RetrogeneDB ID: retro_mmus_65

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:86731986..86732388(-)
• Located in intron of: ENSMUSG00000044937

Retrocopy information

• Ensembl ID: ENSMUSG00000056366
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Fabp3
• Ensembl ID: ENSMUSG00000028773
• Aliases: None
• Description: fatty acid binding protein 3, muscle and heart [Source:MGI Symbol;Acc:MGI:95476]

Sequence

>retro_mmus_65
ATGGCGGACGCCTTTGTCGGTACCTGGAAGCTAGTGGACTGCAAGAATTTTGATGACTACATGAAGTCACTCGGTGTGGG
CTTTGCCACCAGGCAGGTGGCTAGCATGACCAAGCCTACTACCATCATCGAGAAGAACGGGGATACTATCACCATAAAGA
CACAAAGTACCTTCAAGAACACAGAGATCAACTTTCAGCTGGGAATAGAGTTCGACGAGGTGACAGCAGATGACCGGAAG
GTCAAGTCACTGGTGACGCTGGACGGAGGCAAACTCATCCATGTGCAGAAGTGGAATGGGCAGGAGACAACACTAACTAG
GGAGCTAGTTGACAGGAAACTCATCCTGACTCTCACTCATGGCAGTGTGGTGAGCACTCGGACTTATGAGAAGGAGGCGT
GA

Alignment

ORF - retro_mmus_65 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.5 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADAFVGTWKLVDSKNFDDYMKSLGVGFATRQVASMTKPTTIIEKNGDTITIKTQSTFKNTEINFQLGIE
          MADAFVGTWKLVD.KNFDDYMKSLGVGFATRQVASMTKPTTIIEKNGDTITIKTQSTFKNTEINFQLGIE
Retrocopy MADAFVGTWKLVDCKNFDDYMKSLGVGFATRQVASMTKPTTIIEKNGDTITIKTQSTFKNTEINFQLGIE

Parental  FDEVTADDRKVKSLVTLDGGKLIHVQKWNGQETTLTRELVDGKLILTLTHGSVVSTRTYEKEA
          FDEVTADDRKVKSLVTLDGGKLIHVQKWNGQETTLTRELVD.KLILTLTHGSVVSTRTYEKEA
Retrocopy FDEVTADDRKVKSLVTLDGGKLIHVQKWNGQETTLTRELVDRKLILTLTHGSVVSTRTYEKEA

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	0.21 RPM	17.38 RPM
SRP007412_cerebellum	0.17 RPM	14.24 RPM
SRP007412_heart	11.05 RPM	1238.89 RPM
SRP007412_kidney	1.58 RPM	279.45 RPM
SRP007412_liver	0.03 RPM	0.05 RPM
SRP007412_testis	0.87 RPM	24.79 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_65 was not detected

EST

No EST(s) were mapped for retro_mmus_65 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_6858	867 libraries	142 libraries	55 libraries	1 library	7 libraries

The graphical summary, for retro_mmus_65 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_65 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_65 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016819	2 retrocopies	retro_btau_1467, retro_btau_295,
Danio rerio	ENSDARG00000023290	1 retrocopy	retro_drer_33,
Dasypus novemcinctus	ENSDNOG00000000511	2 retrocopies	retro_dnov_1510, retro_dnov_2482,
Equus caballus	ENSECAG00000024852	1 retrocopy	retro_ecab_519,
Homo sapiens	ENSG00000121769	1 retrocopy	retro_hsap_1258,
Gorilla gorilla	ENSGGOG00000014432	1 retrocopy	retro_ggor_990,
Macropus eugenii	ENSMEUG00000012501	6 retrocopies	retro_meug_1037, retro_meug_148, retro_meug_1660, retro_meug_273, retro_meug_563, retro_meug_819,
Microcebus murinus	ENSMICG00000009359	4 retrocopies	retro_mmur_1490, retro_mmur_203, retro_mmur_621, retro_mmur_734,
Myotis lucifugus	ENSMLUG00000013609	2 retrocopies	retro_mluc_1144, retro_mluc_1717,
Mus musculus	ENSMUSG00000027533	4 retrocopies	retro_mmus_1685, retro_mmus_1791, retro_mmus_2084, retro_mmus_3185,
Mus musculus	ENSMUSG00000028773	3 retrocopies	retro_mmus_2804, retro_mmus_3204, retro_mmus_65 ,
Nomascus leucogenys	ENSNLEG00000001586	1 retrocopy	retro_nleu_2097,
Otolemur garnettii	ENSOGAG00000013757	4 retrocopies	retro_ogar_1148, retro_ogar_1312, retro_ogar_1873, retro_ogar_959,
Pongo abelii	ENSPPYG00000001616	1 retrocopy	retro_pabe_1048,
Pan troglodytes	ENSPTRG00000000457	1 retrocopy	retro_ptro_3047,
Rattus norvegicus	ENSRNOG00000012879	1 retrocopy	retro_rnor_2199,
Ictidomys tridecemlineatus	ENSSTOG00000003842	3 retrocopies	retro_itri_1544, retro_itri_640, retro_itri_641,