASKLQFILAEEQFILSQVALLEQVNTLVPMLDSASIKAVPEHAARLQRLAQIHIQQQDQC
          EYIDRIAIPEASKLQFILAEEQFILSQVALLEQVNTLVP.LDSASIKAVPEHAARLQRLAQIHIQQQDQC
Retrocopy EYIDRIAIPEASKLQFILAEEQFILSQVALLEQVNTLVPVLDSASIKAVPEHAARLQRLAQIHIQQQDQC

Parental  VEITEESKALLEEYNKTTMLLSKQFVQWDELLCQLEAAKQVKPAAE
          VEITEESKALLEEYNKTTMLLSKQ.VQWDELLCQLEAAKQVKPAAE
Retrocopy VEITEESKALLEEYNKTTMLLSKQLVQWDELLCQLEAAKQVKPAAE

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	0.22 RPM	32.93 RPM
SRP017611_kidney	0.07 RPM	20.03 RPM
SRP017611_liver	0.00 RPM	7.46 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_562 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_562 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_562 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
Oryctolagus cuniculus	ENSOCUG00000000358	1 retrocopy	retro_ocun_1894,
Rattus norvegicus	ENSRNOG00000014208	1 retrocopy	retro_rnor_562 ,