RetrogeneDB ID: retro_mmus_427

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:30794546..30794908(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tmem213
• Ensembl ID: ENSMUSG00000029829
• Aliases: Tmem213, D630002J15Rik
• Description: transmembrane protein 213 [Source:MGI Symbol;Acc:MGI:1924772]

Sequence

>retro_mmus_427
TTGTTTTCCAGCCTGGGGCACCTCTGCACCAACATGGCCCCGACTGGTGTCTTCCTCTGCAGCCCTGGGTACCTCACCTC
TGCCCCACAGGCCGCCCTCGTCTTCACCTCCTTCTACTTGTCCTGTGATACAGAATCCAGCAGCGGCAATTCAACCCTGA
GTACACACTACTCAGACTCCAGGACCCTGGAGCAGTGTGCCAATGTTGACTTCTGCCCACTAGCCTCCCTGTGTCGCAGA
GCTTCTGTGGACAAATATGGCTGGATTGCTGCAGTGGCTGGAGTTTCTGGTTCCTCATTCTCATCCTGCTGTTCGTGGAC
AAACTGATGAAGTTAACTCCCGAGGAGCCCAAAGACCTGGCC

Alignment

ORF - retro_mmus_427 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.08 %
• Parental protein coverage: 99.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MFSTPGHLCSNMAQSGVFLRNPGHLTSAPQAALLFSLVLTSFHLSCGTETSSSNSTLSAHHPDPGTLEQC
          .FS..GHLC.NMA..GVFL..PG.LTSAPQAAL.F....TSF.LSC.TE.SS.NSTLS.H..D..TLEQC
Retrocopy LFSSLGHLCTNMAPTGVFLCSPGYLTSAPQAALVF----TSFYLSCDTESSSGNSTLSTHYSDSRTLEQC

Parental  ANVDFCPLASLCCRASVDEYGWIAAAVGWS-FWFLTLILLCVDKLMKLTPEEPKDLA
          ANVDFCPLASLC.RASVD.YGWIAA..G.S........L..VDKLMKLTPEEPKDLA
Retrocopy ANVDFCPLASLCRRASVDKYGWIAAVAGVS<WFLILILLF-VDKLMKLTPEEPKDLA

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	0.02 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.02 RPM	17.54 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_427 was not detected

EST

No EST(s) were mapped for retro_mmus_427 retrocopy.

TSS

No TSS is located nearby retro_mmus_427 retrocopy 5' end.

Lab

retro_mmus_427 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_427 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000029829	1 retrocopy	retro_mmus_427 ,
Tarsius syrichta	ENSTSYG00000008448	1 retrocopy	retro_tsyr_2174,