RetrogeneDB ID: retro_mmus_13

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:62664827..62665199(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000048497
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Mmgt1
• Ensembl ID: ENSMUSG00000061273
• Aliases: Mmgt1, 9630048L06Rik, BC032271, Emc5, Tmem32
• Description: membrane magnesium transporter 1 [Source:MGI Symbol;Acc:MGI:2384305]

Sequence

>retro_mmus_13
ATGGTGGCGTGGCTGTGGAAGGTGCTGATGGGCGTCGGTCTCTTCGCCCTCACCCACGCGGCCTTCTCAGCTGCTCAGCA
TCGCTCTCATGCGCGACTGACAGAAAAGAAGTATGAGCCGCTGCCGGCGGATATAGTTCTCCAGACCCTTTTGGCCTTTG
CGCTTACCTGTTACGGCGTGGTTCATACTGCAGGGGACTTTAGAGACAGGGATGCCACTTCGGAACTAAAGGATATGACA
TTTGACACCTTAAGGAATCGCCCGTCTTTTTACGTGTTTCACCGTTCTGGCTACCGACTGTTCCAGCGTCCGGATTCAAC
CCATTCTTCAAACCTCAGCGCGTCATCTTCTGACTTACCGTTGAAGTTTTGA

Alignment

ORF - retro_mmus_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.49 %
• Parental protein coverage: 93.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAPSLWKGLVGVGLFALAHAAFSAAQHRSYMRLTEKEDESLPIDIVLQTLLAFAVTCYGIVHIAGEFKDM
          M...LWK.L.GVGLFAL.HAAFSAAQHRS..RLTEK..E.LP.DIVLQTLLAFA.TCYG.VH.AG.F.D.
Retrocopy MVAWLWKVLMGVGLFALTHAAFSAAQHRSHARLTEKKYEPLPADIVLQTLLAFALTCYGVVHTAGDFRDR

Parental  DATSELKNKTFDTLRNHPSFYVFNHRGRVLFRPSDATNSSNLDALSSNTSLK
          DATSELK..TFDTLRN.PSFYVF...G..LF...D.T.SSNL.A.SS...LK
Retrocopy DATSELKDMTFDTLRNRPSFYVFHRSGYRLFQRPDSTHSSNLSASSSDLPLK

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	3.04 RPM	37.94 RPM
SRP007412_cerebellum	1.56 RPM	33.17 RPM
SRP007412_heart	1.68 RPM	33.37 RPM
SRP007412_kidney	2.95 RPM	46.08 RPM
SRP007412_liver	0.41 RPM	19.31 RPM
SRP007412_testis	0.69 RPM	2.70 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_13 was not detected

EST

No EST(s) were mapped for retro_mmus_13 retrocopy.

TSS

No TSS is located nearby retro_mmus_13 retrocopy 5' end.

Lab

retro_mmus_13 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_13 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000025297	2 retrocopies	retro_btau_1566, retro_btau_864,
Cavia porcellus	ENSCPOG00000013476	3 retrocopies	retro_cpor_104, retro_cpor_1171, retro_cpor_979,
Echinops telfairi	ENSETEG00000005810	1 retrocopy	retro_etel_1671,
Monodelphis domestica	ENSMODG00000028393	1 retrocopy	retro_mdom_281,
Mus musculus	ENSMUSG00000061273	1 retrocopy	retro_mmus_13 ,
Oryctolagus cuniculus	ENSOCUG00000029505	1 retrocopy	retro_ocun_660,
Otolemur garnettii	ENSOGAG00000003462	2 retrocopies	retro_ogar_1112, retro_ogar_2224,
Rattus norvegicus	ENSRNOG00000000881	1 retrocopy	retro_rnor_689,
Sus scrofa	ENSSSCG00000025854	1 retrocopy	retro_sscr_908,
Ictidomys tridecemlineatus	ENSSTOG00000004796	1 retrocopy	retro_itri_1421,
Tupaia belangeri	ENSTBEG00000011209	1 retrocopy	retro_tbel_4115,