RetrogeneDB ID: retro_rnor_2626

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 8:56105405..56105916(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Dctpp1
• Ensembl ID: ENSRNOG00000017850
• Aliases: Dctpp1, RS21-C6, Rs21c6, Xtp3tpa
• Description: dCTP pyrophosphatase 1 [Source:UniProtKB/Swiss-Prot;Acc:Q91VC0]

Sequence

>retro_rnor_2626
ATGTCCCAAGCTGGTACCGGCTGCGTGCGGTAATGGGGGGCAAGAAGACTCTGCTGCTGCCGGCCCATTCAGCTTCAGCC
CAGAGCCCACGCTTGAGGACATCCGACGCCTCCATGCAGAGTTTGCTGCTAAGCGGGACTGGGAGCAGTTCCACCAGCCT
CGGAACCTGCTCCTAGCCTTGGTGGGAGAAGTGGGCGATCTAGCAGAACTCTTTCAGTGAAAGTCTGAGGCAGAGCCTGA
TCCTCAGGCGTGGCAGCCAAAGGAGAGAGCAGCCCTTCAGGAGGAGCTTAGTGACGTCCTCATCTACCTGGTGGCATTAG
CAGCCCGTTGTCATGTGGACTTACCTCGAGCAGTAATCTCCAAAATGGACACCAACCGCCAACGTTACCCAGTCCATCTG
TCCCGGGGCTCTGCCTGCAAGTACACAGACTTGCCCCGTGGGACCCTCTCTGAAAACGAGACTGTGGGGTCTGGAGACCC
TGCCTCTGAGTTGGGAAACCAGGCTTCCACC

Alignment

ORF - retro_rnor_2626 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.32 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSQAGTG-VCGNGGQEDSAAAGPFSFSPEPTLEDIRRLHAEFAAERDWEQFHQPRNLLLALVGEVGELAE
          MSQAGTG..CGNGGQEDSAAAGPFSFSPEPTLEDIRRLHAEFAA.RDWEQFHQPRNLLLALVGEVG.LAE
Retrocopy MSQAGTG>ACGNGGQEDSAAAGPFSFSPEPTLEDIRRLHAEFAAKRDWEQFHQPRNLLLALVGEVGDLAE

Parental  LFQWKSDAEPGPQAWQPKERAALQEELSDVLIYLVALAARCHVDLPRAVISKMDTNRQRYPVHLSRGSAC
          LFQ.KS.AEP.PQAWQPKERAALQEELSDVLIYLVALAARCHVDLPRAVISKMDTNRQRYPVHLSRGSAC
Retrocopy LFQ*KSEAEPDPQAWQPKERAALQEELSDVLIYLVALAARCHVDLPRAVISKMDTNRQRYPVHLSRGSAC

Parental  KYTDLPRGTLSENEAVGSGDPASELGNQAST
          KYTDLPRGTLSENE.VGSGDPASELGNQAST
Retrocopy KYTDLPRGTLSENETVGSGDPASELGNQAST

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	2.16 RPM
SRP017611_kidney	0.00 RPM	1.05 RPM
SRP017611_liver	0.00 RPM	1.34 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2626 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2626 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2626 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016594	1 retrocopy	retro_cfam_887,
Callithrix jacchus	ENSCJAG00000002621	2 retrocopies	retro_cjac_43, retro_cjac_676,
Myotis lucifugus	ENSMLUG00000013774	1 retrocopy	retro_mluc_1052,
Otolemur garnettii	ENSOGAG00000011361	1 retrocopy	retro_ogar_874,
Rattus norvegicus	ENSRNOG00000017850	2 retrocopies	retro_rnor_1173, retro_rnor_2626 ,
Sus scrofa	ENSSSCG00000007796	1 retrocopy	retro_sscr_676,