RetrogeneDB ID: retro_rnor_2739

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 9:69720167..69720481(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000047299
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Nop16
• Ensembl ID: ENSRNOG00000017284
• Aliases: Nop16, RGD1305727
• Description: Nucleolar protein 16 [Source:UniProtKB/Swiss-Prot;Acc:Q1RP77]

Sequence

>retro_rnor_2739
GAGGCCATGGAGGTAGACACCGAGGAGAGACCCAAGGATCTTGTTCGGAAGCCCTATGTGGTAAATGACCTGGAGGCAGA
AGCCAGCCTCCCACAGAAGAAAGGAAATACCTTGTCTCAGGACCTCATCGATTATGTTTATTACGTGGTGGAGAATCACG
GGAGGACTATAAGGCCATGGCCAAGAGAAGAAAAATTACTATCAAGACACCCCAAAACAGATTTGGAACGAGATCAATGT
CTATAAGCGCTTTTAACCCAATGGAATGGCAAGTCTTCATGGATTCTTTGCAGAATAAGAAGATAGAGGTAGAC

Alignment

ORF - retro_rnor_2739 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 58.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KAMEVDTEERPKDLVRKPYVVNDLEAEASLPEKKGNTLSRDLIDYVHYMVENHG-EDYKAMAR-DEKNYY
          .AMEVDTEERPKDLVRKPYVVNDLEAEASLP.KKGNTLS.DLIDYV.Y.VENHG.EDYKAMA....KNYY
Retrocopy EAMEVDTEERPKDLVRKPYVVNDLEAEASLPQKKGNTLSQDLIDYVYYVVENHG<EDYKAMAK<EKKNYY

Parental  QDTPKQIRNKINVYKR-FYPTEWQVFVASLQNKKMEVD
          QDTPKQI.N.INVYKR.F.P.EWQVF..SLQNKK.EVD
Retrocopy QDTPKQIWNEINVYKR>FNPMEWQVFMDSLQNKKIEVD

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	0.07 RPM	22.72 RPM
SRP017611_kidney	0.14 RPM	17.38 RPM
SRP017611_liver	0.07 RPM	10.62 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2739 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2739 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2739 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016694	2 retrocopies	retro_cfam_1790, retro_cfam_1793,
Callithrix jacchus	ENSCJAG00000012315	1 retrocopy	retro_cjac_2208,
Cavia porcellus	ENSCPOG00000026072	1 retrocopy	retro_cpor_129,
Echinops telfairi	ENSETEG00000010391	1 retrocopy	retro_etel_1329,
Myotis lucifugus	ENSMLUG00000003504	1 retrocopy	retro_mluc_2425,
Mustela putorius furo	ENSMPUG00000012552	1 retrocopy	retro_mputfur_381,
Mus musculus	ENSMUSG00000025869	2 retrocopies	retro_mmus_3033, retro_mmus_3258,
Otolemur garnettii	ENSOGAG00000000824	2 retrocopies	retro_ogar_1323, retro_ogar_2299,
Rattus norvegicus	ENSRNOG00000017284	1 retrocopy	retro_rnor_2739 ,
Sus scrofa	ENSSSCG00000029577	1 retrocopy	retro_sscr_510,
Ictidomys tridecemlineatus	ENSSTOG00000004869	1 retrocopy	retro_itri_1124,