RetrogeneDB ID: retro_mmus_3255

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 9:25450710..25452057(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Clpb
• Ensembl ID: ENSMUSG00000001829
• Aliases: Clpb, AL118244, Skd3
• Description: ClpB caseinolytic peptidase B [Source:MGI Symbol;Acc:MGI:1100517]

Sequence

>retro_mmus_3255
TGGGTCTGGGCCAAGGTGCTGGTGGTTCAGTGCTACAAGAATCCATCTAACAAGGATGCAGCTCTAATGGAAGCTGCTCT
GGCCAATAACGTGCAGGAAGTCAGAAGGCTGTTGTCAGAAGGTGCAGATGTCAATGCAAGGTACAAACTTGGCTAGACAG
CATTGATGGTGGCAGCCATCAGCCACAATGAGAGTGTGGTGCAGGTCCTGCTTGCTGCTGAAGCTGACTCAAACCTTGGG
GATGGCTTCAGCAGTGTCTACAAAACTGCCAATGAACAGGGAGTCCATTCTTTGGAAGTCCTAGTCATTCAAGAGGATGA
CTTCAACAACCGATTAAACTACCTGGCTAGCTTCAAAAGCTGCACAGCCCTGCACTATGCTGTCCAGGCCCACAACTACA
GCATCGTCAAGGAGCTGCTGGATGGAGAAGCCAACCCCCTTCAGAGGAATATGATGGGACACACAACCCTGGATTATGCC
CAGGAAGAGGAGGTTATAAAACTTCTGAAAACTTCTGAGACCAAGTATATGGAGAAGCAGAGGAAGCGTGAGGCAGAGGA
GAGGCACCGCTTCCTACTGAGCAGCGACTGAAGGAGCACATCATTGACCAAGAGAGTGCCATCGCCACTATTAGTGCTGA
GATCCAGAGGAAGGAGAATGGCTGGTAGGATGAGGAGCACCCTCTAGTCGTCCTCTTCTTGGGATCATCTGGAATAGGGA
AAAGCGAGCTGGCCAAGCAGACAGCCAAGTATATGCACAAAGATGACAAGAAAGGGCTTCATCTTGCTCAACATATCTGA
GTTCCAGGAGTGACATGATGTAGCAAATTTATCGGCTCTTCAGTAGGCTATATCGGCCATGAAGAGGGTGGCCAGCTGAC
CAAGAAACTGAAACAGTGCCCAAATGCAGTAGTCCTGTTTGATGAGATAGACAAGGCCCATCCAGATGTGCTCACCATCA
TGCTGCAGCTGTTTGATGAGGGCTACCTGACAGATGGCAAAGGGAAGACCATTGACTGCAAGGATGCCATCTTCATCATG
ACTCCCATTGTAGCCAGTGCTGAGATTGCCCAGCATGCATTGCAGCTCAGACAGGAAGCTTTGGAGATGAGCCGAAATTG
AATCGCCGAAAACCTTAGGGATGTCCAGATTAGTGACAAGATCACTATCTTGAAGAACTTTAACGAGAATGTGATCTGAC
CCATCCTGAAAGTTCACTTCCAGAGAGATGAGTTTTTTGGGAGGGATCAAAGAGATCATCTACTTCTTCCCTTTCTGCCA
TTCAGAGCTCCTCCAGCTGGTCAACAAGGAACTTCAGGACCAAGAGAGCCAAACAGAGGCACATCAC

Alignment

ORF - retro_mmus_3255 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.04 %
• Parental protein coverage: 66.47 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  WALAMALVVQCYSKNPSNKDAALMEAARANNVQEVRRLLSEGADVNARHKLGWTALMVASISHNESVVQV
          W..A..LVVQCY.KNPSNKDAALMEAA.ANNVQEVRRLLSEGADVNAR.KLG.TALMVA.ISHNESVVQV
Retrocopy WVWAKVLVVQCY-KNPSNKDAALMEAALANNVQEVRRLLSEGADVNARYKLG*TALMVAAISHNESVVQV

Parental  LLAAGADPNLGDEFSSVYKTANEQGVHSLEVLVTREDDFNNRLNHRASFKGCTALHYAVLADDYSIVKEL
          LLAA.AD.NLGD.FSSVYKTANEQGVHSLEVLV..EDDFNNRLN..ASFK.CTALHYAV.A..YSIVKEL
Retrocopy LLAAEADSNLGDGFSSVYKTANEQGVHSLEVLVIQEDDFNNRLNYLASFKSCTALHYAVQAHNYSIVKEL

Parental  LDRGANPLQRNEMGHTPLDYAREGEVMKLLKTSETKYMEKQRKREAEERRRF-PLEQRLKEHIIGQESAI
          LD..ANPLQRN.MGHT.LDYA.E.EV.KLLKTSETKYMEKQRKREAEER.RF.P.EQRLKEHII.QESAI
Retrocopy LDGEANPLQRNMMGHTTLDYAQEEEVIKLLKTSETKYMEKQRKREAEERHRF<PTEQRLKEHIIDQESAI

Parental  ATVGAAIRRKENGWYDEEHPLVFLFLGSSGIGKTELAKQTAKYMHKDAK-KGFIRLDMSEFQERHEVA-K
          AT..A.I.RKENGW.DEEHPLV.LFLGSSGIGK.ELAKQTAKYMHKD.K.KGFI.L..SEFQE.H.VA.K
Retrocopy ATISAEIQRKENGW*DEEHPLVVLFLGSSGIGKSELAKQTAKYMHKDDK>KGFILLNISEFQE*HDVA<K

Parental  FIGSPPGYIGHEEGGQLTKKLKQCPNAVVLFDEVDKAHPDVLTIMLQLFDEGRLTDGKGKTIDCKDAIFI
          FIGS..GYIGHEEGGQLTKKLKQCPNAVVLFDE.DKAHPDVLTIMLQLFDEG.LTDGKGKTIDCKDAIFI
Retrocopy FIGSSVGYIGHEEGGQLTKKLKQCPNAVVLFDEIDKAHPDVLTIMLQLFDEGYLTDGKGKTIDCKDAIFI

Parental  MTSNVASDEIAQHALQLRQEALEMSRNRIAENLGDVQMSDKITISKNFKENVIRPILKAHFRRDEFLGR-
          MT..VAS.EIAQHALQLRQEALEMSRN.IAENL.DVQ.SDKITI.KNF.ENVI.PILK.HF.RDEF.GR.
Retrocopy MTPIVASAEIAQHALQLRQEALEMSRN*IAENLRDVQISDKITILKNFNENVI*PILKVHFQRDEFFGR>

Parental  INEIVYFLPFCHSELIQLVNKELNFWAKRAKQRH
          I.EI.YF.PFCHSEL.QLVNKEL..........H
Retrocopy IKEIIYFFPFCHSELLQLVNKELQDQESQTEAHH

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	39.46 RPM
SRP007412_cerebellum	0.00 RPM	38.47 RPM
SRP007412_heart	0.03 RPM	75.46 RPM
SRP007412_kidney	0.02 RPM	62.29 RPM
SRP007412_liver	0.00 RPM	39.71 RPM
SRP007412_testis	0.09 RPM	701.82 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3255 was not detected

EST

No EST(s) were mapped for retro_mmus_3255 retrocopy.

TSS

No TSS is located nearby retro_mmus_3255 retrocopy 5' end.

Lab

retro_mmus_3255 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3255 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015121	1 retrocopy	retro_cjac_1271,
Mus musculus	ENSMUSG00000001829	1 retrocopy	retro_mmus_3255 ,