RetrogeneDB ID: retro_mmus_1172

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:9886175..9886631(+)
• Located in intron of: ENSMUSG00000060579

Retrocopy information

• Ensembl ID: ENSMUSG00000089686
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Mnd1
• Ensembl ID: ENSMUSG00000033752
• Aliases: Mnd1, 2610034E18Rik, AI591601, Gaj
• Description: meiotic nuclear divisions 1 homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1924165]

Sequence

>retro_mmus_1172
CTAGTGGATGACGGTATGGTTGACTGCGAGAGGATCGGGACGTCCAATTACTACTGGGCTTTTCCGAGCAAGGCTCTTCA
TGCCAGGAAGCACAAGTTGGAGGCTCTGAACTCTCAGCTGTCAGAGGGAAGCCAGAAGCATGCAGACTTACAGAAGAGCA
TTGAGAAAGCAAGAGTTGGCCGGCAAGAGACGCAAGAACGAACCATGTTTGCAAAAGAACTTTCTTCATTTCGAGACTAA
AGGCAACAACTTAAGGCAGAAGTGGAAAAATATCGAGAATGTGACCCACAGGTTGTGGAAGAGATTCGTGAAGCAAATAA
AGTAGCTAAAGAAGCCGCCAATCGATGGACTGATAACATATTTGCAATAAAATCCTGGGCCAAAAGAAAATTTGGGTTTG
AAGAAAGTAAAATTGATAAAAACTTTGGAATTCCAGAAGACTTTGACTACATAGAC

Alignment

ORF - retro_mmus_1172 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.71 %
• Parental protein coverage: 74.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LVDDGMVDCERIGTSNYYWAFPSKALHARKRKLEALNSQLSEGSQKHADLQKSIEKARVGRQETEERAML
          LVDDGMVDCERIGTSNYYWAFPSKALHARK.KLEALNSQLSEGSQKHADLQKSIEKARVGRQET.ER.M.
Retrocopy LVDDGMVDCERIGTSNYYWAFPSKALHARKHKLEALNSQLSEGSQKHADLQKSIEKARVGRQETQERTMF

Parental  AKELSSFRDQRQQLKAEVEKYRECDPQVVEEIREANKVAKEAANRWTDNIFAIKSWAKRKFGFEESKIDK
          AKELSSFRD.RQQLKAEVEKYRECDPQVVEEIREANKVAKEAANRWTDNIFAIKSWAKRKFGFEESKIDK
Retrocopy AKELSSFRD*RQQLKAEVEKYRECDPQVVEEIREANKVAKEAANRWTDNIFAIKSWAKRKFGFEESKIDK

Parental  NFGIPEDFDYID
          NFGIPEDFDYID
Retrocopy NFGIPEDFDYID

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	0.14 RPM
SRP007412_cerebellum	0.00 RPM	0.17 RPM
SRP007412_heart	0.00 RPM	0.72 RPM
SRP007412_kidney	0.00 RPM	0.60 RPM
SRP007412_liver	0.00 RPM	2.27 RPM
SRP007412_testis	0.00 RPM	5.40 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1172 was not detected

EST

No EST(s) were mapped for retro_mmus_1172 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_32395	748 libraries	222 libraries	92 libraries	8 libraries	2 libraries

The graphical summary, for retro_mmus_1172 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_1172 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1172 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018446	1 retrocopy	retro_amel_1745,
Callithrix jacchus	ENSCJAG00000001993	5 retrocopies	retro_cjac_1495, retro_cjac_1907, retro_cjac_2624, retro_cjac_2946, retro_cjac_3979,
Dipodomys ordii	ENSDORG00000004514	1 retrocopy	retro_dord_99,
Felis catus	ENSFCAG00000022084	1 retrocopy	retro_fcat_1833,
Macaca mulatta	ENSMMUG00000004937	1 retrocopy	retro_mmul_395,
Mus musculus	ENSMUSG00000033752	2 retrocopies	retro_mmus_1172 , retro_mmus_3281,
Nomascus leucogenys	ENSNLEG00000005936	1 retrocopy	retro_nleu_998,
Oryctolagus cuniculus	ENSOCUG00000004594	2 retrocopies	retro_ocun_1865, retro_ocun_360,
Ochotona princeps	ENSOPRG00000015738	1 retrocopy	retro_opri_1121,
Sorex araneus	ENSSARG00000011001	1 retrocopy	retro_sara_417,
Tupaia belangeri	ENSTBEG00000004475	1 retrocopy	retro_tbel_1734,