RetrogeneDB ID: retro_mmus_3544

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:150431505..150431798(+)
• Located in intron of: ENSMUSG00000090483

Retrocopy information

• Ensembl ID: ENSMUSG00000082974
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Lamtor4
• Ensembl ID: ENSMUSG00000050552
• Aliases: Lamtor4, 0910001L09Rik, AV006840
• Description: late endosomal/lysosomal adaptor, MAPK and MTOR activator 4 [Source:MGI Symbol;Acc:MGI:1913346]

Sequence

>retro_mmus_3544
ACTTCTGCACTGACCAAAGGGCTTGAGCAAATCCCAGACCAGTTTGGCTCCCTGGTGCTGAGCGAAGGTGCAGTGCTGGC
ATCATCTGGGGACCTTAAGAATGATAAGCAGGCAGCCAGCGCCATCTCAAAGCTGGTCAGCACAGCCTGTGGCTTCAGGC
TGCACCATGGCACGAACATCCCTTTCAAATGCCTGTCTGTGGTCTTTGGTGAACACACACTGCTGGTGACTGTGTCAGGA
GAGAGGGTGTTTGTGGTGAAGAGACAGAACCAAGGTCCATGCCTATTGATATC

Alignment

ORF - retro_mmus_3544 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.85 %
• Parental protein coverage: 98.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TSALTQGLERIPDQLGYLVLSEGAVLASSGDLENDEQAASAISELVSTACGFQLHHGTNIPFKRLSVVFG
          TSALT.GLE.IPDQ.G.LVLSEGAVLASSGDL.ND.QAASAIS.LVSTACGF.LHHGTNIPFK.LSVVFG
Retrocopy TSALTKGLEQIPDQFGSLVLSEGAVLASSGDLKNDKQAASAISKLVSTACGFRLHHGTNIPFKCLSVVFG

Parental  EHTLLVTVSGQRVFVVKRQNRG-REPIDV
          EHTLLVTVSG.RVFVVKRQN.G...PID.
Retrocopy EHTLLVTVSGERVFVVKRQNQG<SMPIDI

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	21.07 RPM
SRP007412_cerebellum	0.00 RPM	23.19 RPM
SRP007412_heart	0.00 RPM	26.34 RPM
SRP007412_kidney	0.04 RPM	32.90 RPM
SRP007412_liver	0.03 RPM	36.29 RPM
SRP007412_testis	0.00 RPM	4.12 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3544 was not detected

EST

No EST(s) were mapped for retro_mmus_3544 retrocopy.

TSS

No TSS is located nearby retro_mmus_3544 retrocopy 5' end.

Lab

retro_mmus_3544 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3544 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014561	1 retrocopy	retro_cfam_1491,
Cavia porcellus	ENSCPOG00000013370	1 retrocopy	retro_cpor_119,
Mus musculus	ENSMUSG00000050552	1 retrocopy	retro_mmus_3544 ,
Ochotona princeps	ENSOPRG00000003476	1 retrocopy	retro_opri_640,
Pteropus vampyrus	ENSPVAG00000011987	1 retrocopy	retro_pvam_1449,