RetrogeneDB ID: retro_mmus_2710

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 5:148183444..148184389(-)
• Located in intron of: ENSMUSG00000029651

Retrocopy information

• Ensembl ID: ENSMUSG00000066554
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Fus
• Ensembl ID: ENSMUSG00000030795
• Aliases: Fus, D430004D17Rik, D930039C12Rik, Fus1, Tls
• Description: fused in sarcoma [Source:MGI Symbol;Acc:MGI:1353633]

Sequence

>retro_mmus_2710
AATTTTGGGGACATGGCTTCAAACGACTATACCCAACAAGCAACTCAAAGCTACGGGGCCTATCCTACCCAGCCTGGGCA
GGGCTACTCCCAACAGAGCAATCAGCCCTATGGCCAATCAGCTGACACTTCAGGATACGGCCAGATCAGCTATGGTTCCT
CTTCTGGACAGACCCAAAACACAGGCTATGGAACTCAGTCAGCTCCCCAGGGATATGGTTCCACTGGAGGCTATGGCAGC
AGCCAAAGTTCCCAATCTTCTTATGGGCAGCAGTCCTCCTACCCTGGCTATGGCCAACAGCCAGCTCCTAGCAGCACCTC
AGGAAGTTATGGTGGCAGTTCTCAGAGCAGCAGCTATGGGCAACCCCAGAGTTATGGTCAACAGTCTGGCTATGGTGGAC
AGCAACAAAGCTATGGACAACAACAAAGCTCCTATAACCCACCTCAGGGTTATGGACAACAGAACCAGTACAACAGCAGC
AGCGGAGGTGGTGGAGGGGGTGGTGGAGGCAACTATGGCCAAGATCAGTCCTCTATGAGTGGCGGCGGTGGTGGTTATGG
CAATCAGGACTAGAGTGGTGGCGGTGGTGGTGGCTACGGGGGAGGCCAGCAGGATCGTGGGGGCCGTGACAGGGGCAGTG
GAGGTGGTTACAACCGAAGCAGTGGTGGCTATGAACCCAGAGGCTGTGGAGGTAACCGAGGAGGCAGAGGCGTCATGGGC
GGAAGTGACCGTGGTGACTTCAATAAATTTGGTGGTCCTCGGGATCAAGGATCTCGTCATGATTCTGAACAGGATAATTC
AGACAACAATACCATCTTCGTGCAAGGCCTAGGCGAGAATGTTACAATTGAATCTGTGGCTGATTACTTCAAGCAGATTG
GAATTATTAAGACAAACAAGAAAACGGGACAGCCTATGATTAATTTGTACACAGACAGGGAAACT

Alignment

ORF - retro_mmus_2710 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.09 %
• Parental protein coverage: 61.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DYTQQATQSYGAYPTQPGQGYSQQSSQPYGQQSYSGYGQSADTSGYGQSSYGSSYGQTQNTGYGTQSAPQ
          .....A...Y....TQ....Y..Q..Q.Y.QQS...YGQSADTSGYGQ.SYGSS.GQTQNTGYGTQSAPQ
Retrocopy NFGDMASNDYTQQATQSYGAYPTQPGQGYSQQSNQPYGQSADTSGYGQISYGSSSGQTQNTGYGTQSAPQ

Parental  GYGSTGGYGSSQSSQSSYGQQSSYPGYGQQPAPSSTSGSYGGSSQSSSYGQPQSGGYGQQSGYGGQQQSY
          GYGSTGGYGSSQSSQSSYGQQSSYPGYGQQPAPSSTSGSYGGSSQSSSYGQPQS..YGQQSGYGGQQQSY
Retrocopy GYGSTGGYGSSQSSQSSYGQQSSYPGYGQQPAPSSTSGSYGGSSQSSSYGQPQS--YGQQSGYGGQQQSY

Parental  GQQQSSYNPPQGYGQQNQYNSSSGGGGGGGGGNYGQDQSSMSGGGGGGGYGNQDQSGGGGGGYGGGQQDR
          GQQQSSYNPPQGYGQQNQYNSSSGGGGGGGGGNYGQDQSSMSGGGGG..YGNQD.SGGGGGGYGGGQQDR
Retrocopy GQQQSSYNPPQGYGQQNQYNSSSGGGGGGGGGNYGQDQSSMSGGGGG--YGNQD*SGGGGGGYGGGQQDR

Parental  GGRGRGGGGGYNRSSGGYEPRGRGGGRGGRGGMGGSDRGGFNKFGGPRDQGSRHDSEQDNSDNNTIFVQG
          GGR.RG.GGGYNRSSGGYEPRG.GG.RGGRG.MGGSDRG.FNKFGGPRDQGSRHDSEQDNSDNNTIFVQG
Retrocopy GGRDRGSGGGYNRSSGGYEPRGCGGNRGGRGVMGGSDRGDFNKFGGPRDQGSRHDSEQDNSDNNTIFVQG

Parental  LGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRET
          LGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRET
Retrocopy LGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRET

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	1.92 RPM	227.18 RPM
SRP007412_cerebellum	1.65 RPM	283.28 RPM
SRP007412_heart	1.81 RPM	182.67 RPM
SRP007412_kidney	1.19 RPM	174.92 RPM
SRP007412_liver	0.49 RPM	64.45 RPM
SRP007412_testis	1.83 RPM	233.13 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2710 was not detected

EST

No EST(s) were mapped for retro_mmus_2710 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_112135	235 libraries	443 libraries	380 libraries	7 libraries	7 libraries

The graphical summary, for retro_mmus_2710 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_2710 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2710 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000000968	1 retrocopy	retro_meug_1986,
Myotis lucifugus	ENSMLUG00000004806	3 retrocopies	retro_mluc_1934, retro_mluc_608, retro_mluc_638,
Macaca mulatta	ENSMMUG00000019637	1 retrocopy	retro_mmul_153,
Mus musculus	ENSMUSG00000009079	1 retrocopy	retro_mmus_1379,
Mus musculus	ENSMUSG00000030795	2 retrocopies	retro_mmus_2710 , retro_mmus_2952,
Rattus norvegicus	ENSRNOG00000023360	4 retrocopies	retro_rnor_1439, retro_rnor_2727, retro_rnor_2894, retro_rnor_913,