RetrogeneDB ID: retro_mmus_3238

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:126476103..126476805(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000074026
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Tk1
• Ensembl ID: ENSMUSG00000025574
• Aliases: Tk1, D530002A18Rik, Tk-1, Tk1a, Tk1b
• Description: thymidine kinase 1 [Source:MGI Symbol;Acc:MGI:98763]

Sequence

>retro_mmus_3238
ATGAGCTACATCAATCTACCCACCGTGCTGCCCAGCTCCCCCAGCAAGACCCGGGGGCAGATTCAGGTGATTTTCGGGCC
CATGTTCTCAGGGAAAAGCACGGAGCTGATGAGAAGAGTCCGGCGCTTCCAGATCGCCCAGTACAAGTGCCTGGTCATCA
AGTATGCCAAAGACACGCGCTATAGCAACAGCTTCTCCACACATGATCGGAACACCATTGACGCATTGCCAGCCTGCATG
CTCCGCGATGTGACCCAGGAGTCCTTGAGTGTGGCCGTCATTGGCATCGATGAGGGGCAGTTTTTTCCTGACATTGTGGA
TTTCTGTGAAATGATGGCCAACGAGGGCAAGACAGTAATTGTGGCAGCACTGGATGGGACCTTCCAGAGGAAGGCTTTCG
GCAGCATCTTGAACCTGGTGCCCCTGGCGGAGAGTGTGGTGAAGCTCACCGCTGTGTGCATGGAGTGCTTCCGAGAAGCT
GCCTACACGAAGAGGCTGGGTCTGGAGAAAGAGGTGGAGGTGATTGGCGGAGCCGACAAGTATCACTCCGTGTGCCGCCT
GTGCTACTTTAAGAAGTCTTCAGCCCAGGCTGCTGGGTCAGACAACAAAGAGAACTGTCTGGTGCTGGGGCAGCCGGGAG
AGGCCTTGGCTGTCAAGAAGCTCTTTGCCTCTCAGCAAGTCCTACAATACAACTCTGCCAAC

Alignment

ORF - retro_mmus_3238 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.01 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSYINLPTVLPSSPSKTRGQIQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYSNSFSTHDR
          MSYINLPTVLPSSPSKTRGQIQVI.GPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYSNSFSTHDR
Retrocopy MSYINLPTVLPSSPSKTRGQIQVIFGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYSNSFSTHDR

Parental  NTMDALPACMLRDVTQESLGVAVIGIDEGQFFPDIVDFCEMMANEGKTVIVAALDGTFQRKAFGSILNLV
          NT.DALPACMLRDVTQESL.VAVIGIDEGQFFPDIVDFCEMMANEGKTVIVAALDGTFQRKAFGSILNLV
Retrocopy NTIDALPACMLRDVTQESLSVAVIGIDEGQFFPDIVDFCEMMANEGKTVIVAALDGTFQRKAFGSILNLV

Parental  PLAESVVKLTAVCMECFREAAYTKRLGLEKEVEVIGGADKYHSVCRLCYFKKSSAQTAGSDNK-NCLVLG
          PLAESVVKLTAVCMECFREAAYTKRLGLEKEVEVIGGADKYHSVCRLCYFKKSSAQ.AGSDNK.NCLVLG
Retrocopy PLAESVVKLTAVCMECFREAAYTKRLGLEKEVEVIGGADKYHSVCRLCYFKKSSAQAAGSDNKENCLVLG

Parental  QPGEALVVRKLFASQQVLQYNSAN
          QPGEAL.V.KLFASQQVLQYNSAN
Retrocopy QPGEALAVKKLFASQQVLQYNSAN

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
SRP007412_brain	0.00 RPM	1.17 RPM
SRP007412_cerebellum	0.00 RPM	1.04 RPM
SRP007412_heart	0.00 RPM	4.61 RPM
SRP007412_kidney	0.38 RPM	19.04 RPM
SRP007412_liver	1.23 RPM	43.94 RPM
SRP007412_testis	0.14 RPM	2.79 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3238 was not detected

EST

No EST(s) were mapped for retro_mmus_3238 retrocopy.

TSS

No TSS is located nearby retro_mmus_3238 retrocopy 5' end.

Lab

retro_mmus_3238 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3238 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,