RetrogeneDB ID: retro_mmus_579

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:82431042..82432394(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Map3k7
• Ensembl ID: ENSMUSG00000028284
• Aliases: Map3k7, B430101B05, C87327, Tak1
• Description: mitogen-activated protein kinase kinase kinase 7 [Source:MGI Symbol;Acc:MGI:1346877]

Sequence

>retro_mmus_579
GCCTTACTACACTGCTGCTCATGCAGTGAGCTGGTGTTTACAGCTTACCTGCACAGCATGCAGCCCAAAGCTCTAATTCA
CAGGGACCTCAAGCCTCCAAACTTGCTGCTGGTTGCAGGAGGGACAGTTCTAAAAATCTGCGATTTTGATACAGCTTGTG
ACATCCAGACACACATGACCAATAATAAAGGGAGTGCTGCTTGGATGGTCCCCGAAGTGTTTGAAGGTAGCAATTACAGT
GAAAAGTGTGATGTCTTCAGCTGGGGTATTATCCTCTGGGAAGTGATAACACGCTGGAAACCCGATGAGATCGGTGGCCC
AGCTTTCAGATTCATGTGGACTGTTCATAATGGCACTCGACCACCACTGATCAAAAATTTACCTAAGCCCATTGAGAGCT
TGATGACACACTGTTGGTCTAAGGATCCTTCTCAACGCCCTTCAATGGAGGAAATTGTGAAAATAATGACTCACTTGATG
CGGTACTTCCCAGGAGCGGATGAGCCATTACAGTATCCTTGTCAGTACTCTGATGAAGGGCAGAGCAACTCAGCCACCAG
CACAGGCTCATTCATGGACATTGCTTCTACAAATACCAGTAATAAAAGTAACACAAATATGGAACAGATTCCTGCCACAA
ACAACACTATTAAACGCTTGGAGTCAAAACTGTTGATAAACCAGGCAAAGGAACAGAGTGAATGTGGACGCCTGAGTTTG
GAGCCTCTCATGGGAGCAGTGTGGAGAGCTTGCCCCCCACTTCTGAGGGCAAGAGGACGAGTGCTGACATGTCTGAAATA
GAAGCCAGGATTGTGGCGACTGCAGGTAATGGGCAACCAAGGCGTAGATCCATTCAAGACTTGACTGTTACTGGGACAGA
ACCTGGTCAGGTGAGCAGTCGGTCATCCAGCCCTAGAGTTGGAATGATCACTATCTCAGGACCAACCTCAGAGAAGCCAG
CTCGAAGTCACCCGTGGAACCCTGATGATTCCACAGATACCAATGGCTTAGATAACTCCATCCCAATGGCATATCTTACA
CTGGATCACCAGCTACAGCCTCTAGCGCCGTGCCCAAACTCCAAATAATTCATGGCAGTGTTTGAACAACATTGTAAAAT
GGCACAGGAGTATATGAAAGTTCAAACCGAAATCGCATTGTTACTACAGAGAAAGCAAGAAGTAGTTGCAGAATTGGACC
AGGATGAAAAGGACCAGCAAAATACATCTCGTCTGGTACAGGAACATAAAAAGCTTTTAGATGAAAACAAAAGCCTTTCT
ACTTATTACCAGCAATGCAAAAAACAACTAGAGGTTATCAGAAGCCAACAGCAGAAACGACAAGGCACTTCA

Alignment

ORF - retro_mmus_579 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.72 %
• Parental protein coverage: 77.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AMSWCLQCSQGV--AYLHSMQPKALIHRDLKPPNLLLVAGGTVLKICDFGTACDIQTHMTNNKGSAAWMA
          A...C..CS..V..AYLHSMQPKALIHRDLKPPNLLLVAGGTVLKICDF.TACDIQTHMTNNKGSAAWM.
Retrocopy ALLHCCSCSELVFTAYLHSMQPKALIHRDLKPPNLLLVAGGTVLKICDFDTACDIQTHMTNNKGSAAWMV

