RetrogeneDB ID: retro_mmus_476

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:106888135..106888897(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083613
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Pou2f3
• Ensembl ID: ENSMUSG00000032015
• Aliases: Pou2f3, Epoc-1, Oct-11a, Oct11, Otf-11, Otf11, Skin, Skin-1a, Skn-1a, Skn-li
• Description: POU domain, class 2, transcription factor 3 [Source:MGI Symbol;Acc:MGI:102565]

Sequence

>retro_mmus_476
GGCCACTTGCAGTCCGTATCCCAGTTCCTGCTTTCCCAGACCCCACCTGGACAGCAAGGTCTGCAGCTGAATCTTCTCTC
CTTTCCACAGCAACAAAGCACTCTACTCCTCCCACATACAGGGCCTGGCCTTGCCTCCCAGGCAGTTTGGGCGCCCTGGG
ATGTCAGCATCCTTTTTAGAGCCCCACCTGGATGCTCCTCAGCACCTGCCAGGGCCCAAGCAACTGCCTGGCCCCGGAGG
GAATGACTGACCTGGAGGAGCTGGAGAAGTTTGCCAAGACCTTCAAGCAGAGACGCATTAAGCTAGGCTTCACACAGGGA
GGTGTGGGATTGGCGATGAGAAAGCTATATGGCAATGATTTTAGCCAGACTACCATCTCTCTATTTGAGGCCCTCAACCT
GAGCTTCAAAAATATGTGCAAACTAAAGCAGCTGCTGGAGAAGTGGCTGAACAATGCAGAGTCCTCCCAGCCAGATACTT
CAGCGAGCACACCCAGCTCCTACCCCACTCTCAGCGAAGTGTTTGACACTAAGAGGAAGAAACAGACCAGCATCGAGACC
AACATCAGCCTGACTTTGGAGAAGATATTTCAAGATAAACCTCAACCCAGCTCGGAAGAGATTTCCTTGATTGCGGAGCA
GTTATCCATGGAGACGGAGGTGGTTAGAGTCTAGATCTGCAATCGACACCAAAAGGAAAAGAGAATCAACTGCCCCGTGG
CCACCCCTGTTAAGACCACCCATCTACAACTCCTGGCTTGTC

Alignment

ORF - retro_mmus_476 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.94 %
• Parental protein coverage: 61.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GHLQSVSQFLLSQTPPGQQGLQPNLLSFPQQQSTLLLPQTGPGLASQAV-GRPGLSGSSLEPHLDAPQHL
          GHLQSVSQFLLSQTPPGQQGLQ.NLLSFPQQQSTLLLP.TGPGLASQAV.GRPG.S.S.LEPHLDAPQHL
Retrocopy GHLQSVSQFLLSQTPPGQQGLQLNLLSFPQQQSTLLLPHTGPGLASQAV>GRPGMSASFLEPHLDAPQHL

Parental  PG-PKHLPGPGGNDEPTDLEELEKFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSF
          PG.P.....P.G....TDLEELEKFAKTFKQRRIKLGFTQG.VGLAM.KLYGNDFSQTTIS.FEALNLSF
Retrocopy PG>PSNCLAPEGM---TDLEELEKFAKTFKQRRIKLGFTQGGVGLAMRKLYGNDFSQTTISLFEALNLSF

Parental  KNMCKLKPLLEKWLNDAESSPSDPSASTPSSYPTLSEVFGRKRKKRTSIETNIRLTLEKRFQDNPKPSSE
          KNMCKLK.LLEKWLN.AESS..D.SASTPSSYPTLSEVF..KRKK.TSIETNI.LTLEK.FQD.P.PSSE
Retrocopy KNMCKLKQLLEKWLNNAESSQPDTSASTPSSYPTLSEVFDTKRKKQTSIETNISLTLEKIFQDKPQPSSE

Parental  EISMIAEQLSMEKEVVRVWFCNRRQKEKRINCPVATPVK-PPIYNSRLV
          EIS.IAEQLSME.EVVRV..CNR.QKEKRINCPVATPVK.PPIYNS.LV
Retrocopy EISLIAEQLSMETEVVRV*ICNRHQKEKRINCPVATPVK>PPIYNSWLV

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	0.12 RPM
SRP007412_cerebellum	0.00 RPM	0.04 RPM
SRP007412_heart	0.00 RPM	0.12 RPM
SRP007412_kidney	0.00 RPM	0.40 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	5.53 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_476 was not detected

EST

No EST(s) were mapped for retro_mmus_476 retrocopy.

TSS

No TSS is located nearby retro_mmus_476 retrocopy 5' end.

Lab

retro_mmus_476 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_476 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000024406	2 retrocopies	retro_mmus_2201, retro_mmus_250,
Mus musculus	ENSMUSG00000032015	1 retrocopy	retro_mmus_476 ,