RetrogeneDB ID: retro_rnor_1026

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 14:105141954..105142401(+)
• Located in intron of: ENSRNOG00000005548

Retrocopy information

• Ensembl ID: ENSRNOG00000025903
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Dck
• Ensembl ID: ENSRNOG00000003296
• Aliases: None
• Description: deoxycytidine kinase [Source:RefSeq peptide;Acc:NP_077072]

Sequence

>retro_rnor_1026
ATGGCCACCCCACCTAAGAGGTTCTGCCCTTCTCCCTTGACCAGCTCTGAGGGCACCCGCATCAAGATCTCCATCGATGG
GAACATCGCTGCTGGGAAGTCAACGTTTGTGAATATCCTAAAGCGAGTCTGTGAGGATTGGGGCGTGGTTCCTCAGCCCG
TCGCCAGGTGGTGCAATGTGCAGAACACCCAAGGCAACCCTGAGGAGTTGACAGCATCTCCGAAGAGCGGTGGGAATGCT
CTTCAGATGATGTATGAGAAACCCGAGCGGTGGTCTTTTACCTTCCAATCATACACCTGTCTCAGCCGGATCCGAGCCCA
GCTTGCCTCTCTCAACGGCAGGCTCAAGGATGCAGAGAAACCTGTATTATTTTTGGAACGATCTGTGTATAGTGACAGGT
GTACTTTTGCATCCAATTTGTATGAATCTGACTGCATGAACGAAACA

Alignment

ORF - retro_rnor_1026 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.67 %
• Parental protein coverage: 57.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATPPKRFCSSPSTSSEGTRIKKISIEGNIAAGKSTFVNILKQVCEDWEVVPEPVARWCNVQSTQDEFEE
          MATPPKRFC.SP.TSSEGTRIK.ISI.GNIAAGKSTFVNILK.VCEDW.VVP.PVARWCNVQ.TQ...EE
Retrocopy MATPPKRFCPSPLTSSEGTRIK-ISIDGNIAAGKSTFVNILKRVCEDWGVVPQPVARWCNVQNTQGNPEE

Parental  LTTSQKSGGNVLQMMYEKPERWSFIFQSYACLSRIRAQLASLNGRLRDAEKPVLFFERSVYSDRYIFASN
          LT.S.KSGGN.LQMMYEKPERWSF.FQSY.CLSRIRAQLASLNGRL.DAEKPVLF.ERSVYSDR..FASN
Retrocopy LTASPKSGGNALQMMYEKPERWSFTFQSYTCLSRIRAQLASLNGRLKDAEKPVLFLERSVYSDRCTFASN

Parental  LYESDCMNET
          LYESDCMNET
Retrocopy LYESDCMNET

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	53.35 RPM
SRP017611_kidney	0.00 RPM	3.91 RPM
SRP017611_liver	0.00 RPM	2.89 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1026 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1026 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1026 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000022606	1 retrocopy	retro_fcat_1830,
Myotis lucifugus	ENSMLUG00000005844	1 retrocopy	retro_mluc_2007,
Mus musculus	ENSMUSG00000029366	1 retrocopy	retro_mmus_2735,
Oryctolagus cuniculus	ENSOCUG00000001265	1 retrocopy	retro_ocun_1247,
Pan troglodytes	ENSPTRG00000016139	1 retrocopy	retro_ptro_427,
Pteropus vampyrus	ENSPVAG00000004341	1 retrocopy	retro_pvam_32,
Rattus norvegicus	ENSRNOG00000003296	1 retrocopy	retro_rnor_1026 ,
Xenopus tropicalis	ENSXETG00000018331	1 retrocopy	retro_xtro_9,