RetrogeneDB ID: retro_mmus_426

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:30642076..30642316(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: 1110001A16Rik
• Ensembl ID: ENSMUSG00000062691
• Aliases: None
• Description: RIKEN cDNA 1110001A16 gene [Source:MGI Symbol;Acc:MGI:1915804]

Sequence

>retro_mmus_426
ATGGCTTGGACCATGGAACCTCTGGCAAGGAAGATCTTTAAAGGAGTTTTAGCAGCTGAGCTTGTGGGTGTTGCTGGAGC
TCACTTTTTGTTTAAAAAGATGAACTCCAGCCAAGATTTCAGACAAACAATGAGCAAGAAATTTCCCTTCATTTTGGAAG
TTTATTACAAATCCATTGAACAGTCTGGAATGTATGGAGTTCGAGAGAAAGATCAGGAAAAATGGTTGACTAGCAAAAAC

Alignment

ORF - retro_mmus_426 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.5 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MARIMEPLARKIFKGVLAAELVGVAGAYCLFKKMHSSQDFRQTMSKKFPFILEVYYKSIEQSGMYGVREK
          MA..MEPLARKIFKGVLAAELVGVAGA..LFKKM.SSQDFRQTMSKKFPFILEVYYKSIEQSGMYGVREK
Retrocopy MAWTMEPLARKIFKGVLAAELVGVAGAHFLFKKMNSSQDFRQTMSKKFPFILEVYYKSIEQSGMYGVREK

Parental  DEEKWLTSKN
          D.EKWLTSKN
Retrocopy DQEKWLTSKN

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	3.15 RPM
SRP007412_cerebellum	0.00 RPM	2.17 RPM
SRP007412_heart	0.00 RPM	6.16 RPM
SRP007412_kidney	0.00 RPM	3.85 RPM
SRP007412_liver	0.00 RPM	3.47 RPM
SRP007412_testis	0.00 RPM	1.60 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_426 was not detected

EST

No EST(s) were mapped for retro_mmus_426 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_73763	284 libraries	414 libraries	367 libraries	7 libraries	0 libraries

The graphical summary, for retro_mmus_426 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_426 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_426 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017579	1 retrocopy	retro_amel_629,
Choloepus hoffmanni	ENSCHOG00000013008	2 retrocopies	retro_chof_328, retro_chof_49,
Felis catus	ENSFCAG00000023228	2 retrocopies	retro_fcat_1289, retro_fcat_1750,
Homo sapiens	ENSG00000218739	2 retrocopies	retro_hsap_2312, retro_hsap_4294,
Gorilla gorilla	ENSGGOG00000025368	2 retrocopies	retro_ggor_1755, retro_ggor_2869,
Mus musculus	ENSMUSG00000062691	2 retrocopies	retro_mmus_426 , retro_mmus_509,
Pongo abelii	ENSPPYG00000029876	2 retrocopies	retro_pabe_2045, retro_pabe_3499,
Pan troglodytes	ENSPTRG00000033858	2 retrocopies	retro_ptro_1687, retro_ptro_2911,
Rattus norvegicus	ENSRNOG00000040303	2 retrocopies	retro_rnor_1144, retro_rnor_973,
Sus scrofa	ENSSSCG00000020689	2 retrocopies	retro_sscr_328, retro_sscr_434,
Tursiops truncatus	ENSTTRG00000006884	7 retrocopies	retro_ttru_1069, retro_ttru_1866, retro_ttru_1946, retro_ttru_274, retro_ttru_526, retro_ttru_57, retro_ttru_832,