RetrogeneDB ID: retro_mmus_2869

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:122792583..122793324(-)
• Located in intron of: ENSMUSG00000003153

Retrocopy information

• Ensembl ID: ENSMUSG00000092076
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Uck1
• Ensembl ID: ENSMUSG00000002550
• Aliases: Uck1, URK1, Umpk
• Description: uridine-cytidine kinase 1 [Source:MGI Symbol;Acc:MGI:98904]

Sequence

>retro_mmus_2869
GGCACCGCTAGTGGCAAGTCAACAGTGTGTGAGAAGATCATGGAGCTGCTGGGACAGAACGAAGTGGACCGCCGGCAGCG
CAAGTTGGTCATCCTGAGCCAGGATTGCTTCTACAAGGTTCTGACGGCCGAGCAGAAGGCCAAGGCTTTGAAGGGACAGT
ACAATTTTGACCACCCAGATGCTTTTGATAATGATCTGATGCACAAGACCCTGAAAAACATTGTTGAAGGCAAAACTGTC
GAGGTCCCTACCTATGATTTTGTGACCCACTCAAGGTTACCAGAGACCACTGTGGTCTACCCAGCTGATGTGGTTCTGTT
CGAGGGCATCTTGGTATTCTACACCCGGGAGATCCGGGACATGTTCCACCTGCGCCTCTTTGTGGACACAGACTCTGATG
TTAGGCTGTCTCGAAGAGTTCTCCGGGATGTGCAACGAGGAAGGGACCTGGAACAGATCCTGACTCAGTATACCGCCTTT
GTGAAACCAGCCTTTGAGGAGTTCTGCCTGCCGACTAAGAAGTACGCTGACGTGATCATCCCTCGAGGAGTTGATAATAT
GGTGGCCATCAACCTGATCGTGCAACACATCCAGGACATCCTCAACGGGGACCTGTGCAAGCAGCACCGAGGCGGGCCCA
ACGGGCGCAACCACAAGAGGACCTTCCCCGAGCCAGGAGATCACCCTGGGGTGTTGGCCACTGGCAAGCGCTCACACCTG
GAGTCTAGCAGCAGACCCCAT

Alignment

ORF - retro_mmus_2869 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.19 %
• Parental protein coverage: 87.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GTASGKSTVCEKIMELLGQNEVDRRQRKLVILSQDCFYKVLTAEQKAKALKGQYNFDHPDAFDNDLMHKT
          GTASGKSTVCEKIMELLGQNEVDRRQRKLVILSQDCFYKVLTAEQKAKALKGQYNFDHPDAFDNDLMHKT
Retrocopy GTASGKSTVCEKIMELLGQNEVDRRQRKLVILSQDCFYKVLTAEQKAKALKGQYNFDHPDAFDNDLMHKT

Parental  LKNIVEGKTVEVPTYDFVTHSRLPETTVVYPADVVLFEGILVFYTQEIRDMFHLRLFVDTDSDVRLSRRV
          LKNIVEGKTVEVPTYDFVTHSRLPETTVVYPADVVLFEGILVFYT.EIRDMFHLRLFVDTDSDVRLSRRV
Retrocopy LKNIVEGKTVEVPTYDFVTHSRLPETTVVYPADVVLFEGILVFYTREIRDMFHLRLFVDTDSDVRLSRRV

Parental  LRDVQRGRDLEQILTQYTAFVKPAFEEFCLPTKKYADVIIPRGVDNMVAINLIVQHIQDILNGDLCKRHR
          LRDVQRGRDLEQILTQYTAFVKPAFEEFCLPTKKYADVIIPRGVDNMVAINLIVQHIQDILNGDLCK.HR
Retrocopy LRDVQRGRDLEQILTQYTAFVKPAFEEFCLPTKKYADVIIPRGVDNMVAINLIVQHIQDILNGDLCKQHR

Parental  GGPNGRNHKRTFPEPGDHPGVLATGKRSHLESSSRPH
          GGPNGRNHKRTFPEPGDHPGVLATGKRSHLESSSRPH
Retrocopy GGPNGRNHKRTFPEPGDHPGVLATGKRSHLESSSRPH

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	0.02 RPM	16.31 RPM
SRP007412_cerebellum	0.04 RPM	17.50 RPM
SRP007412_heart	0.06 RPM	9.87 RPM
SRP007412_kidney	0.13 RPM	29.49 RPM
SRP007412_liver	0.00 RPM	14.04 RPM
SRP007412_testis	0.05 RPM	9.42 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2869 was not detected

EST

No EST(s) were mapped for retro_mmus_2869 retrocopy.

TSS

No TSS is located nearby retro_mmus_2869 retrocopy 5' end.

Lab

retro_mmus_2869 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2869 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000004903	1 retrocopy	retro_mmur_782,
Mus musculus	ENSMUSG00000002550	2 retrocopies	retro_mmus_2869 , retro_mmus_3145,
Otolemur garnettii	ENSOGAG00000028797	1 retrocopy	retro_ogar_2882,