RetrogeneDB ID: retro_rnor_1173

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 16:3900233..3900722(+)
• 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_1173
GTGCGTGGTAATGCGGGGCAAGAAGACTCTGCTGCTGCCGGCCAGTTCAGCTTCAGCCTGGAGCCCACGCTTGAGGACAT
CTGACGCCTCCATGCAGAATTTGCTGCTGAGCGAGACTGGGAGCAGTTCCACCAGCCTCGGAACCTGCTCCTAACTTTGG
TGGGAGAAGTGGGCAAGCTGGCAGAACTCTTTCAGTGGAAGTCTGACGAAGAGCCTGGTCCTCAGGCGTGGCAGCCAAAG
GAGAGAGCAGCCCTTCAGAAGGAGCTTAGTGATGTCCTCATTTACCTGGTGGCATTAGCAGCCCGTTGCCATGTGGACTT
ACCTCGAGCAGTAATTTCCAAAATGGACACCAACCGCCAACGTTACCCAGTCCATCTGTCCCGAGGTTCTGCCTGCAAGT
ACACAGACTTGCCCCGTGGGACCCTCTCTGAAAACAAGGCTGTGGGATCTGGAGGCCCTGCCTCTGAGTTGAGAAACCAG
GCTTCCACC

Alignment

ORF - retro_rnor_1173 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.64 %
• Parental protein coverage: 95.88 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VCGNGGQEDSAAAGPFSFSPEPTLEDIRRLHAEFAAERDWEQFHQPRNLLLALVGEVGELAELFQWKSDA
          V.GN.GQEDSAAAG.FSFS.EPTLEDI.RLHAEFAAERDWEQFHQPRNLLL.LVGEVG.LAELFQWKSD.
Retrocopy VRGNAGQEDSAAAGQFSFSLEPTLEDI*RLHAEFAAERDWEQFHQPRNLLLTLVGEVGKLAELFQWKSDE

Parental  EPGPQAWQPKERAALQEELSDVLIYLVALAARCHVDLPRAVISKMDTNRQRYPVHLSRGSACKYTDLPRG
          EPGPQAWQPKERAALQ.ELSDVLIYLVALAARCHVDLPRAVISKMDTNRQRYPVHLSRGSACKYTDLPRG
Retrocopy EPGPQAWQPKERAALQKELSDVLIYLVALAARCHVDLPRAVISKMDTNRQRYPVHLSRGSACKYTDLPRG

Parental  TLSENEAVGSGDPASELGNQAST
          TLSEN.AVGSG.PASEL.NQAST
Retrocopy TLSENKAVGSGGPASELRNQAST

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_1173 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1173 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1173 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,