RetrogeneDB ID: retro_mmus_3347

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:63801192..63801583(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Commd9
• Ensembl ID: ENSMUSG00000027163
• Aliases: Commd9, 1810029F08Rik, AA409293
• Description: COMM domain containing 9 [Source:MGI Symbol;Acc:MGI:1923751]

Sequence

>retro_mmus_3347
ACTAGGCTGGTGGCCTTTGTGGCCTGTCCTCTGCTGAGGCGATTCTGGCTCTCTTTCCAGAAAGTTTCCACCCAAACCTC
AAAACCTGCTGACAAAAATCATCCTGGAGCACATATCAACATGGCAAACCGAAGCCCAAGGAAACCAGATCTCTCGGCCA
CGCCCGGTGGACCTGGACTGGAGCGTGGATAGCAAAACCTCCTCTGACAGCATCAGCCGAATGGCTGTCCCCATATGCCT
GCTCCAGATGAAGATCTAGGAGGATCCTAGTCTGTGTGGAGAGAAACCCTCCATCTCGGCTGTGACCATGGAGCTGAGCA
AAGAGACTCTGGATACCTTGTTAGACGGGCTGGGTCGCATTCGGGACCAGCTTTCTGCTGTAGCTAATAAG

Alignment

ORF - retro_mmus_3347 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.47 %
• Parental protein coverage: 66.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TRLVAFR-DLSSAEAILALFPENFHQNLK-NLLTKIIVEHISTWRAEAQANQISLPRLVDLDWRVDIKTS
          TRLVAF...LSSAEAILALFPE.FH.NLK.NLLTKII.EHISTW..EAQ.NQIS.PR.VDLDW.VD.KTS
Retrocopy TRLVAFV<GLSSAEAILALFPESFHPNLK<NLLTKIILEHISTWQTEAQGNQISRPRPVDLDWSVDSKTS

Parental  SDNISRMAVPTCLLQMKIQEDPSLCGEKPSISAVTMELSKETLDTMLDGLGRIRDQLSAVANK
          SD.ISRMAVP.CLLQMKI.EDPSLCGEKPSISAVTMELSKETLDT.LDGLGRIRDQLSAVANK
Retrocopy SDSISRMAVPICLLQMKI*EDPSLCGEKPSISAVTMELSKETLDTLLDGLGRIRDQLSAVANK

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	12.06 RPM
SRP007412_cerebellum	0.00 RPM	13.03 RPM
SRP007412_heart	0.00 RPM	11.11 RPM
SRP007412_kidney	0.00 RPM	16.30 RPM
SRP007412_liver	0.00 RPM	8.85 RPM
SRP007412_testis	0.00 RPM	12.49 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3347 was not detected

EST

No EST(s) were mapped for retro_mmus_3347 retrocopy.

TSS

No TSS is located nearby retro_mmus_3347 retrocopy 5' end.

Lab

retro_mmus_3347 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3347 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000027163	2 retrocopies	retro_mmus_3347 , retro_mmus_731,
Ochotona princeps	ENSOPRG00000010271	2 retrocopies	retro_opri_848, retro_opri_94,