RetrogeneDB ID: retro_mmus_2347

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:49342247..49342575(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000096476
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Tusc2
• Ensembl ID: ENSMUSG00000010054
• Aliases: Tusc2, 1190001E22Rik, AA407686, Fus1, Lgcc, PAP, Pdap2
• Description: tumor suppressor candidate 2 [Source:MGI Symbol;Acc:MGI:1931086]

Sequence

>retro_mmus_2347
ATGGGCGCCAGTGGCTCCAAAGCTCGGGGTCTTTGGCCCTTTGCCTCCACTATGAGGGACGGCGGCCCAGAGGCAGCAGG
CTCTGAGCAGTCTTTGGTGTGGCCTCGAGGCCGAGCACTGCCTCCCTTCGTATTCATGCTCAGTGGCTCCATGTTCTATG
ATGAAGATAGAGATCTAGCTCACGAATTCTATGAGGAGACAATCGTCACCAAGAATGGGCAGAAGCGAGCCAAGCTGAGG
CAGGTACATAAGAATTGGATTCCTCAGGGCATCGTGAAGCTGGATCCCCCGAATCCACATGGATTTCCCCATGATCCTCT
ATGAAGTA

Alignment

ORF - retro_mmus_2347 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.88 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGASGSKARGLWPFASTPGGGGPEAAGSEQSLVRSRARAVPPFVFTRRGSMFYDEDGDLAHEFYEETIVT
          MGASGSKARGLWPFAST...GGPEAAGSEQSLV..R.RA.PPFVF...GSMFYDED.DLAHEFYEETIVT
Retrocopy MGASGSKARGLWPFASTMRDGGPEAAGSEQSLVWPRGRALPPFVFMLSGSMFYDEDRDLAHEFYEETIVT

Parental  KNGQKRAKLRRVHKNLIPQGIVKLDPPRIHVDFP-VILYEV
          KNGQKRAKLR.VHKN.IPQGIVKLDPP..H..FP..ILYEV
Retrocopy KNGQKRAKLRQVHKNWIPQGIVKLDPPNPH-GFP>MILYEV

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	46.24 RPM
SRP007412_cerebellum	0.00 RPM	45.51 RPM
SRP007412_heart	0.00 RPM	19.77 RPM
SRP007412_kidney	0.00 RPM	31.80 RPM
SRP007412_liver	0.00 RPM	24.77 RPM
SRP007412_testis	0.00 RPM	16.33 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2347 was not detected

EST

No EST(s) were mapped for retro_mmus_2347 retrocopy.

TSS

No TSS is located nearby retro_mmus_2347 retrocopy 5' end.

Lab

retro_mmus_2347 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2347 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000007859	2 retrocopies	retro_dord_20, retro_dord_590,
Mus musculus	ENSMUSG00000010054	2 retrocopies	retro_mmus_2347 , retro_mmus_2349,
Oryctolagus cuniculus	ENSOCUG00000005259	1 retrocopy	retro_ocun_1687,
Rattus norvegicus	ENSRNOG00000021528	1 retrocopy	retro_rnor_2952,