RetrogeneDB ID: retro_mmus_246

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:21272402..21272909(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000096375
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Cetn4
• Ensembl ID: ENSMUSG00000045031
• Aliases: None
• Description: centrin 4 [Source:MGI Symbol;Acc:MGI:2677454]

Sequence

>retro_mmus_246
ATGGCATCCAGCCAGCGCATAACTTTAGACCAATGGAAGAAAAAAGCAGCAAAAGTTGAACTGAATGACACCCAGAAGCA
AGAAATTAAAGAGGCCTTTGACTTATTCGATATTGATGGATCTGGAACCATAGATCTGAAAGAACTGAAGATTGCAATGC
GGGCCTTAGGCTTTGAGCCAAAGAAAGAAGAAGTAAAACAACTGATCGCTGAAATCGACAAGGAAGGGACTGGCACCATT
TGTTTTGAAGATTTTTTTGCCATCATGAGCGTAAAAATGAGTGAAAAAGATGAAAAAGAAGAAATACTGAAGGCATTTAA
ATTATTTGATGACGATGCTACGGGAAGCATATCACTAAATAACATCAAGAGGGTTGCCAAGGAGCTAGGGGAAAACTTAA
CCGAAGATGAATTACAGGAAATGCTTGATGAAGCTGATCCTGACGGGGATGGAGAGATTAATGAGGAAGAATTCTTGAAG
ATGATGAAGAAGACCAGCCTTTATTAG

Alignment

ORF - retro_mmus_246 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.4 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASSQRITLDQWKKKAAKVELNDTQKQEIKEAFDLFDIDGSGTIDLKELKIAMRALGFEPKKEEVKQLIA
          MASSQRITLDQWKKKAAKVELNDTQKQEIKEAFDLFDIDGSGTIDLKELKIAMRALGFEPKKEEVKQLIA
Retrocopy MASSQRITLDQWKKKAAKVELNDTQKQEIKEAFDLFDIDGSGTIDLKELKIAMRALGFEPKKEEVKQLIA

Parental  EIDKEGTGTICFEDFFAIMSVKMSEKDEKEEILKAFKLFDDDATGSISLNNIKRVAKELGENLTEDELQE
          EIDKEGTGTICFEDFFAIMSVKMSEKDEKEEILKAFKLFDDDATGSISLNNIKRVAKELGENLTEDELQE
Retrocopy EIDKEGTGTICFEDFFAIMSVKMSEKDEKEEILKAFKLFDDDATGSISLNNIKRVAKELGENLTEDELQE

Parental  MLDEADRDGDGEINEEEFLKMMKKTSLY
          MLDEAD.DGDGEINEEEFLKMMKKTSLY
Retrocopy MLDEADPDGDGEINEEEFLKMMKKTSLY

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	3.85 RPM
SRP007412_cerebellum	0.04 RPM	1.43 RPM
SRP007412_heart	0.00 RPM	0.25 RPM
SRP007412_kidney	0.02 RPM	2.83 RPM
SRP007412_liver	0.00 RPM	0.14 RPM
SRP007412_testis	6.31 RPM	152.77 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_246 was not detected

EST

No EST(s) were mapped for retro_mmus_246 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_73635	835 libraries	216 libraries	17 libraries	1 library	3 libraries

The graphical summary, for retro_mmus_246 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_246 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_246 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000018901	2 retrocopies	retro_mdom_182, retro_mdom_325,
Mus musculus	ENSMUSG00000031347	2 retrocopies	retro_mmus_107, retro_mmus_838,
Mus musculus	ENSMUSG00000045031	1 retrocopy	retro_mmus_246 ,