RetrogeneDB ID: retro_mmus_1923

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:58108059..58108569(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000053472
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Nudt15
• Ensembl ID: ENSMUSG00000033405
• Aliases: Nudt15, 6530403O17, A730068G11Rik, MTH2
• Description: nudix (nucleoside diphosphate linked moiety X)-type motif 15 [Source:MGI Symbol;Acc:MGI:2443366]

Sequence

>retro_mmus_1923
ATGGCCGCTAACGCAGAGCCGAGGCGGCGGCCAGGAGTTGGGGTCGGCGTGGTGGTGCTGAGCTGCGAGCATCCTCGCTG
CGTCCTTCTGGGGAAAAGGAAAGGATCGTTTGGAGCCGGCAGTTTCCAGCTTCCTGGGGGCCATTTGGAATTCGGTGAGA
CCTGGGAAGAATGTGCTCAGAGAGAAACCTGGGAAGAAGCTGGGCTTCACCTGAAAAATGTGCGCTTTGCCTCTGTGGTA
AATTCTTTTGTTGAGAAGGAGAATTACCATTATGTTACCATATTAATGAAAGGAGAGGTGGATATGACTCATGATTCGGA
GCCGAGGAATATGGAGCCTGAAAAGAATGAAAGTTGGGAGTGGGTTCCATGGGAAGAATTCCCTCCCTTAGACCAGCTTT
TCTGGGCTCTCCGCTGTCTAAAAGAGCAAGGTTATGACCCATTTAAAGAGGACCTGAACCACCTGGAAGGGTACCGAGGA
GAGCACCTTGAAAGGACCACGAAGACTCCT

Alignment

ORF - retro_mmus_1923 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.41 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAANAEPRRRPGVGVGVVVLSCEHPRCVLLGKRKGSFGAGSFQLPGGHLEFGETWEECAQRETWEEAGLH
          MAANAEPRRRPGVGVGVVVLSCEHPRCVLLGKRKGSFGAGSFQLPGGHLEFGETWEECAQRETWEEAGLH
Retrocopy MAANAEPRRRPGVGVGVVVLSCEHPRCVLLGKRKGSFGAGSFQLPGGHLEFGETWEECAQRETWEEAGLH

Parental  LKNVCFASVVNSFVEKENYHYVTILMKGEVDMTHDSEPRNMEPEKNESWEWVPWEEFPPLDQLFWALRCL
          LKNV.FASVVNSFVEKENYHYVTILMKGEVDMTHDSEPRNMEPEKNESWEWVPWEEFPPLDQLFWALRCL
Retrocopy LKNVRFASVVNSFVEKENYHYVTILMKGEVDMTHDSEPRNMEPEKNESWEWVPWEEFPPLDQLFWALRCL

Parental  KEQGYDPFKEDLNHLEGYRGEHLERTTKTP
          KEQGYDPFKEDLNHLEGYRGEHLERTTKTP
Retrocopy KEQGYDPFKEDLNHLEGYRGEHLERTTKTP

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	0.44 RPM
SRP007412_cerebellum	0.00 RPM	0.65 RPM
SRP007412_heart	0.00 RPM	1.06 RPM
SRP007412_kidney	0.10 RPM	0.50 RPM
SRP007412_liver	0.00 RPM	0.27 RPM
SRP007412_testis	0.14 RPM	0.37 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1923 was not detected

EST

No EST(s) were mapped for retro_mmus_1923 retrocopy.

TSS

No TSS is located nearby retro_mmus_1923 retrocopy 5' end.

Lab

retro_mmus_1923 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1923 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019501	1 retrocopy	retro_btau_559,
Callithrix jacchus	ENSCJAG00000009274	1 retrocopy	retro_cjac_1497,
Homo sapiens	ENSG00000136159	2 retrocopies	retro_hsap_1822, retro_hsap_4063,
Gorilla gorilla	ENSGGOG00000008232	3 retrocopies	retro_ggor_2171, retro_ggor_2257, retro_ggor_2729,
Microcebus murinus	ENSMICG00000009583	1 retrocopy	retro_mmur_962,
Mus musculus	ENSMUSG00000033405	1 retrocopy	retro_mmus_1923 ,
Nomascus leucogenys	ENSNLEG00000002957	2 retrocopies	retro_nleu_2878, retro_nleu_563,
Pongo abelii	ENSPPYG00000005353	2 retrocopies	retro_pabe_1490, retro_pabe_3337,
Pan troglodytes	ENSPTRG00000042329	1 retrocopy	retro_ptro_82,
Tarsius syrichta	ENSTSYG00000006960	1 retrocopy	retro_tsyr_146,