RetrogeneDB ID: retro_mmus_878

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:81709143..81709516(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Lamtor2
• Ensembl ID: ENSMUSG00000028062
• Aliases: Lamtor2, 2010111E04Rik, AL022628, Mapbpip, P14, Rab25, Robld3
• Description: late endosomal/lysosomal adaptor, MAPK and MTOR activator 2 [Source:MGI Symbol;Acc:MGI:1932697]

Sequence

>retro_mmus_878
ATGCTGCATCTCAAGGCTTTGACGAAAGTGCTAAGCCAAGCCAACACTGGGGGAGTCCAAAGCACCCTGCTGCTAAATAA
AATGGATTGCTGCTGGCCTACTCCAGTTATGGGGACACAGATGCCTGGGTCACTGCAGCCATCGCCAGTAACGTCTGGGC
CATGTATGATAAGATCGGGAACCAGCATTTAACGAAGCCGGTCTCAAATTTATTCTGATGGACTGCATGGAGGGCAGTGT
AGCCATTACGAGGGTGATCAACCTTCTGCTATCTATGAATGCCAAGGAAACCATAGGCTTTGGAATGCTCAAGGCCAAGG
CTCAGGCCTTGGTGCAGTACCTGGAGTAACCCCTCACCCAAGTAGCAGCATCA

Alignment

ORF - retro_mmus_878 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.68 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MLRPKALTQVLSQANTGGVQSTLLLNN-EGSLLAYSGYGDTDARVTAAIASNIWAAYDRNGNQ-AFNEDS
          ML..KALT.VLSQANTGGVQSTLLLN...G.LLAYS.YGDTDA.VTAAIASN.WA.YD..GNQ.AFNE..
Retrocopy MLHLKALTKVLSQANTGGVQSTLLLNK<NGLLLAYSSYGDTDAWVTAAIASNVWAMYDKIGNQ<AFNEAG

Parental  LKFILMDCMEGRVAITRVANLLLCMYAKETVGFGMLKAKAQALVQYLEEPLTQVAAS
          LKFILMDCMEG.VAITRV.NLLL.M.AKET.GFGMLKAKAQALVQYLE.PLTQVAAS
Retrocopy LKFILMDCMEGSVAITRVINLLLSMNAKETIGFGMLKAKAQALVQYLE*PLTQVAAS

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	23.85 RPM
SRP007412_cerebellum	0.00 RPM	33.13 RPM
SRP007412_heart	0.06 RPM	31.63 RPM
SRP007412_kidney	0.00 RPM	44.39 RPM
SRP007412_liver	0.00 RPM	41.67 RPM
SRP007412_testis	0.05 RPM	10.66 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_878 was not detected

EST

No EST(s) were mapped for retro_mmus_878 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_25112	484 libraries	199 libraries	373 libraries	15 libraries	1 library

The graphical summary, for retro_mmus_878 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_878 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_878 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000009193	1 retrocopy	retro_ecab_629,
Felis catus	ENSFCAG00000028596	1 retrocopy	retro_fcat_872,
Myotis lucifugus	ENSMLUG00000023871	1 retrocopy	retro_mluc_237,
Mus musculus	ENSMUSG00000028062	1 retrocopy	retro_mmus_878 ,
Otolemur garnettii	ENSOGAG00000016953	2 retrocopies	retro_ogar_2919, retro_ogar_910,
Pteropus vampyrus	ENSPVAG00000010328	1 retrocopy	retro_pvam_748,
Rattus norvegicus	ENSRNOG00000019908	3 retrocopies	retro_rnor_1037, retro_rnor_2493, retro_rnor_847,
Tursiops truncatus	ENSTTRG00000013344	1 retrocopy	retro_ttru_1782,