RetrogeneDB ID: retro_mmus_724

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:73389915..73390317(+)
• Located in intron of: ENSMUSG00000069824

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ly6e
• Ensembl ID: ENSMUSG00000022587
• Aliases: Ly6e, 9804, Ly67, RIG-E, Sca-2, TSA-1, Tsa1
• Description: lymphocyte antigen 6 complex, locus E [Source:MGI Symbol;Acc:MGI:106651]

Sequence

>retro_mmus_724
ATGTCTACCACTTCCAGCATGAGGGTCTTCTCAATTGTGTTGCAGGCACACCTTCTGGGTGTGGAGCTAGTCCCTTCTCT
GATATGCTCCTCCTGCACCCATCAGAAGAGCAATATAAACCCCCCGTGGCCAGTTGCATGCAAGGACACAGGCAATTACT
GTATCATGTTATTTTCTGCTGTTGGCTTTGGGAATGTCAACCTTGGCTATACCCTGAATACGGGCTGCTCCCAGTCCTGC
CCCCATGAAAACATCAATATCAACCCTGGTGTGGCATCTGTGAATAGCTACCAAAGCTCCTTCTGCAATTTCAGCAATGC
TTGCCTCTGACTTCATGCCAGTGTCCCACTACTGGGCCTTGGACTCCTGCTCAGCTAGCTGGCTCTGCTGCAGCTGAGCC
CC

Alignment

ORF - retro_mmus_724 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.59 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSATSNMRVFLPVLLAALLGMEQVHSLMCFSCTDQKNNINCLWPVSCQEKDHYCITLSAAAGFGNVNLGY
          MS.TS.MRVF..VL.A.LLG.E.V.SL.C.SCT.QK.NIN..WPV.C.....YCI.L..A.GFGNVNLGY
Retrocopy MSTTSSMRVFSIVLQAHLLGVELVPSLICSSCTHQKSNINPPWPVACKDTGNYCIMLFSAVGFGNVNLGY

Parental  TLNKGCSPICPSENVNLNLGVASVNSYCCQSSFCNFSAAGLGLRASIPLLGLGLLLSLLALLQLSP
          TLN.GCS..CP.EN.N.N.GVASVNSY..QSSFCNFS.A.L.L.AS.PLLGLGLLLS.LALLQLSP
Retrocopy TLNTGCSQSCPHENININPGVASVNSY--QSSFCNFSNACL*LHASVPLLGLGLLLS*LALLQLSP

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	116.51 RPM
SRP007412_cerebellum	0.00 RPM	81.81 RPM
SRP007412_heart	0.00 RPM	124.09 RPM
SRP007412_kidney	0.00 RPM	172.28 RPM
SRP007412_liver	0.00 RPM	278.49 RPM
SRP007412_testis	0.00 RPM	17.38 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_724 was not detected

EST

No EST(s) were mapped for retro_mmus_724 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_16532	605 libraries	279 libraries	173 libraries	7 libraries	8 libraries

The graphical summary, for retro_mmus_724 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_724 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_724 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021460	2 retrocopies	retro_cjac_2250, retro_cjac_808,
Mus musculus	ENSMUSG00000022587	1 retrocopy	retro_mmus_724 ,
Pongo abelii	ENSPPYG00000018927	1 retrocopy	retro_pabe_2122,
Tursiops truncatus	ENSTTRG00000001986	2 retrocopies	retro_ttru_1323, retro_ttru_742,