RetrogeneDB ID: retro_mmus_3299

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:94416588..94416855(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tctex1d2
• Ensembl ID: ENSMUSG00000014075
• Aliases: Tctex1d2, 0610012D17Rik, 2410011K15Rik
• Description: Tctex1 domain containing 2 [Source:MGI Symbol;Acc:MGI:1913311]

Sequence

>retro_mmus_3299
GGCTTGTGCGAGGTGGACAAGAACTCAGAGGAGCCTGAGAACACCTATATTCTGAGGCTCATTGTCCAGCAAAAGTTTAA
ACTCTCTGTGGTTAAAGACTGCATCCATGCTGTGCTCAAGGAAGAATTGGCAAGCACTGAATATTCTTCAGATAAAATGA
TTCAACTCACAAAACATCTATCAGAAATGATTAGAGATAAGCTAAAAGCACGACTGCTCACTGTTTCTGGGATGCAGACA
CCAACAACTACATTCACAATGTTTGCA

Alignment

ORF - retro_mmus_3299 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.65 %
• Parental protein coverage: 85.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GLSEVDKNSGEPENTYILRPIFQQRFRPSVVKDCIHTVLKEELASAEYSPDEMPQLTKRLSEMIKDKLKA
          GL.EVDKNS.EPENTYILR.I.QQ.F..SVVKDCIH.VLKEELAS.EYS.D.M.QLTK.LSEMI.DKLKA
Retrocopy GLCEVDKNSEEPENTYILRLIVQQKFKLSVVKDCIHAVLKEELASTEYSSDKMIQLTKHLSEMIRDKLKA

Parental  WLLAVSGMQTRTTTLTMFS
          .LL.VSGMQT.TTT.TMF.
Retrocopy RLLTVSGMQTPTTTFTMFA

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	6.96 RPM
SRP007412_cerebellum	0.00 RPM	5.04 RPM
SRP007412_heart	0.00 RPM	3.77 RPM
SRP007412_kidney	0.00 RPM	5.52 RPM
SRP007412_liver	0.00 RPM	0.46 RPM
SRP007412_testis	0.00 RPM	88.64 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3299 was not detected

EST

No EST(s) were mapped for retro_mmus_3299 retrocopy.

TSS

No TSS is located nearby retro_mmus_3299 retrocopy 5' end.

Lab

retro_mmus_3299 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3299 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012543	1 retrocopy	retro_chof_845,
Mus musculus	ENSMUSG00000014075	2 retrocopies	retro_mmus_2987, retro_mmus_3299 ,