RetrogeneDB ID: retro_mmus_2970

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:122838086..122838286(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Tbca
• Ensembl ID: ENSMUSG00000042043
• Aliases: Tbca, Tbca13
• Description: tubulin cofactor A [Source:MGI Symbol;Acc:MGI:107549]

Sequence

>retro_mmus_2970
GCTGAAGATGGAGAAAACGACCCCATTAAGAAGCAGACAGATATCCTGTAAGAGTCCCGGATGATGACCCCAGATTGCCA
GCGTCGGTTAGAAGCTGCATATACTGATCTTCAACAGATATTAGAAAGTGAAAAAGACTTGGAAGAAACTGAAGAGTATA
AAGAAGCCCTGTAGTGCTGGATTCTGTGAAGCTAGAAGCC

Alignment

ORF - retro_mmus_2970 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.76 %
• Parental protein coverage: 62.04 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AEDGENYAIKKQAEILQESRMMIPDCQRRLEAAYTDLQQILESEKDLEEAEEYKEA-RVVLDSVKLEA
          AEDGEN..IKKQ..IL.ESRMM.PDCQRRLEAAYTDLQQILESEKDLEE.EEYKEA..VVLDSVKLEA
Retrocopy AEDGENDPIKKQTDIL*ESRMMTPDCQRRLEAAYTDLQQILESEKDLEETEEYKEA<PVVLDSVKLEA

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	0.00 RPM	15.65 RPM
SRP007412_cerebellum	0.00 RPM	13.98 RPM
SRP007412_heart	0.00 RPM	16.47 RPM
SRP007412_kidney	0.02 RPM	30.09 RPM
SRP007412_liver	0.05 RPM	33.13 RPM
SRP007412_testis	0.09 RPM	41.44 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2970 was not detected

EST

No EST(s) were mapped for retro_mmus_2970 retrocopy.

TSS

No TSS is located nearby retro_mmus_2970 retrocopy 5' end.

Lab

retro_mmus_2970 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2970 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014223	4 retrocopies	retro_acar_11, retro_acar_130, retro_acar_142, retro_acar_195,
Callithrix jacchus	ENSCJAG00000019848	4 retrocopies	retro_cjac_114, retro_cjac_2160, retro_cjac_2173, retro_cjac_2974,
Cavia porcellus	ENSCPOG00000012187	1 retrocopy	retro_cpor_930,
Echinops telfairi	ENSETEG00000016572	1 retrocopy	retro_etel_93,
Homo sapiens	ENSG00000171530	3 retrocopies	retro_hsap_3065, retro_hsap_346, retro_hsap_4667,
Macaca mulatta	ENSMMUG00000011853	1 retrocopy	retro_mmul_229,
Mus musculus	ENSMUSG00000042043	3 retrocopies	retro_mmus_1486, retro_mmus_2839, retro_mmus_2970 ,
Otolemur garnettii	ENSOGAG00000010198	1 retrocopy	retro_ogar_3193,
Ochotona princeps	ENSOPRG00000002460	4 retrocopies	retro_opri_550, retro_opri_727, retro_opri_879, retro_opri_91,
Pongo abelii	ENSPPYG00000015579	2 retrocopies	retro_pabe_2540, retro_pabe_350,
Pan troglodytes	ENSPTRG00000017013	2 retrocopies	retro_ptro_2067, retro_ptro_274,
Rattus norvegicus	ENSRNOG00000048342	1 retrocopy	retro_rnor_140,
Sorex araneus	ENSSARG00000009943	1 retrocopy	retro_sara_699,
Ictidomys tridecemlineatus	ENSSTOG00000009840	1 retrocopy	retro_itri_246,
Tupaia belangeri	ENSTBEG00000006034	6 retrocopies	retro_tbel_1073, retro_tbel_113, retro_tbel_1286, retro_tbel_2336, retro_tbel_2905, retro_tbel_756,
Tarsius syrichta	ENSTSYG00000000514	1 retrocopy	retro_tsyr_1038,