RetrogeneDB ID: retro_mmus_340

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:83314512..83315297(+)
• Located in intron of: ENSMUSG00000026163

Retrocopy information

• Ensembl ID: ENSMUSG00000079140
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Mrrf
• Ensembl ID: ENSMUSG00000026887
• Aliases: Mrrf, 2400002D02Rik, MRFF, MTRRF, RRF
• Description: mitochondrial ribosome recycling factor [Source:MGI Symbol;Acc:MGI:1915121]

Sequence

>retro_mmus_340
ATGGCCTTGGGAATAAGATGCCTTCGCCTGCTGCACCCTGCTTTTCGCAGTTACCATGCTGCTTTGACCAGACCTGTTTC
AGAAGTTTCCATGAAGACAGTGAGTGGAAGACAACATGACCATAGGCAGTACTCAGCCTACCCAGCAGTACCAGTTCGCC
ATTTTGCAATCAAGAAAGCCAAAGCTAAAGGGAAAGGACAGCCCCAGGCCAGGGTGAACATTAATAGAGCCTTTGTTGAG
GATATAATCAGCTTGGAAGAGGTGGATGAAGACATGAAATCTGTGATGGAAGCACTTAAGGATAATTTCAATAGGACTCT
CAACATAAGGACTGCATCAGGATCCCTTGATCATATTACTGTGGTAACTGCTGATGGGAAGGTTGCTCTAAGTCAGATTG
GCCAGATCTCCATGAAGTCGCCACAGGTGATTCTGGTGAATATGGCCATCTTCCCAGAGTGCACAGCTGCAGCTATCAAG
GCTATAAGAGGAAGTAGAATGAATCTGAACCCAGAAGTGGAAGGAACACTAATTCGGGTACCCATTCCTAAATTAACCAG
GGAACACAGAGAAATGCTGGTAAAATTGGCCAAACAGAACACCAACAAGGCCAAAGAAAATTTACGGAAGGTTTGCACTA
ATGCAATGAATAAACTGAAGAAGTCAAAGGACAAAACCTCGGAGGACACCATTAGACTCATGGAGAAGCAGATCAGCCAA
ATTGCAGACGACACGGTGGCAGAGTTGGACCAGCATCTGGCAGCAAGACCAAAGAACTCCTTGGA

Alignment

ORF - retro_mmus_340 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.78 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASGIRCFRLLHPAFRSYHAALTRPVSEVSMKTVSGRQHGHRQYSAYPAVPVRHFATKKAKAKGKGQPQA
          MA.GIRC.RLLHPAFRSYHAALTRPVSEVSMKTVSGRQH.HRQYSAYPAVPVRHFA.KKAKAKGKGQPQA
Retrocopy MALGIRCLRLLHPAFRSYHAALTRPVSEVSMKTVSGRQHDHRQYSAYPAVPVRHFAIKKAKAKGKGQPQA

Parental  RVTVNRALVEDIISLEEVDEDMKSVVEALKDNFNKTLNIRTAPGSLDHITVVTADGKVALNQIGQISMKS
          RV..NRA.VEDIISLEEVDEDMKSV.EALKDNFN.TLNIRTA.GSLDHITVVTADGKVAL.QIGQISMKS
Retrocopy RVNINRAFVEDIISLEEVDEDMKSVMEALKDNFNRTLNIRTASGSLDHITVVTADGKVALSQIGQISMKS

Parental  PQVILVNMASFPECTAAAIKAIRESGMNLNPEVEGTLIRVPIPKVTREHREMLVKLAKQNTNKAKENLRK
          PQVILVNMA.FPECTAAAIKAIR.S.MNLNPEVEGTLIRVPIPK.TREHREMLVKLAKQNTNKAKENLRK
Retrocopy PQVILVNMAIFPECTAAAIKAIRGSRMNLNPEVEGTLIRVPIPKLTREHREMLVKLAKQNTNKAKENLRK

Parental  VRTNAMNKLKKSKDKTSEDTIRLIEKQISQMADDTVAELDQHLAA-KTKELLG
          V.TNAMNKLKKSKDKTSEDTIRL.EKQISQ.ADDTVAELDQHLAA.KTKELLG
Retrocopy VCTNAMNKLKKSKDKTSEDTIRLMEKQISQIADDTVAELDQHLAA<KTKELLG

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	0.05 RPM	13.22 RPM
SRP007412_cerebellum	0.48 RPM	10.07 RPM
SRP007412_heart	0.06 RPM	29.26 RPM
SRP007412_kidney	0.06 RPM	20.77 RPM
SRP007412_liver	0.03 RPM	15.46 RPM
SRP007412_testis	0.27 RPM	28.86 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_340 was not detected

EST

No EST(s) were mapped for retro_mmus_340 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_76803	89 libraries	59 libraries	736 libraries	169 libraries	19 libraries

The graphical summary, for retro_mmus_340 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_340 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_340 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000007351	1 retrocopy	retro_cpor_877,
Homo sapiens	ENSG00000148187	1 retrocopy	retro_hsap_4897,
Gorilla gorilla	ENSGGOG00000023499	1 retrocopy	retro_ggor_98,
Mus musculus	ENSMUSG00000026887	1 retrocopy	retro_mmus_340 ,
Nomascus leucogenys	ENSNLEG00000017177	1 retrocopy	retro_nleu_1263,
Pongo abelii	ENSPPYG00000019570	1 retrocopy	retro_pabe_80,
Pan troglodytes	ENSPTRG00000021324	1 retrocopy	retro_ptro_3265,
Rattus norvegicus	ENSRNOG00000025997	2 retrocopies	retro_rnor_1477, retro_rnor_2654,
Sarcophilus harrisii	ENSSHAG00000012469	2 retrocopies	retro_shar_610, retro_shar_704,
Tupaia belangeri	ENSTBEG00000016569	1 retrocopy	retro_tbel_4411,