RetrogeneDB ID: retro_rnor_1914

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:120723144..120723786(-)
• Located in intron of: ENSRNOG00000017291

Retrocopy information

• Ensembl ID: ENSRNOG00000047508
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Tk1
• Ensembl ID: ENSRNOG00000047314
• Aliases: None
• Description: Thymidine kinase, cytosolic [Source:UniProtKB/Swiss-Prot;Acc:P27158]

Sequence

>retro_rnor_1914
ATGAGTTACATCAACCTGCCCACCATGCTGCCCATCTCCCCCAGCAATACCCGGGGGCATATCCAGGTGATTCTCAGGCC
CATGTTCTCAGGGAAAAGCATAGAGCTGATGAGGAGAGCACGGCACTTCCAGATCGCCCAGTACAAGTGCCTGGTCATCA
AGTATGCCAAAGACACGTGCTATAGCAGCAACTTCTCAACACATGATCGGAACACCATGGATGCACTGCCAGCCTGCATG
CTCCGGGATGTGGCCCAGGAGGCCTTGAGAGTGGCCGTCGTTGGCATCGATGAAGGGCAGTTTTTCCCTGACATTGTGGA
TTTCTGTGAAACGATAGCCAATGCAGGCAAGACAGTGATTGTGGCGGCGCTGGACGGAACCTTCCAGAGGAAGGCTTTCA
GCAGCATCTTGAACCTGGTGCCCTTGGCCAAGAGTGTGGTGAAGCTCACTGCCATGTGCACGGAGCCCTTTCATGAAGCT
GCCTACACCAAGAGGCTGAGCCTGGAGGAAGAGGGGGAGGTGATTGGCGGAGCAGATAAGTACCTAAGAAGTCTTCAGCC
CAGACTGCAGACAACAAAGAGAACTGCCCAGTGCTGGGGCAGCCGGGAGAGGCCCCGGCTGTCAGGAAGCTCTTTGTCTC
TC

Alignment

ORF - retro_rnor_1914 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.7 %
• Parental protein coverage: 91.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSYINLPTVLPISPSKTRGQIQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYSNSFSTHDR
          MSYINLPT.LPISPS.TRG.IQVIL.PMFSGKS.ELMRR.R.FQIAQYKCLVIKYAKDT.YS..FSTHDR
Retrocopy MSYINLPTMLPISPSNTRGHIQVILRPMFSGKSIELMRRARHFQIAQYKCLVIKYAKDTCYSSNFSTHDR

Parental  NTMDALPACMLKDVAQEALGVAVIGIDEGQFFPDIVDFCETMANTGKTVIVAALDGTFQRKAFGSILNLV
          NTMDALPACML.DVAQEAL.VAV.GIDEGQFFPDIVDFCET.AN.GKTVIVAALDGTFQRKAF.SILNLV
Retrocopy NTMDALPACMLRDVAQEALRVAVVGIDEGQFFPDIVDFCETIANAGKTVIVAALDGTFQRKAFSSILNLV

Parental  PLAESVVKLTAVCMECFREASYTKRLGLEKEVEVIGGADKY-HSVCRLCYFKKSSAQTADNKENYSVLGQ
          PLA.SVVKLTA.C.E.F.EA.YTKRL.LE.E.EVIGGADKY..S........K..AQ.....E.....G.
Retrocopy PLAKSVVKLTAMCTEPFHEAAYTKRLSLEEEGEVIGGADKYLRSLQPRLQTTKRTAQCWGSRERPRLSGS

Parental  PIEI
          ....
Retrocopy SLSL

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	8.23 RPM
SRP017611_liver	0.27 RPM	9.01 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1914 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1914 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1914 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000002133	1 retrocopy	retro_etel_332,
Macropus eugenii	ENSMEUG00000002886	1 retrocopy	retro_meug_129,
Monodelphis domestica	ENSMODG00000001854	2 retrocopies	retro_mdom_227, retro_mdom_691,
Mus musculus	ENSMUSG00000025574	1 retrocopy	retro_mmus_3238,
Rattus norvegicus	ENSRNOG00000047314	2 retrocopies	retro_rnor_1914 , retro_rnor_2057,