RetrogeneDB ID: retro_mmus_2576

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:69461062..69461738(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000043484
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Cmpk1
• Ensembl ID: ENSMUSG00000028719
• Aliases: None
• Description: cytidine monophosphate (UMP-CMP) kinase 1 [Source:MGI Symbol;Acc:MGI:1913838]

Sequence

>retro_mmus_2576
ATGCTGAGCAGCTGTCCTCGCCTGCTGCCGCACGTCCTGGTCCCGAGCTGCCTGCCGCTGACCCGCAGACTGCTGCTCTT
CCCACCACATGAAGCCATTGGTCTTGTTCATTTTGGGCGGGCCCGGTGCGGGCAAGGGGACCCAGTGTGTGTGCATTGTC
GAGAAATATGGCTCCACACACCTTTCTGCAGGAGAGCTTCTTCGTGATGAAAGGAAGAATCCAGACTCTCAGTATGATGA
GCTTATTGAAAAGTACATTAAAGAAGGAAAGATTGTACCAGTTGAGATAACCATCAGTTTATTAAGGAGGGAAATGGACC
AAACAATGGCTGCCAATGCTCAGAAGAATAAATTCTTGATTGATGGATTTCCGAGAAATCAAGACAACGTTCAAGGCTGG
AACAAAACCATGGATGGAAAAGCAGATGTATCTTTTGTTCTGTTTTTTGACTGTAATAATGAGATCTGTATTGAACGATG
TCCTGAAAGGGGAAAAAGTAGTGGTAAGAGTGACGACAACAGAGAGAGCTTGGAAAAGAGAATTCAGACTTACTTTGAAT
CACCAAAACCAATTATTGACTTATATGAAGAAATGGGGAAAGTCAAGAAGATAGATGTTTCTAAGTCTGTTGATGAAGTT
TTTGGTGAAGTTGTGAAGATTTTTGACAAAGAAGGC

Alignment

ORF - retro_mmus_2576 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.47 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLSSCRRLLPHVLVPSCPPLTRTLRLFPL-HLMKPLVVFVLGGPGAGKGTQCARIVEKYGYTHLSAGELL
          MLSSC.RLLPHVLVPSC..L..T.RL....H.MKPLV.F.LGGPGAGKGTQC..IVEKYG.THLSAGELL
Retrocopy MLSSCPRLLPHVLVPSC--LPLTRRLLLF>HHMKPLVLFILGGPGAGKGTQCVCIVEKYGSTHLSAGELL

Parental  RDERKNPDSQYGELIEKYIKEGKIVPVEITISLLKREMDQTMAANAQKNKFLIDGFPRNQDNLQGWNKTM
          RDERKNPDSQY.ELIEKYIKEGKIVPVEITISLL.REMDQTMAANAQKNKFLIDGFPRNQDN.QGWNKTM
Retrocopy RDERKNPDSQYDELIEKYIKEGKIVPVEITISLLRREMDQTMAANAQKNKFLIDGFPRNQDNVQGWNKTM

Parental  DGKADVSFVLFFDCNNEICIERCLERGKSSGRSDDNRESLEKRIQTYLESTKPIIDLYEEMGKVKKIDAS
          DGKADVSFVLFFDCNNEICIERC.ERGKSSG.SDDNRESLEKRIQTY.ES.KPIIDLYEEMGKVKKID.S
Retrocopy DGKADVSFVLFFDCNNEICIERCPERGKSSGKSDDNRESLEKRIQTYFESPKPIIDLYEEMGKVKKIDVS

Parental  KSVDEVFGEVVKIFDKEG
          KSVDEVFGEVVKIFDKEG
Retrocopy KSVDEVFGEVVKIFDKEG

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	0.09 RPM	45.86 RPM
SRP007412_cerebellum	0.04 RPM	30.00 RPM
SRP007412_heart	0.00 RPM	18.30 RPM
SRP007412_kidney	0.10 RPM	66.64 RPM
SRP007412_liver	0.03 RPM	52.49 RPM
SRP007412_testis	0.00 RPM	8.00 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2576 was not detected

EST

No EST(s) were mapped for retro_mmus_2576 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_115095	454 libraries	125 libraries	393 libraries	76 libraries	24 libraries

The graphical summary, for retro_mmus_2576 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_2576 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2576 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004030	1 retrocopy	retro_cfam_1729,
Choloepus hoffmanni	ENSCHOG00000004014	2 retrocopies	retro_chof_609, retro_chof_840,
Cavia porcellus	ENSCPOG00000014747	4 retrocopies	retro_cpor_1070, retro_cpor_1295, retro_cpor_417, retro_cpor_799,
Macaca mulatta	ENSMMUG00000017375	2 retrocopies	retro_mmul_1572, retro_mmul_66,
Mustela putorius furo	ENSMPUG00000012394	1 retrocopy	retro_mputfur_1061,
Mus musculus	ENSMUSG00000026817	1 retrocopy	retro_mmus_3666,
Mus musculus	ENSMUSG00000028719	1 retrocopy	retro_mmus_2576 ,
Rattus norvegicus	ENSRNOG00000007775	1 retrocopy	retro_rnor_1940,
Sus scrofa	ENSSSCG00000003885	1 retrocopy	retro_sscr_454,