RetrogeneDB ID: retro_mmus_157

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:68618834..68619575(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000094854
• Aliases: Gm5334, EG384639
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Tspan7
• Ensembl ID: ENSMUSG00000058254
• Aliases: Tspan7, 1200014P11Rik, A15, AI323365, Cd231, Mxs1, PE31, R74651, TALLA, Tm4sf2
• Description: tetraspanin 7 [Source:MGI Symbol;Acc:MGI:1298407]

Sequence

>retro_mmus_157
ACTGTGGCACCGAGGAAAATGGAGACTAAATTTGTGGTATCCTGTCTCAAAATCTTCCTCCTCATCTACTGCTTTGGCTT
CTGGAGCACTGGGGTTATCTTGTTGGTTTTTGGAGTCTGGGGACAGCTTACTCTGGGCGTGTATCTCTCTCTTCTTGCCA
TAGATGTTCCCACTGTGCTCATTGGAACTGGTATCGTGATTATCATTTTTGGTTTATTTGGATGCTTTTCTACATGCCGA
GGAAGCCCAAGGATGCTGAAGCTGTATTCCCTGTTTCTGTCACTGGTGTTCCTGGCTGAGCTTGCTGCTAGCATCTCAGG
GGTTTTACTTCACCGTGAGATCAAGAACAGATTCCTGAAAATTTATACCAATGCTGTACGGAATTATAACAGCAATGATA
GGAAGAGCCAGGCCGTGGACCAGGTGCAGTATAGTCTAATGTGCTGTGGGGTGAAGAACTACACAGACTGGAATGACAAC
CCCTACTTCCTGAATCATGGTATCCCCCCGAGTTGCTGCAAGGATGAAGCTGACTGTAGTCTCCAGGATCGACAGAATCT
GACCGCGGTTGCCACCAAAGTTAACCAGAGGGGCTGCTATGTTCTGATGGTAGGTTTCTTAGAGGCAAACATGGTCATCA
TCATTGGAGTGCTGTTTACAGTCACATTTTCCCAGTTGATTGGCGTGAGGTTGTCCTGTTGTCTATCTCGGCTCATCATG
ACCCAACACTATGAGACAGTG

Alignment

ORF - retro_mmus_157 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.05 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASRRMETKPVITCLKTLLIIYSFVFWITGVILLAVGVWGKLTLGTYISLIAENSTNAPYVLIGTGTTIV
          .A.R.METK.V..CLK..L.IY.F.FW.TGVILL..GVWG.LTLG.Y.SL.A......P.VLIGTG..I.
Retrocopy VAPRKMETKFVVSCLKIFLLIYCFGFWSTGVILLVFGVWGQLTLGVYLSLLA---IDVPTVLIGTGIVII

Parental  VFGLFGCFATCRGSPWMLKLYAMFLSLVFLAELVAGISGFVFRHEIKDTFLRTYTDAMQNYNGNDERSRA
          .FGLFGCF.TCRGSP.MLKLY..FLSLVFLAEL.A.ISG.....EIK..FL..YT.A..NYN.ND..S.A
Retrocopy IFGLFGCFSTCRGSPRMLKLYSLFLSLVFLAELAASISGVLLHREIKNRFLKIYTNAVRNYNSNDRKSQA

Parental  VDHVQRSLSCCGVQNYTNWSSSPYFLDHGIPPSCCMNETDCNPLDLHNLTVAATKVNQKGCYDLVTSFME
          VD.VQ.SL.CCGV.NYT.W...PYFL.HGIPPSCC..E.DC...D..NLT..ATKVNQ.GCY.L...F.E
Retrocopy VDQVQYSLMCCGVKNYTDWNDNPYFLNHGIPPSCCKDEADCSLQDRQNLTAVATKVNQRGCYVLMVGFLE

Parental  TNMGIIAGVAFGIAFSQLIGMLLACCLSRFITANQYEMV
          .NM.II.GV.F...FSQLIG..L.CCLSR.I....YE.V
Retrocopy ANMVIIIGVLFTVTFSQLIGVRLSCCLSRLIMTQHYETV

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	891.88 RPM
SRP007412_cerebellum	0.00 RPM	519.23 RPM
SRP007412_heart	0.00 RPM	113.56 RPM
SRP007412_kidney	0.00 RPM	57.31 RPM
SRP007412_liver	0.03 RPM	25.81 RPM
SRP007412_testis	17.75 RPM	3.06 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_157 was not detected

EST

No EST(s) were mapped for retro_mmus_157 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_136811	1065 libraries	4 libraries	0 libraries	1 library	2 libraries
TSS #2	TSS_136812	1065 libraries	3 libraries	1 library	1 library	2 libraries

The graphical summary, for retro_mmus_157 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_157 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_157 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_131

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000002809	1 retrocopy	retro_meug_1563,
Mus musculus	ENSMUSG00000025351	1 retrocopy	retro_mmus_1722,
Mus musculus	ENSMUSG00000058254	1 retrocopy	retro_mmus_157 ,
Otolemur garnettii	ENSOGAG00000008547	2 retrocopies	retro_ogar_1615, retro_ogar_3124,
Rattus norvegicus	ENSRNOG00000003229	1 retrocopy	retro_rnor_131,