RetrogeneDB ID: retro_mmus_1564

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:32730988..32731806(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Nsmce1
• Ensembl ID: ENSMUSG00000030750
• Aliases: Nsmce1, 2510027N19Rik
• Description: non-SMC element 1 homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1914961]

Sequence

>retro_mmus_1564
CTGGTTTGCACTCCCTCCAACATGCAGGGCAACAGGAGGAGAGCAGAAGACATGACAGATGTGCACCGGTGCTTCTTCCC
GCTGTTCATGACCCACTGTGTGCTGGAGGAATGGGAAGTTTGGCCTCTGCAGAACCACTGCTATCAGGTCCATGACTGAA
ATGCTATTGTAGATAAGCTGGAGACCTCATCAACAACATCAACAGTGTCCTGGAGTCTCTGTATATTGAGATAAAGAAAG
GGGTCACGGAAGACGATGCGAGACCCATTTATGCACTGGTGAATCTTGCTACAATTTCAGTTTCCAAAATGGCTACGGAT
TTTGCAGAGAACGAGCTGGACCTGTTTAGAAAGGCTTTGGAACTGATCATTGACTCAGAAACTGGCTTTGCTTCTTCTAC
AAACATTTTGAACCTAGTTAATTAACTCAAAGGCAAAAAGATGAGGAAGAAGTAGGTGGAACAGGTGCCCCAGAAGTTTG
TGCAGAGCAAGTGGCTGATTGAGAAGGAGGGAGAGTTCGCCTTACATGGCCAGGCTATCTTGGAGATGGAACAGTTCATC
CTAGAGAGCTACCCAGATGCTGTGAAGATATGCAACATCTGCCATGGCTTCCTCATCCAGGGTCAAAGCTGTGAGACATG
TGGAATTAGGATGCATTTGCCTTGTGTGGCCAAATACTTCCAGTCCACCCCTGAACTACACTGCCCCCACTGTAATGACT
ACTGGCCCCATGATATACCAGAAGTCTATGACCCTGAGAAGGAGAGGGAGGCTGGCATCTCCAAGTCGAGCAGAAAGTCC
TTGCAAACCCGACAGCAC

Alignment

ORF - retro_mmus_1564 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.59 %
• Parental protein coverage: 97.5 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LVCAPSNMQGSTRRAGAMTDVHRRFLQLLMTHGVLEEWEVRRLQNHCYQVHDRNATVDKLE-DFINNINS
          LVC.PSNMQG..RRA..MTDVHR.F..L.MTH.VLEEWEV..LQNHCYQVHD.NA.VDKLE.D.INNINS
Retrocopy LVCTPSNMQGNRRRAEDMTDVHRCFFPLFMTHCVLEEWEVWPLQNHCYQVHD*NAIVDKLE<DLINNINS

Parental  VLESLYIEIKKGVTEDDGRPIYALVNLATTSVSKMATDFAENELDLFRKALELIVDSETGFASSTNILNL
          VLESLYIEIKKGVTEDD.RPIYALVNLAT.SVSKMATDFAENELDLFRKALELI.DSETGFASSTNILNL
Retrocopy VLESLYIEIKKGVTEDDARPIYALVNLATISVSKMATDFAENELDLFRKALELIIDSETGFASSTNILNL

Parental  VDQLKGKKMRKKEAEQVLQKFVQSKWLIEKEGEFTLHGRAILEMEQFIRESYPDSVKMCNICHGLLIQGQ
          V..LKGKKMRKK..EQV.QKFVQSKWLIEKEGEF.LHG.AILEMEQFI.ESYPD.VK.CNICHG.LIQGQ
Retrocopy VN*LKGKKMRKK*VEQVPQKFVQSKWLIEKEGEFALHGQAILEMEQFILESYPDAVKICNICHGFLIQGQ

Parental  SCETCGIRMHLPCVAKYFQSIPEPHCPHCNDYWPHDIPEVYNPEKEREAGISKSSRKSLRTRQH
          SCETCGIRMHLPCVAKYFQS.PE.HCPHCNDYWPHDIPEVY.PEKEREAGISKSSRKSL.TRQH
Retrocopy SCETCGIRMHLPCVAKYFQSTPELHCPHCNDYWPHDIPEVYDPEKEREAGISKSSRKSLQTRQH

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	8.76 RPM
SRP007412_cerebellum	0.00 RPM	8.51 RPM
SRP007412_heart	0.00 RPM	26.93 RPM
SRP007412_kidney	0.00 RPM	18.86 RPM
SRP007412_liver	0.00 RPM	9.37 RPM
SRP007412_testis	0.00 RPM	109.91 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1564 was not detected

EST

No EST(s) were mapped for retro_mmus_1564 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_52408	255 libraries	502 libraries	307 libraries	7 libraries	1 library

The graphical summary, for retro_mmus_1564 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_1564 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1564 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011003	2 retrocopies	retro_chof_1394, retro_chof_339,
Callithrix jacchus	ENSCJAG00000020515	1 retrocopy	retro_cjac_2191,
Dasypus novemcinctus	ENSDNOG00000013271	1 retrocopy	retro_dnov_641,
Mus musculus	ENSMUSG00000030750	2 retrocopies	retro_mmus_1564 , retro_mmus_2488,
Ochotona princeps	ENSOPRG00000011452	1 retrocopy	retro_opri_732,