Parental  PEVFEGSNYSEKCDVFSWGIILWEVITRRKPFDEIGGPAFRIMWAVHNGTRPPLIKNLPKPIESLMTRCW
          PEVFEGSNYSEKCDVFSWGIILWEVITR.KP.DEIGGPAFR.MW.VHNGTRPPLIKNLPKPIESLMT.CW
Retrocopy PEVFEGSNYSEKCDVFSWGIILWEVITRWKP-DEIGGPAFRFMWTVHNGTRPPLIKNLPKPIESLMTHCW

Parental  SKDPSQRPSMEEIVKIMTHLMRYFPGADEPLQYPCQYSDEGQSNSATSTGSFMDIASTNTSNKSDTNMEQ
          SKDPSQRPSMEEIVKIMTHLMRYFPGADEPLQYPCQYSDEGQSNSATSTGSFMDIASTNTSNKS.TNMEQ
Retrocopy SKDPSQRPSMEEIVKIMTHLMRYFPGADEPLQYPCQYSDEGQSNSATSTGSFMDIASTNTSNKSNTNMEQ

Parental  VPATNDTIKRLESKLLKNQAKQQSESGRLSL-GASRGSSVESLPPTSEGKRMSADMSEIEARIVATAGNG
          .PATN.TIKRLESKLL.NQAK.QSE.GRLSL.GAS.GSSVESLPPTSEGKR.SADMSEIEARIVATAGNG
Retrocopy IPATNNTIKRLESKLLINQAKEQSECGRLSL<GASHGSSVESLPPTSEGKRTSADMSEIEARIVATAGNG

Parental  QPRRRSIQDLTVTGTEPGQVSSRSSSPSVRMITTSGPTSEKPARSHPWTPDDSTDTNGSDNSIPMAYLTL
          QPRRRSIQDLTVTGTEPGQVSSRSSSP.V.MIT.SGPTSEKPARSHPW.PDDSTDTNG.DNSIPMAYLTL
Retrocopy QPRRRSIQDLTVTGTEPGQVSSRSSSPRVGMITISGPTSEKPARSHPWNPDDSTDTNGLDNSIPMAYLTL

Parental  DHQLQPLAPCPNSKESMAVFEQHCKMAQEYMKVQTEIALLLQRKQELVAELDQDEKDQQNTSRLVQEHKK
          DHQLQPLAPCPNSK..MAVFEQHCKMAQEYMKVQTEIALLLQRKQE.VAELDQDEKDQQNTSRLVQEHKK
Retrocopy DHQLQPLAPCPNSK*FMAVFEQHCKMAQEYMKVQTEIALLLQRKQEVVAELDQDEKDQQNTSRLVQEHKK

Parental  LLDENKSLSTYYQQCKKQLEVIRSQQQKRQGTS
          LLDENKSLSTYYQQCKKQLEVIRSQQQKRQGTS
Retrocopy LLDENKSLSTYYQQCKKQLEVIRSQQQKRQGTS

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	0.63 RPM	58.94 RPM
SRP007412_cerebellum	0.22 RPM	48.37 RPM
SRP007412_heart	0.16 RPM	64.91 RPM
SRP007412_kidney	1.06 RPM	66.47 RPM
SRP007412_liver	0.30 RPM	45.58 RPM
SRP007412_testis	0.41 RPM	42.49 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_579 was not detected

EST

No EST(s) were mapped for retro_mmus_579 retrocopy.

TSS

No TSS is located nearby retro_mmus_579 retrocopy 5' end.

Lab

retro_mmus_579 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_579 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001962	1 retrocopy	retro_chof_1819,
Myotis lucifugus	ENSMLUG00000003344	1 retrocopy	retro_mluc_1173,
Mus musculus	ENSMUSG00000028284	1 retrocopy	retro_mmus_579 ,
Mus musculus	ENSMUSG00000030890	1 retrocopy	retro_mmus_1119,