RetrogeneDB ID: retro_mmus_1179

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:15910503..15911254(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Arhgap1
• Ensembl ID: ENSMUSG00000027247
• Aliases: Arhgap1, B230365D05Rik, C76222, Cdc42GAP, p50rhoGAP
• Description: Rho GTPase activating protein 1 [Source:MGI Symbol;Acc:MGI:2445003]

Sequence

>retro_mmus_1179
CCAGAAGCAGCCATGGACCCTCTCTCAGAGCTGCACGATGACCTGACCCTGGATGACACCAGCCAAGCTCTGAACCAGTT
GAAGCTGGCCTCCACTGATAAGAAGAACTGGCCTTCTGATGAAATGCCAGACTTCCCCAAGTCAGATGACTCCAAAAGCA
GCTCTCCAGAACCTGTGACACACCTGAAGTGGGATGACCCTTACTATGACATTGCCCGGCACCAGATTTTGGAAGTAGTG
GGTGATGATAAGTATGGGTGGAAGATCATTGTATTCAGTGCTTGCAGGATGCCCCCCTAGCCACCAGCTGGACCACAGCA
AGCTCTTGGGATACTTGAAACACACACTGGACCAGTATGTGGAGAGTGACTACACACTCCTGTACCTGCACCATAGCCTG
ACCAGTGACAACAATCCCTCCCTCAGCTGGCTATGGGATGCCTACAGAGAGTTTGACCGCAAGTACAAGAAGAACATCAA
GGCTCTGTACATAGTGCACCCAACCATGTTTATCAAAACTCTGCTTATCCTCTTTAAGCCTCTCATCAGTTTCAAGTTTG
GATGGAAGATCTTCTACGTGAATTACCTGAGTGAGTTGAGCAAGCACGTGAAGCTGGAACAGTTGGGGATCCCTTGCCAA
GTGCTCAAGTATGATGACTTCCTCAAATCCACACAGAAGAGTCCTGCAACAGCTCCCAAGCCCATGGCACCATGGCACAT
CCTGCCCAATCAGCAGTTTGGAGTCTCCTTA

Alignment

ORF - retro_mmus_1179 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.83 %
• Parental protein coverage: 52.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PERAMDPLSELQDDLTLDDTSQALNQLKLASIDEKNWPSDEMPDFPKSDDSKSSSPEPVTHLKWDDPYYD
          PE.AMDPLSEL.DDLTLDDTSQALNQLKLAS.D.KNWPSDEMPDFPKSDDSKSSSPEPVTHLKWDDPYYD
Retrocopy PEAAMDPLSELHDDLTLDDTSQALNQLKLASTDKKNWPSDEMPDFPKSDDSKSSSPEPVTHLKWDDPYYD

Parental  IARHQIVEVAGDDKYGRKIIVFSACRMPP-SHQLDHSKLLGYLKHTLDQYVESDYTLLYLHHGLTSDNKP
          IARHQI.EV.GDDKYG.KIIVFSACRMPP.SHQLDHSKLLGYLKHTLDQYVESDYTLLYLHH.LTSDN.P
Retrocopy IARHQILEVVGDDKYGWKIIVFSACRMPP>SHQLDHSKLLGYLKHTLDQYVESDYTLLYLHHSLTSDNNP

Parental  SLSWLRDAYREFDRKYKKNIKALYIVHPTMFIKTLLILFKPLISFKFGRKIFYVNYLSELSEHVKLEQLG
          SLSWL.DAYREFDRKYKKNIKALYIVHPTMFIKTLLILFKPLISFKFG.KIFYVNYLSELS.HVKLEQLG
Retrocopy SLSWLWDAYREFDRKYKKNIKALYIVHPTMFIKTLLILFKPLISFKFGWKIFYVNYLSELSKHVKLEQLG

Parental  IPRQVLKYDDFLKSTQKSPATAPKPMPPRPPLPNQQFGVSL
          IP.QVLKYDDFLKSTQKSPATAPKPM.P...LPNQQFGVSL
Retrocopy IPCQVLKYDDFLKSTQKSPATAPKPMAPWHILPNQQFGVSL

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	0.02 RPM	55.56 RPM
SRP007412_cerebellum	0.00 RPM	27.83 RPM
SRP007412_heart	0.00 RPM	20.61 RPM
SRP007412_kidney	0.12 RPM	46.20 RPM
SRP007412_liver	0.00 RPM	14.17 RPM
SRP007412_testis	0.41 RPM	13.72 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1179 was not detected

EST

No EST(s) were mapped for retro_mmus_1179 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_33004	167 libraries	153 libraries	704 libraries	46 libraries	2 libraries

The graphical summary, for retro_mmus_1179 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_1179 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1179 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000017628	1 retrocopy	retro_mluc_618,
Mus musculus	ENSMUSG00000027247	1 retrocopy	retro_mmus_1179 ,