RetrogeneDB ID: retro_mmus_2538

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:152157007..152157490(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081544
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Lamtor1
• Ensembl ID: ENSMUSG00000030842
• Aliases: Lamtor1, 2400001E08Rik, Pdro, p18
• Description: late endosomal/lysosomal adaptor, MAPK and MTOR activator 1 [Source:MGI Symbol;Acc:MGI:1913758]

Sequence

>retro_mmus_2538
ATGGGGTGCTGCTATAGCAGCAAAAATGAAGACTCGGACCAGGATCGGGAGGAGAGGAAGCTGTTGCTGGACCCCAGTAG
CACCCCTACCAAAGCCCTCAATGGAGCCAAGCCCAACTACCATAGCCTACCTTCAGCTCCCACAGATGAGTAGGCCCTGC
TTTCCTCCATCCTTGCCAAGACAGCTAGCAACATCATTGATGTGTCTGCCGCAGACTCCCAGGGCATGGAACAGCATGAG
TACACGGACCGAGCAAGGCAGTACAGTACCCGCTTGGCTGTGCTTAGCAGCAGTCTGACCCATTGGAAGAAGCTGCCACC
GCTGCCATCTCTCACCAGCCAGCCCCACCAAGTGCTGGCCAGCGAGCCTATCCCCTTCTCTGACTTGCAGCAGGTCTCTA
AGATAGCTGCATATGCCTATAGTGCACTTTCTCAGATCTGCGTGGACGAGAAAGAAGAGCTGGTTGTACAGTTTGGGATC
CCA

Alignment

ORF - retro_mmus_2538 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.03 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGCCYSSENEDSDQDREERKLLLDPSSTPTKALNGAEPNYHSLPSARTDEQALLSSILAKTASNIIDVSA
          MGCCYSS.NEDSDQDREERKLLLDPSSTPTKALNGA.PNYHSLPSA.TDE.ALLSSILAKTASNIIDVSA
Retrocopy MGCCYSSKNEDSDQDREERKLLLDPSSTPTKALNGAKPNYHSLPSAPTDE*ALLSSILAKTASNIIDVSA

Parental  ADSQGMEQHEYMDRARQYSTRLAVLSSSLTHWKKLPPLPSLTSQPHQVLASEPIPFSDLQQVSRIAAYAY
          ADSQGMEQHEY.DRARQYSTRLAVLSSSLTHWKKLPPLPSLTSQPHQVLASEPIPFSDLQQVS.IAAYAY
Retrocopy ADSQGMEQHEYTDRARQYSTRLAVLSSSLTHWKKLPPLPSLTSQPHQVLASEPIPFSDLQQVSKIAAYAY

Parental  SALSQIRVDAKEELVVQFGIP
          SALSQI.VD.KEELVVQFGIP
Retrocopy SALSQICVDEKEELVVQFGIP

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	36.33 RPM
SRP007412_cerebellum	0.04 RPM	31.26 RPM
SRP007412_heart	0.06 RPM	60.11 RPM
SRP007412_kidney	0.04 RPM	48.80 RPM
SRP007412_liver	0.00 RPM	30.34 RPM
SRP007412_testis	0.00 RPM	19.35 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2538 was not detected

EST

No EST(s) were mapped for retro_mmus_2538 retrocopy.

TSS

No TSS is located nearby retro_mmus_2538 retrocopy 5' end.

Lab

retro_mmus_2538 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2538 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010854	2 retrocopies	retro_amel_1176, retro_amel_436,
Macropus eugenii	ENSMEUG00000003560	1 retrocopy	retro_meug_17,
Mus musculus	ENSMUSG00000030842	2 retrocopies	retro_mmus_1805, retro_mmus_2538 ,
Rattus norvegicus	ENSRNOG00000020016	1 retrocopy	retro_rnor_2788,
Tarsius syrichta	ENSTSYG00000014730	2 retrocopies	retro_tsyr_1324, retro_tsyr_33,