RetrogeneDB ID: retro_mmus_3204

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:61112173..61112523(-)
• Located in intron of: ENSMUSG00000031644

Retrocopy information

• Ensembl ID: ENSMUSG00000080956
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_3204
ATGGTGGACACCTTCGTCAGCACTGGAAGCTAGTGGACAGCAAGAATTTTGATGACTACATGAAGTCACTTGGTGTGGGC
TTTGCCACCAGGCAGGTGGCAAGCATGACCAAGCCTACCACAGTCATTGAGAAGAGTGGGGATACTATCACCATAAAGAT
ACATAGTACCTTCAAGAGCACAGAGATCAGTTTTCATCTGGGGGTAGATTTTGAAGAGGTAACGGCAGATGACAGGAAGG
TTAAGTCAGTCCTAACACTGGGCAGAGGCAAAGTTGTCCATGTGCAGAAGTAGAACAGGCAGGAGAGTATGCTTACAAGG
GAGCTAAGCGACGGGAAAGTCATTCTGACT

Alignment

ORF - retro_mmus_3204 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.97 %
• Parental protein coverage: 87.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADAFVGT-WKLVDSKNFDDYMKSLGVGFATRQVASMTKPTTIIEKNGDTITIKTQSTFKNTEINFQLGI
          M.D.FV.T.WKLVDSKNFDDYMKSLGVGFATRQVASMTKPTT.IEK.GDTITIK..STFK.TEI.F.LG.
Retrocopy MVDTFVST<WKLVDSKNFDDYMKSLGVGFATRQVASMTKPTTVIEKSGDTITIKIHSTFKSTEISFHLGV

Parental  EFDEVTADDRKVKSLVTLDGGKLIHVQKWNGQETTLTRELVDGKLILT
          .F.EVTADDRKVKS..TL..GK..HVQK.N.QE..LTREL.DGK.ILT
Retrocopy DFEEVTADDRKVKSVLTLGRGKVVHVQK*NRQESMLTRELSDGKVILT

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	0.05 RPM	17.38 RPM
SRP007412_cerebellum	0.04 RPM	14.24 RPM
SRP007412_heart	0.19 RPM	1238.89 RPM
SRP007412_kidney	0.06 RPM	279.45 RPM
SRP007412_liver	0.00 RPM	0.05 RPM
SRP007412_testis	0.05 RPM	24.79 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3204 was not detected

EST

No EST(s) were mapped for retro_mmus_3204 retrocopy.

TSS

No TSS is located nearby retro_mmus_3204 retrocopy 5' end.

Lab

retro_mmus_3204 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3204 has 0 orthologous retrocopies within eutheria group .

---

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,