RetrogeneDB ID: retro_mmus_3257

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:27611801..27612119(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Naa20
• Ensembl ID: ENSMUSG00000002728
• Aliases: Naa20, 1500004D14Rik, 2900026I01Rik, AU041458, D2Ertd186e, Nat5
• Description: N(alpha)-acetyltransferase 20, NatB catalytic subunit [Source:MGI Symbol;Acc:MGI:1915127]

Sequence

>retro_mmus_3257
ATATCAAAGCTCTCTGTCTATCCTGATTTTCACCGTCCTGGCTTGGCTGCTAAAATTATAGAGTTACTAGAGGAAATTTC
AGAAAGAAACGGTGGATTTTTTGTTGATCTCTTCATAAGAGTATCCAATCAAGTTACTGTCAGCATGTATAAGCAGTTGG
GTTACAGTGTCTACAGGACAGTCATAGAGTACGTACTACTCAGCCAGCAACGGGGAGCCTGATGAGGATGCCTATGAGAT
GAGGAAAGCACTTTCCAGGGACACTGAGAAGAAATCCATCATACCATTACCTTATTCTTGAGGCCTGAGGACATTGAA

Alignment

ORF - retro_mmus_3257 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.78 %
• Parental protein coverage: 55.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VTALSVAPEFRRLGLAAKLMELLEEISERKGGFFVDLFVRVSNQVAVNMYKQLGYSVYRTVIEY-YSASN
          ...LSV.P.F.R.GLAAK..ELLEEISER.GGFFVDLF.RVSNQV.V.MYKQLGYSVYRTVIEY.Y....
Retrocopy ISKLSVYPDFHRPGLAAKIIELLEEISERNGGFFVDLFIRVSNQVTVSMYKQLGYSVYRTVIEY>YYSAS

Parental  -GEPDEDAYDMRKALSRDTEKKSIIPLPHP-VRPEDIE
          .GEPDEDAY.MRKALSRDTEKKSIIPLP....RPEDIE
Retrocopy NGEPDEDAYEMRKALSRDTEKKSIIPLPYS<LRPEDIE

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	24.46 RPM
SRP007412_cerebellum	0.00 RPM	21.58 RPM
SRP007412_heart	0.00 RPM	24.31 RPM
SRP007412_kidney	0.00 RPM	17.15 RPM
SRP007412_liver	0.00 RPM	6.53 RPM
SRP007412_testis	0.00 RPM	10.57 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3257 was not detected

EST

No EST(s) were mapped for retro_mmus_3257 retrocopy.

TSS

No TSS is located nearby retro_mmus_3257 retrocopy 5' end.

Lab

retro_mmus_3257 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3257 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001144	1 retrocopy	retro_btau_899,
Canis familiaris	ENSCAFG00000032025	1 retrocopy	retro_cfam_768,
Callithrix jacchus	ENSCJAG00000005377	4 retrocopies	retro_cjac_1099, retro_cjac_1629, retro_cjac_2984, retro_cjac_439,
Gorilla gorilla	ENSGGOG00000004247	1 retrocopy	retro_ggor_374,
Microcebus murinus	ENSMICG00000006044	1 retrocopy	retro_mmur_540,
Macaca mulatta	ENSMMUG00000007708	1 retrocopy	retro_mmul_479,
Mustela putorius furo	ENSMPUG00000001228	2 retrocopies	retro_mputfur_1495, retro_mputfur_321,
Mus musculus	ENSMUSG00000002728	3 retrocopies	retro_mmus_1228, retro_mmus_3146, retro_mmus_3257 ,
Nomascus leucogenys	ENSNLEG00000009855	1 retrocopy	retro_nleu_2267,
Oryctolagus cuniculus	ENSOCUG00000015481	1 retrocopy	retro_ocun_1331,
Otolemur garnettii	ENSOGAG00000011542	1 retrocopy	retro_ogar_2007,
Pongo abelii	ENSPPYG00000010746	1 retrocopy	retro_pabe_342,
Pan troglodytes	ENSPTRG00000013299	1 retrocopy	retro_ptro_284,
Ictidomys tridecemlineatus	ENSSTOG00000014733	1 retrocopy	retro_itri_1656,
Tupaia belangeri	ENSTBEG00000000969	1 retrocopy	retro_tbel_567,