RetrogeneDB ID: retro_mmus_1976

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:138871984..138872511(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081009
• 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_1976
ACACCTTTTCTCCAGGGTGAATTACTTTATATCACATTGTCAGGAGAAGATTAGAAGAATTTTTTGATGACCCAAAGAAT
TGGGGGGTGGAAGGAAGAAAAGTCAAATCTGGAGCTTCACATACCTGGTAGCAACTGAGAAACAAAAGTAATGAAAATTT
ACATAAGCTTTGACATATACTTCTGAAGGAAAGAACCATGCTTCTAACTCTAGAGCAGGAGGCCAAGTGACAGAGATTGC
CAATGCCAAGTCCAGAGTGGTTAGAAAAGGTTGTTGATTCCATGATGCCTTAGATAAAGTTGTCCAGGAGAGAGAAGATG
CTTTGAGGCTTCTTCAGACCAGTCAAGAAAATCCAAGACCTGGTGCTTGGGAGAAGGGACAGCTTTGGCCAAATCATCAG
GTGCAAATTCAAGCAGTGACCTATACCTTGCTATCTAAATAAAAGATATAACAGAAGGCAGTTCTTTGTAATGCCTTATG
TGGATTGCTTTGCCAGACTGAGAGTTGAGAAACATGTCCTCACTGAA

Alignment

ORF - retro_mmus_1976 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.54 %
• Parental protein coverage: 69.05 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TSFLQCKLLHTTLS-RKGLEEFFDDPKNWGEE--KVKSGASWTCQQLRNKSNEDLHKLWYVLLKERNMLL
          T.FLQ..LL..TLS.R..LEEFFDDPKNWG.E..KVKSGAS.T..QLRNKSNE.LHKL...LLKER.MLL
Retrocopy TPFLQGELLYITLS<RRRLEEFFDDPKNWGVEGRKVKSGASHTW*QLRNKSNENLHKL*HILLKERTMLL

Parental  TLEQEAKRQRLPMPSPERLEKVVDSM-DNVDKVVQEREDALRLLQTGQEKPRPGAW-RRDIFGRIVWHKF
          TLEQEAK.QRLPMPSPE.LEKVVDSM.D..DKVVQEREDALRLLQT.QE.PRPGAW.RRD.FG.I...KF
Retrocopy TLEQEAK*QRLPMPSPEWLEKVVDSM<DALDKVVQEREDALRLLQTSQENPRPGAW>RRDSFGQIIRCKF

Parental  KQWPIPWYLNKRYNRRRFFAMPYVDRFIRLRIEKHARIE
          KQ.PIP.YLNKRYNRR.FF.MPYVD.F.RLR.EKH...E
Retrocopy KQ*PIPCYLNKRYNRRQFFVMPYVDCFARLRVEKHVLTE

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	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_1976 was not detected

EST

No EST(s) were mapped for retro_mmus_1976 retrocopy.

TSS

No TSS is located nearby retro_mmus_1976 retrocopy 5' end.

Lab

retro_mmus_1976 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1976 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_1829

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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,