RetrogeneDB ID: retro_mmus_2952

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:95461990..95463153(+)
• Located in intron of: None

Retrocopy information

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

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_2952
ATGGCTTCAACCAACTATACCCAATAAGATACTCAAAGCTACGGGGCCTATCTTACCCAGCCTGGGCAGGGCTACTCCCA
ACAAAGTAGTCAGACCAATGGCCAGCAGAGTTACAGTGGTTATGGCCAATCAGCTGACACTTCAGGGATATGGCCAGAAC
AGCTATGGCCTTCTTATGGACAGACCCAAACCACAGGCTATGGAACTCAGCTCCCCAGGGATATGGTTCCACTGGAGGCT
ATGGAAGCAGCCAAAGTTCCCAATCTTCTTATGGGCAGCAGTCCTCCTACCTTGACTATGGCCAACAGCCAACTCCTAGT
AGCACCTCAGGAAGTTATGGTGGCAGCTCTCAGAACAGCAGCTATGGGCAGCCCCAGAGTGGAGGTTATGGTTAACAGTC
TGGCTATGGTTGGACAGCAGCAAAGCTACGGACAGCAACCAAGCTCCTGTAACCCACCTCAGGATTATGGACAACAGAAC
CACTACAACAGCAGCAGTGGAGGAAGTGGAGGGGGTGGTGGAGGCAACTATGGCCAAGATCAGACCTCTATGAGTGGCGG
CGGTGGTGGTTATGGCAATCACGACCAAAGTGGTGGCAGCGGTAGTGGCTACGGGGGAGGCCAGCAGGATCGTGGGGGCT
ATGGCAGAGGTGGTGGAGGTGGTTACACCCGAAGCAGTGGTGAATATGACCCCAGAGGCTGTGGAGGTAGCCAAGGAGGC
AAAGGCGGCATGGGAGGAAGTGACCATGGTGGCTTCAATAAAGTTGGTCCTCGGGATCAAGGATCTCGTCATGATTCTGA
GCAGGATAATTCAGACGAAAATACCATCTTTGTGCAAGGCCTAGGTGAGAATCTTACAGTTAAATCTGTGGCTGACTACT
TCAAGCATATTGGAATTAAGACAAATAAGAAAACTCGACAGTCTATGATTAATTTGTATACAGACAGGGAAACTGGCAAG
TTGAAGGGTGAGGCAACAGTTTCATTTGATGACCCACCTTCTGCTAAAGCAGCTACAGACTGGTTTGATGGTAAAAAATT
CTCTGTAAATCCTATTAAAATTTCATTTGCTACCCTCATAGTTGACTTCAATCAGGGTGGTGGAAATGGTCGTGGAGGTT
GAGGGCGAGGAGAAACATGGGCCGTGGAGGCTATGGTGGTGGC

Alignment

ORF - retro_mmus_2952 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.63 %
• Parental protein coverage: 75.82 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MASNDYTQQATQSYGAYPTQPGQGYSQQSSQPYGQQSYSGYGQSADTSG-YGQSSYG-SSYGQTQ-NSYG
          MAS..YTQ..TQSYGAY.TQPGQGYSQQSSQ..GQQSYSGYGQSADTSG.YGQ.SYG..SYGQTQ.N...
Retrocopy MASTNYTQ*DTQSYGAYLTQPGQGYSQQSSQTNGQQSYSGYGQSADTSG>YGQNSYG<PSYGQTQ<NHRL

Parental  TQSAPQGYGSTGGYGSSQSSQSSYGQQSSYPGYGQQPAPSSTSGSYGGSSQSSSYGQPQSGGYGQQSGYG
          ..SAPQGYGSTGGYGSSQSSQSSYGQQSSY..YGQQP.PSSTSGSYGGSSQ.SSYGQPQSGGYG.QSGYG
Retrocopy WNSAPQGYGSTGGYGSSQSSQSSYGQQSSYLDYGQQPTPSSTSGSYGGSSQNSSYGQPQSGGYG*QSGYG

Parental  -GQQQSYGQQQSSYNPPQGYGQQNQYNSSSGGGGGGGGGNYGQDQSSMSGGGGGGGYGNQDQSGGGGGGY
          .GQQQSYGQQ.SS.NPPQ.YGQQN.YNSSSGG.GGGGGGNYGQDQ.SMSGGGGG..YGN.DQSGG.G.GY
Retrocopy >GQQQSYGQQPSSCNPPQDYGQQNHYNSSSGGSGGGGGGNYGQDQTSMSGGGGG--YGNHDQSGGSGSGY

Parental  GGGQQDRGGRGRGGGGGYNRSSGGYEPRGRGGGRGGRGGMGGSDRGGFNKFGGPRDQGSRHDSEQDNSDN
          GGGQQDRGG.GRGGGGGY.RSSG.Y.PRG.GG..GG.GGMGGSD.GGFNK..GPRDQGSRHDSEQDNSD.
Retrocopy GGGQQDRGGYGRGGGGGYTRSSGEYDPRGCGGSQGGKGGMGGSDHGGFNKV-GPRDQGSRHDSEQDNSDE

Parental  NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWF
          NTIFVQGLGEN.T..SVADYFK.IG.IKTNKKT.Q.MINLYTDRETGKLKGEATVSFDDPPSAKAA.DWF
Retrocopy NTIFVQGLGENLTVKSVADYFKHIG-IKTNKKTRQSMINLYTDRETGKLKGEATVSFDDPPSAKAATDWF

Parental  DGKEFSGNPIKVSFATRRADFNRGGGNGRGGRGRGGP-MGRGGYGGG
          DGK.FS.NPIK.SFAT...DFN.GGGNGRGG.GRG...MGRGGYGGG
Retrocopy DGKKFSVNPIKISFATLIVDFNQGGGNGRGG*GRGET<MGRGGYGGG

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	0.05 RPM	227.18 RPM
SRP007412_cerebellum	0.00 RPM	283.28 RPM
SRP007412_heart	0.00 RPM	182.67 RPM
SRP007412_kidney	0.04 RPM	174.92 RPM
SRP007412_liver	0.00 RPM	64.45 RPM
SRP007412_testis	0.00 RPM	233.13 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2952 was not detected

EST

No EST(s) were mapped for retro_mmus_2952 retrocopy.

TSS

No TSS is located nearby retro_mmus_2952 retrocopy 5' end.

Lab

retro_mmus_2952 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2952 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,