RetrogeneDB ID: retro_mmus_1986

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:150305760..150306516(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000084320
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Mrpl47
• Ensembl ID: ENSMUSG00000037531
• Aliases: None
• Description: mitochondrial ribosomal protein L47 [Source:MGI Symbol;Acc:MGI:1921850]

Sequence

>retro_mmus_1986
ATGGCTGCGACCAGTCTAGTGGGTATTTGTAGAAGAGCCCCAGCGTTCCTGAAGGCTGCTTGCTCCCTAGTAAATCCCAA
GGACCCTTCTCACTCAGGTCACAGGTCTTCTCTTAGTTTGTTGCATAAGAACACACCACATGTCACATCTTTTCTCCAGT
GTAAATTACTTCATACCACACTGCCAAGGAGAGGACTAGCAGAATTTTTTGATGATCCAAAGAATGGGGGAGGAGGGAGA
AAAAGTCAAATCTGGAGCTTTATGGACCTGCCAGCAGCTGAGAAACAAAAGCAATGAAAACTTACAGAAGCTTTGGTATG
CGCTTCTGAAGGAAAGAACCATGCTTCTAACTCTAGAACAGGAGGCCACGTGATGAGATTGCCAATGCCAAGTCCAGAGT
GGTTAGAAAAGGTTGTTGATTCCATGGATGCCTTAGATAAAGTTGTCTAGGAGAGGGAAGATGCTTTAGGCTTCTTCAGA
TTGGTCAAGAAAAACCAAGACCTGATGCTTGGAAAAGCATCTTTGGACGAATCGTCTGGCACAAATTCAAGCACTGGCCT
ATACTTTGGTGCCTAAATAAAAGATACAACAGGAGGCGGTTCTTCGCAGTGCCTTATGTGGATCGATTTATCAGACTAAG
CATTGAGAAACACACCCGTATTGAAGCAAGAAAGGGAAGTTTACAGAAAAAGAAAGAAAGAATTCTCCAGGAAAAAGTTC
CCACATCTCTCTCAAGACTAGAAATCAAGTACCGTC

Alignment

ORF - retro_mmus_1986 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.63 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MAATSLVGICRRASAFLKAACSLVNPKDAAHSGCRSSLSLLHKNTPHVTSFLQCKLLHTTLSRKGLEEFF
          MAATSLVGICRRA.AFLKAACSLVNPKD..HSG.RSSLSLLHKNTPHVTSFLQCKLLHTTL.R.GL.EFF
Retrocopy MAATSLVGICRRAPAFLKAACSLVNPKDPSHSGHRSSLSLLHKNTPHVTSFLQCKLLHTTLPRRGLAEFF

Parental  DDP-KNW-GEE--KVKSGASWTCQQLRNKSNEDLHKLWYVLLKERNMLLTLEQEAK-RQRLPMPSPERLE
          DDP.K.W.GEE..KVKSGA.WTCQQLRNKSNE.L.KLWY.LLKER.MLLTLEQEA....RLPMPSPE.LE
Retrocopy DDP<KEW<GEEGEKVKSGALWTCQQLRNKSNENLQKLWYALLKERTMLLTLEQEAT<VMRLPMPSPEWLE

Parental  KVVDSMDNVDKVVQEREDAL-RLLQTGQEKPRPGAWRRDIFGRIVWHKFKQWPIPWYLNKRYNRRRFFAM
          KVVDSMD..DKVV.EREDAL.RLLQ.GQEKPRP.AW...IFGRIVWHKFK.WPI.W.LNKRYNRRRFFA.
Retrocopy KVVDSMDALDKVV*EREDAL<RLLQIGQEKPRPDAWK-SIFGRIVWHKFKHWPILWCLNKRYNRRRFFAV

Parental  PYVDRFIRLRIEKHARIEARKRSLQKKKEKIL-HAKFPHLSQERKSSSV
          PYVDRFIRL.IEKH.RIEARK.SLQKKKE.IL...KFPHLSQ..KSS.V
Retrocopy PYVDRFIRLSIEKHTRIEARKGSLQKKKERIL>RKKFPHLSQD*KSSTV

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	0.09 RPM	11.89 RPM
SRP007412_cerebellum	0.00 RPM	11.16 RPM
SRP007412_heart	0.00 RPM	16.41 RPM
SRP007412_kidney	0.00 RPM	12.24 RPM
SRP007412_liver	0.00 RPM	8.93 RPM
SRP007412_testis	0.00 RPM	30.46 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1986 was not detected

EST

No EST(s) were mapped for retro_mmus_1986 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_81383	484 libraries	223 libraries	342 libraries	18 libraries	5 libraries

The graphical summary, for retro_mmus_1986 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_1986 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1986 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011380	1 retrocopy	retro_cfam_1085,
Cavia porcellus	ENSCPOG00000002312	2 retrocopies	retro_cpor_1219, retro_cpor_885,
Felis catus	ENSFCAG00000031548	1 retrocopy	retro_fcat_235,
Macropus eugenii	ENSMEUG00000012649	2 retrocopies	retro_meug_1039, retro_meug_146,
Monodelphis domestica	ENSMODG00000021301	3 retrocopies	retro_mdom_1361, retro_mdom_1879, retro_mdom_562,
Mustela putorius furo	ENSMPUG00000017214	1 retrocopy	retro_mputfur_495,
Mus musculus	ENSMUSG00000037531	3 retrocopies	retro_mmus_1976, retro_mmus_1986 , retro_mmus_2753,
Otolemur garnettii	ENSOGAG00000016957	2 retrocopies	retro_ogar_1900, retro_ogar_3015,
Pteropus vampyrus	ENSPVAG00000004284	1 retrocopy	retro_pvam_150,
Rattus norvegicus	ENSRNOG00000011639	2 retrocopies	retro_rnor_1829, retro_rnor_2523,
Sorex araneus	ENSSARG00000006898	2 retrocopies	retro_sara_269, retro_sara_721,
Tursiops truncatus	ENSTTRG00000008909	1 retrocopy	retro_ttru_420,