RetrogeneDB ID: retro_mmus_941

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:59317082..59318103(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Snip1
• Ensembl ID: ENSMUSG00000050213
• Aliases: Snip1, 2410133M08Rik
• Description: Smad nuclear interacting protein 1 [Source:MGI Symbol;Acc:MGI:2156003]

Sequence

>retro_mmus_941
AGCCCCGAACCCAGCGCTCCAGCTGCTAGCCTGTCCACCGCCAAGCCCAATGCTAGTCGGTCCCCAGACAAAAAGAAAAG
GAAGTCCTCCGGGAGAAGAAGCAAGTCCCCTCCAACTAAGAGAAGCCGGAGTCCCCACTACTCCATGGTCAAAGTGAAGC
AGGAACGTGAGGACCATCCGCTGAGAGGACGAGAGGATCCACAACCCCGGGAGCCATCAGAACAGGAACACAGGAGAGCT
AGGAACAGTGATGAGCGAGCCCGGCACCGGAGCCATTCCCGCCAAAGGAGGAGCTCTGATGAGAGGCCTGTCAGTGGACA
GGGCCGGGATAGAGACAGCCAGAACCTGAAGGCTCAGGAAGAAGAGAGGGACTTTCATAATGCCAGGCGCCAGGAGCATC
GCCAGCAGAATGGAAGTGCTGGCAGCGGTGAGGTTCAAGAAGAGGTGATCCCTCACCCTGCTGGTAACAGAAGCAAAGAG
GTGCCCGTTAAAGAAAAACCATGCTTTGAACTTTCTGGGGCACTTCTTGAGGACACTAATACCTTCCAGGGTGTGGTTAT
TAAATACAATGAGCCCCCAGAAGCCCGGATCCCCAAAAAACGGTGGCGTCTCTACCCCTTTAAAAATGATGAGCTGCTTC
CAGTCTTGTACATCCATCGGCAAAGTGCATACCTTCTGGGTAGACATCGACGCATCGCAGACATTCCCATTGACCATCCC
TCTTGCTCAAAGCAACATGCTGTCTTCCAGTACCGGCTTGTGGAGTCCACCCGTGCTGATGGCACGGTTGATCGGAGTGT
GAAGCCCTTCATCATTGATCTCTGCTCAGCCAACGGAACGTTCTTAAACAACAAGCGTATTGAGCCACAGAGATACTATG
AACTGAAAGAAAGTGATGTACTTAAATTTGGATTCAGTAGCCGAGATTACGTCTTGCTTCATGAGTCTTCAGACATCTCT
GAACTTGAAGAAGGAAGATGAGGGGGAGGAGGAGGAGAAGGAGGAAATGGTACCCCACAGC

Alignment

ORF - retro_mmus_941 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.52 %
• Parental protein coverage: 87.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SLSPPAAEPGHSGHRGSRARSPAKKKSKSSGRRSKSPRTKRSQSPHYPMVKVKQEREDHPRRGREDRQHR
          S..P.A.....S.......RSP.KKK.KSSGRRSKSP.TKRS.SPHY.MVKVKQEREDHP.RGRED.Q.R
Retrocopy SPEPSAPAASLSTAKPNASRSPDKKKRKSSGRRSKSPPTKRSRSPHYSMVKVKQEREDHPLRGREDPQPR

Parental  EPSEQEHRRARNS-ERDRHRGHSRQGRSSDERPVSGQDRDRDSQNLQAQEEERDFHNARRREHRQQNESA
          EPSEQEHRRARNS.ER.RHR.HSRQ.RSSDERPVSGQ.RDRDSQNL.AQEEERDFHNARR.EHRQQN.SA
Retrocopy EPSEQEHRRARNSDERARHRSHSRQRRSSDERPVSGQGRDRDSQNLKAQEEERDFHNARRQEHRQQNGSA

Parental  GSEA--QEVIPRPAGNRSKEVPVKEKPSFELSGALLEDTNTFRGVVIKYSEPPEARIPKKRWRLYPFKND
          GS.....EVIP.PAGNRSKEVPVKEKP.FELSGALLEDTNTF.GVVIKY.EPPEARIPKKRWRLYPFKND
Retrocopy GSGEVQEEVIPHPAGNRSKEVPVKEKPCFELSGALLEDTNTFQGVVIKYNEPPEARIPKKRWRLYPFKND

Parental  EVLPVMYIHRQSAYLLGRHRRIADIPIDHPSCSKQHAVFQYRLVEYTRADGTVGRRVKPYIIDLGSGNGT
          E.LPV.YIHRQSAYLLGRHRRIADIPIDHPSCSKQHAVFQYRLVE.TRADGTV.R.VKP.IIDL.S.NGT
Retrocopy ELLPVLYIHRQSAYLLGRHRRIADIPIDHPSCSKQHAVFQYRLVESTRADGTVDRSVKPFIIDLCSANGT

Parental  FLNNKRIEPQRYYELKEKDVLKFGFSSREYVLLHESSDTSELD-RKEDEDDEE-EEMVSDS
          FLNNKRIEPQRYYELKE.DVLKFGFSSR.YVLLHESSD.SEL.........EE.EEMV..S
Retrocopy FLNNKRIEPQRYYELKESDVLKFGFSSRDYVLLHESSDISELE>KEDEGEEEEKEEMVPHS

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	10.21 RPM
SRP007412_cerebellum	0.00 RPM	10.73 RPM
SRP007412_heart	0.00 RPM	8.00 RPM
SRP007412_kidney	0.02 RPM	9.49 RPM
SRP007412_liver	0.00 RPM	10.73 RPM
SRP007412_testis	0.00 RPM	30.19 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_941 was not detected

EST

No EST(s) were mapped for retro_mmus_941 retrocopy.

TSS

No TSS is located nearby retro_mmus_941 retrocopy 5' end.

Lab

retro_mmus_941 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_941 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001963	1 retrocopy	retro_cjac_1094,
Myotis lucifugus	ENSMLUG00000017132	2 retrocopies	retro_mluc_1400, retro_mluc_159,
Mus musculus	ENSMUSG00000050213	2 retrocopies	retro_mmus_3038, retro_mmus_941 ,
Otolemur garnettii	ENSOGAG00000008634	2 retrocopies	retro_ogar_2306, retro_ogar_893,