RetrogeneDB ID: retro_mmus_424

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:28801132..28802477(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081557
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rpap3
• Ensembl ID: ENSMUSG00000022466
• Aliases: Rpap3, 2310042P20Rik, D15Ertd682e
• Description: RNA polymerase II associated protein 3 [Source:MGI Symbol;Acc:MGI:1277218]

Sequence

>retro_mmus_424
ACGAAAAACAGAATAAAATCTTATGACTATGATGCCTGGGCAAAACTTGATGTAGACAGGATCCTCGAGGAGCCTGACAA
AGAAGACAGCAACCATGATTCTCTGTCCCAGGAGTCAGAGTCGGATGAAGATGGCATTCCTGTGGATTCCCAGAAGGCCC
TTGTTCTAAAAGAAAAGGGCAATAAGTACTTCAAGCAAGGAAAATACAATGAAGCCATTGAATGCTACACGAAAGGCATG
GATGCTGTCCCCTATAATCCCGTGCTGCCAACAAATAGAGTCTCAGCTTACTTCAGATTGAAAAAGTTTGCTGTTGCTGA
GTCTGACTGTAACTTGGCAATTGCCTTGAGCAGGCCTTACACCAAGGCTTACACTAGACGAGGTGCAGCTCGGTTTGCTC
TGCAGAAGTTAGAGGACGCCAGAAAAGATTATGAGAATGTGTTAGATCTGGAGATAGATAACTTTGAAGCAACAAATGAA
CTCAGGAAAATTAATCAGGCTTTAACATCCAAGGAAAACTCCGGTCCTAAAAAAGCTGCTGCTGCCGAGAGTAAGCCAGC
TGCAGGAGAGAAAAAAACCAACGGGCGATCAGCATGGCAGGCAGAAGGCCATTGTGGAGAAAGACCTGGGCAACGGAGTT
TTCAAAGAGAGGAAATACGAGCAAGCAATTGAATGCTATACCCGCGGGATAGCAGCAGACCGCACCAACACCCTGCCCCC
AGATAACAGAGCGATGGCCTATCTTAAGATTCAGAGATATGAAGAAGCTGAAAGAGACCTGCACACAAGCTATCGTACTA
GATGGCTCATACTCAAAAAGCGTTTGCCACAAGAGGAACCGCAAGGACATTTTTGGGAAAGATCAACGAGGCCAAGCAAG
ATTTTGAAACTGTTTTACTTCTGGAACCTGGAAATAAACAAGCGGCAACCGAGCTTTCCAGAATCAAAAGGAACTAATTG
AGAAAGGCCGTTGGGATGATGTCTTCCTTGACTCCACACAGAGACACAATGTGGTGAAAGCTGTGGATAAGCCTCCTTCT
CCTCAGGGATCACCTAAAGCACTCAAGAAGGTTTTTATTGAAGAAACTGGCAATTTGATAGAGACTGTTGATGCACCAGA
TAGTTCTGCCACTGTCCCCAAGAGTGATCGAGCAATGGCGGCCGTGGGCCCTGGAAGCAAGAAGAATTCAAGCCAGGGCG
TCTCTCGCCTGCAGGGGATAGGCCCAGAGCTAAAGTGTTGAAAATAGAAGCAATCAATGACGCTTCAGCCCCACAAGCAC
GGGTGGAGGTGAAGCAGGATGCGCGTCAGCCTGTGAGTGAGAAGGCCTCCATGAGGGCAAAGCAG

Alignment

ORF - retro_mmus_424 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.96 %
• Parental protein coverage: 67.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  TKNRIKSYDYDAWAKLDVDRILDELDKEDSTHDSLSQESESDEDGIRVDSQKALVLKEKGNKYFKQGKYD
          TKNRIKSYDYDAWAKLDVDRIL.E.DKEDS.HDSLSQESESDEDGI.VDSQKALVLKEKGNKYFKQGKY.
Retrocopy TKNRIKSYDYDAWAKLDVDRILEEPDKEDSNHDSLSQESESDEDGIPVDSQKALVLKEKGNKYFKQGKYN

Parental  EAIECYTKGMDADPYNPVLPTNRASAYFRLKKFAVAESDCNLAIALSRTYTKAYARRGAARFALQKLEDA
          EAIECYTKGMDA.PYNPVLPTNR.SAYFRLKKFAVAESDCNLAIALSR.YTKAY.RRGAARFALQKLEDA
Retrocopy EAIECYTKGMDAVPYNPVLPTNRVSAYFRLKKFAVAESDCNLAIALSRPYTKAYTRRGAARFALQKLEDA

Parental  RKDYEKVLELEPDNFEATNELRKINQALTSKENSGPGAAAAAESKPAAGE-SKPTGGQQGRQKAIAEKDL
          RKDYE.VL.LE.DNFEATNELRKINQALTSKENSGP..AAAAESKPAAGE..KPTG.Q.GRQKAI.EKDL
Retrocopy RKDYENVLDLEIDNFEATNELRKINQALTSKENSGPKKAAAAESKPAAGE>KKPTGDQHGRQKAIVEKDL

Parental  GNGFFKEGKYEQAIECYTRGIAADRTNALLPANRAMAYLKIQRYEEAERD-CTQAIVLDGSYS-KAFARR
          GNG.FKE.KYEQAIECYTRGIAADRTN.L.P.NRAMAYLKIQRYEEAERD.CTQAIVLDGSYS.KAFA.R
Retrocopy GNGVFKERKYEQAIECYTRGIAADRTNTLPPDNRAMAYLKIQRYEEAERD>CTQAIVLDGSYS>KAFATR

Parental  GTARTFLGKINEAKQDFETVLLLEPGNKQAATELSRIK-KELIEKGHWDDVFLDSTQRHHVVKAVDNP--
          GTARTFLGKINEAKQDFETVLLLEPGNKQAATELSRIK.KELIEKG.WDDVFLDSTQRH.VVKAVD.P..
Retrocopy GTARTFLGKINEAKQDFETVLLLEPGNKQAATELSRIK<KELIEKGRWDDVFLDSTQRHNVVKAVDKPPS

Parental  PRGSPKALKKVFIEETGNLIETVDAPDSSATVPESDRATAAVGTGTKKNPSEGVS-LPAGDRPRAKVLKI
          P.GSPKALKKVFIEETGNLIETVDAPDSSATVP.SDRA.AAVG.G.KKN.S.GVS..PAGDRPRAKVLKI
Retrocopy PQGSPKALKKVFIEETGNLIETVDAPDSSATVPKSDRAMAAVGPGSKKNSSQGVS<SPAGDRPRAKVLKI

Parental  EAVSDTSAPQAQVGVKQDARQPGSEKASVRAEQ
          EA..D.SAPQA.V.VKQDARQP.SEKAS.RA.Q
Retrocopy EAINDASAPQARVEVKQDARQPVSEKASMRAKQ

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	18.15 RPM
SRP007412_cerebellum	0.00 RPM	18.11 RPM
SRP007412_heart	0.00 RPM	12.76 RPM
SRP007412_kidney	0.00 RPM	15.13 RPM
SRP007412_liver	0.00 RPM	6.55 RPM
SRP007412_testis	0.27 RPM	10.52 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_424 was not detected

EST

No EST(s) were mapped for retro_mmus_424 retrocopy.

TSS

No TSS is located nearby retro_mmus_424 retrocopy 5' end.

Lab

retro_mmus_424 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_424 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000022466	2 retrocopies	retro_mmus_3000, retro_mmus_424 ,