RetrogeneDB ID: retro_mmus_752

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:105876203..105876916(+)
• Located in intron of: ENSMUSG00000053580

Retrocopy information

• Ensembl ID: ENSMUSG00000081270
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Snupn
• Ensembl ID: ENSMUSG00000055334
• Aliases: Snupn, 0610031A09Rik, Rnut1, Snupn1
• Description: snurportin 1 [Source:MGI Symbol;Acc:MGI:1913319]

Sequence

>retro_mmus_752
TTGGGGTAAGAGTGGATTGTGGTTGTGTGTCCTGTTGGGAAAAAATCCCTTATCATGGCCTCCAGGGGTTCAACCAGTGC
CTACACCAAGAATAGCTACTGTGTCAATAGGTTTTTTTTCCCTTCTGCCAGGAGGCAACAGGAGAAACTCAATAACAGCC
AAAGACTACACCATAACATTTAAAGTGAGGTAAACTAGACCGACTATGTTTTGGATGTAATGTGTTAGTGGGGACACCTT
TTCTATGACTGTCAAACTGATTTCCAGCTCTACTGTGTACATTCAAAGTTGACAGAAGAACTCTGAGAGAAAACCAAGAT
TAATCCTTTTAAGTGTATGGGACTAAAGGATTTCCTGTGTACCCCCTGAGAGCCTATGTAAGGTGATGTCTGGATTTTTC
CTTTGAGGTAAATGGTCTTCTCTTCTATCATAAGCAGACCCACGATAGCCCTGGGAGTCTTCCCTGTGTGGGCTGCCTAT
GCTTCTACATGAGACCAGATATCCTAGGTGTAGCTGTGCCAGCTGGTCCACTGGCCACCAAGCCAGACTATGCTGGGTAC
CAACTCCATCAGATTATTGAGCATAAGATGAGCCAGGAGTACATGAAGGAAAAACTCATATACAGTGTTTCTGAGAATGG
GCACTATGAGCTGGAGCACCTATGCACTCCCAAGTTGAGTCCTCCCCACAAATCTGAGAGCCTCATGGATGAC

Alignment

ORF - retro_mmus_752 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.98 %
• Parental protein coverage: 67.88 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LGQEWIVVVCPVGKRALIVASRGSTSAYTKSGYCVNRFSSLLPGGNRRNSTTAKDYTILDCIYSEVNQTY
          LG.EWIVVVCPVGK..LI.ASRGSTSAYTK..YCVNR.....P...R..............I.SEVN.T.
Retrocopy LG*EWIVVVCPVGKKSLIMASRGSTSAYTKNSYCVNRXXX--PSARRQQEKLNNSQRLHHNI*SEVN*TD

Parental  YVLDVMCWRGHPFYDCQTDFRFYWMHSKLPEEEGLGEKTKINPFKFVGLKN-FPCTPESLCEVLSMDFPF
          YVLDVMC..GH.FYDCQTDF..Y..HSKL.EE..L.EKTKINPFK..GLK..FP..P.........DF.F
Retrocopy YVLDVMC*WGHLFYDCQTDFQLYCVHSKLTEE--L*EKTKINPFKCMGLKD<FPVYPLRAYVR*CLDFSF

Parental  EVDGLLFYHKQTHYSPGSTPLVGWLRPYMVSDILGVAVPAGPLTTKPEYAGHQLQQIIEHKRSQEDTKEK
          EV.GLLFYHKQTH.SPGS.P.VG.L..YM..DILGVAVPAGPL.TKP.YAG.QL.QIIEHK.SQE..KEK
Retrocopy EVNGLLFYHKQTHDSPGSLPCVGCLCFYMRPDILGVAVPAGPLATKPDYAGYQLHQIIEHKMSQEYMKEK

Parental  LTHKASENGHYELEHLSTPKLRNPPHSSESLMDN
          L....SENGHYELEHL.TPKL..PPH.SESLMD.
Retrocopy LIYSVSENGHYELEHLCTPKL-SPPHKSESLMDD

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	0.07 RPM	8.60 RPM
SRP007412_cerebellum	0.04 RPM	8.60 RPM
SRP007412_heart	0.00 RPM	8.12 RPM
SRP007412_kidney	0.02 RPM	6.99 RPM
SRP007412_liver	0.00 RPM	4.94 RPM
SRP007412_testis	0.05 RPM	20.03 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_752 was not detected

EST

No EST(s) were mapped for retro_mmus_752 retrocopy.

TSS

No TSS is located nearby retro_mmus_752 retrocopy 5' end.

Lab

retro_mmus_752 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_752 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000014501	1 retrocopy	retro_meug_1444,
Mus musculus	ENSMUSG00000055334	1 retrocopy	retro_mmus_752 ,
Otolemur garnettii	ENSOGAG00000004915	1 retrocopy	retro_ogar_1420,
Rattus norvegicus	ENSRNOG00000005426	2 retrocopies	retro_rnor_2283, retro_rnor_714,