RetrogeneDB ID: retro_mmus_1332

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 15:20423360..20423663(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Slmo1
• Ensembl ID: ENSMUSG00000024530
• Aliases: Slmo1, A230074A19Rik, BC019561
• Description: slowmo homolog 1 (Drosophila) [Source:MGI Symbol;Acc:MGI:2442865]

Sequence

>retro_mmus_1332
AACAGGACCTTGCCATTAATCAGAGAACACCATGATTGGTATCCGGCTATAAGGAAAATAGAGCTGTTTTTCACCAGAAT
CATGTTCAAGAATCAGGTGTCAGTGAATGAGAGATTGGTGTAGACACCTCATCCAGTAAACACTGAAAAGACTATGCCCT
CCCAAGAAGCTATCATCACCGTGAGGAACATTAGACTTAGAAACTAGCTGAAAAGTCTAATGGCGAACATGATATCTTCC
AAGGCATAGAAAGGGTGGCCTACCATTGCATAGATAATTGAACACCCTGAGTGCTCTGTAAAC

Alignment

ORF - retro_mmus_1332 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.43 %
• Parental protein coverage: 58.72 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NRTLTYIKERSVVDPAARKMELCSTNITLTNLVSVNERLVYTPHPENPEKTVLTQEAIITVKGISLGSYL
          NRTL..I.E.....PA.RK.EL..T.I...N.VSVNERLV.TPHP.N.EKT...QEAIITV..I.L...L
Retrocopy NRTLPLIREHHDWYPAIRKIELFFTRIMFKNQVSVNERLV*TPHPVNTEKTMPSQEAIITVRNIRLRN*L

Parental  ESLMATTISSNAKKGWAAIEWIIEHSESAIS
          .SLMA..ISS.A.KGW..I..IIEH.E....
Retrocopy KSLMANMISSKA*KGWPTIA*IIEHPECSVN

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	29.76 RPM
SRP007412_cerebellum	0.00 RPM	26.75 RPM
SRP007412_heart	0.00 RPM	0.31 RPM
SRP007412_kidney	0.00 RPM	0.44 RPM
SRP007412_liver	0.00 RPM	0.03 RPM
SRP007412_testis	0.00 RPM	4.53 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1332 was not detected

EST

No EST(s) were mapped for retro_mmus_1332 retrocopy.

TSS

No TSS is located nearby retro_mmus_1332 retrocopy 5' end.

Lab

retro_mmus_1332 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1332 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012800	2 retrocopies	retro_amel_1395, retro_amel_330,
Mus musculus	ENSMUSG00000016257	2 retrocopies	retro_mmus_2725, retro_mmus_630,
Mus musculus	ENSMUSG00000024530	1 retrocopy	retro_mmus_1332 ,
Oryctolagus cuniculus	ENSOCUG00000022237	1 retrocopy	retro_ocun_723,
Procavia capensis	ENSPCAG00000001084	1 retrocopy	retro_pcap_66,