RetrogeneDB ID: retro_mmus_3309

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:120246758..120247098(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Nenf
• Ensembl ID: ENSMUSG00000037499
• Aliases: Nenf, 1110060M21Rik, SCIRP10, Spuf
• Description: neuron derived neurotrophic factor [Source:MGI Symbol;Acc:MGI:1913458]

Sequence

>retro_mmus_3309
GCTCACTGTAGCAATGAAGAGGAGAATCAGTTCATCTATTTAATGGCAGAGGGAGTAGTGTCTGATGTCAGTTTGGGAAA
GGACTTTCATAAGAATAGCAGCCTCATACAGTCCCTTGACTGTGAAGGACTCCACCTAAGGCGTGGCCAAGATGTCCCTG
GATTCTGCAGGCGTCACCCATGATTCTACAGGACTCATGGCCAAGGAGTTGGAGTCCCTGGGTGACATCTGTAGCAGGAT
GTCCAAAGCCAAACACCCTATTGTTGGCTACGTGGCCCACAGGACCCTTAAGGAGGATGGCAGCCCTAACCTGGACTCCA
AGCCTGAAGATCAGCTCCAT

Alignment

ORF - retro_mmus_3309 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.4 %
• Parental protein coverage: 66.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ARYGGEEEDQPIYLAVKGVVFDVTSGKEFYGRG-APYNALAGKDSSRGVAKMSLDPADLTHDTTGLTAKE
          A....EEE.Q.IYL...GVV.DV..GK.F.....A.Y..L..KDS..GVAKMSLD.A..THD.TGL.AKE
Retrocopy AHCSNEEENQFIYLMAEGVVSDVSLGKDFHKNS>ASYSPLTVKDST*GVAKMSLDSAGVTHDSTGLMAKE

Parental  LEALDDVFSKVYKAKYPIVGYTARRILNEDGSPNLDFKPEDQPH
          LE.L.D..S...KAK.PIVGY.A.R.L.EDGSPNLD.KPEDQ.H
Retrocopy LESLGDICSRMSKAKHPIVGYVAHRTLKEDGSPNLDSKPEDQLH

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	26.45 RPM
SRP007412_cerebellum	0.00 RPM	33.00 RPM
SRP007412_heart	0.00 RPM	49.34 RPM
SRP007412_kidney	0.00 RPM	28.34 RPM
SRP007412_liver	0.00 RPM	7.29 RPM
SRP007412_testis	0.00 RPM	7.91 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3309 was not detected

EST

No EST(s) were mapped for retro_mmus_3309 retrocopy.

TSS

No TSS is located nearby retro_mmus_3309 retrocopy 5' end.

Lab

retro_mmus_3309 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3309 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001341	1 retrocopy	retro_amel_836,
Bos taurus	ENSBTAG00000000759	1 retrocopy	retro_btau_1238,
Dasypus novemcinctus	ENSDNOG00000003399	1 retrocopy	retro_dnov_1256,
Felis catus	ENSFCAG00000031796	1 retrocopy	retro_fcat_1171,
Homo sapiens	ENSG00000117691	2 retrocopies	retro_hsap_3288, retro_hsap_379,
Gorilla gorilla	ENSGGOG00000025197	1 retrocopy	retro_ggor_830,
Macaca mulatta	ENSMMUG00000002142	2 retrocopies	retro_mmul_2064, retro_mmul_490,
Mus musculus	ENSMUSG00000037499	1 retrocopy	retro_mmus_3309 ,
Nomascus leucogenys	ENSNLEG00000002893	1 retrocopy	retro_nleu_1354,
Ochotona princeps	ENSOPRG00000014204	2 retrocopies	retro_opri_127, retro_opri_775,
Pongo abelii	ENSPPYG00000000236	2 retrocopies	retro_pabe_2717, retro_pabe_328,
Pan troglodytes	ENSPTRG00000001961	2 retrocopies	retro_ptro_2224, retro_ptro_295,
Sus scrofa	ENSSSCG00000015597	1 retrocopy	retro_sscr_393,
Ictidomys tridecemlineatus	ENSSTOG00000022293	2 retrocopies	retro_itri_1876, retro_itri_340,
Tarsius syrichta	ENSTSYG00000001880	3 retrocopies	retro_tsyr_1189, retro_tsyr_411, retro_tsyr_549,