RetrogeneDB ID: retro_mmus_1109

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 13:62967407..62968578(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tubb1
• Ensembl ID: ENSMUSG00000016255
• Aliases: None
• Description: tubulin, beta 1 class VI [Source:MGI Symbol;Acc:MGI:107814]

Sequence

>retro_mmus_1109
ATCGACCCCACTGGCAGTTACCATGGCGACAGTGACTTGCAGCTGGAGAGAATCAATGTGTACTACAATGAAGCTGCTGG
CAACAAATATGTACCTTGGGCCATCCTAGTGGACCTGGAGCCTGGCACCATGGACTCCGTGAGGTCGGGACCATTCGGCC
AGATCTTCAGGTCAGACAACTTTGTGCTCGGCCAGAGTGATGCAGGAAATAACTGGGCAAAGGGCCACTACAGAAAGGGG
GCCGAGCTAGTGGACTCTGTCCTGGACGTGGTGAGGAAGGAATCAGAAAGCTGTGACTGTCTCCAGGGCTTCCAGCTGAC
CCACTTACTGGGGGGAGGCACTGGCTCAGGCATGGGGACCCTGCTCATCAGCAAGATCAGAGAGGAGTACCCAGACCGCA
TCATGAAGACCTTCAGCGTCATGCCCTCACCCAAGGTCTCTGACACTGTGGTGGAGCCCTATAATGTCACCCTCTGAGTG
CACCAGCTGGTAGAGAACACAGATGAAACCTAGTCTATCGACAATTAGGCTCTGTAGGACATCTGCTTCCGCACCCTGAA
GCTGACCACACCCACCTATGGCGATCTCAACCACCTGGTGTCAGCCACCATGAGTGAAGTGACCACCTGCCTGCGCTTCC
CAGGCCAGCTGAACGCAGACCTGCACAAGCTGGCTGTGAACATGGTGCCATTCCCACGCCTGCACTTCTTCATGCCAGGC
TTTGCACCTCTGACCAGCCAGGGCAGCCAACAGTACCGAGCCCTGACAGTGCCCGAGCTGACCCAGCCTATGTTCAACTC
CAAGAACATGATGGCTGTCTGCGACCCTCGCCATGGCCGCTACCTGACCATGGCCATTTTCCGTGGCCGCATGTCCATGA
AGGAGGTGGATGAGCAGATGCTCAACGTGCAGAACAAGAACGAACAGCAGCTACTTCGTGGAGTGGATCCCCAACAATGT
CAAGACGGCCGTGTGTGACATCCCTCCTCGTGGCCTCAAGATGTCAGCCACCTTCATTGGCAATAGCATTGCTATCCAGG
AGCTGTTCAAGCGCATCTCTGAGCAGTTCACTGCCATGTTCCAGCGCAAGGCTTTCCTGCACTGATACACGGGCGAGGGC
ATGGACGAGATGGAGTTCACCGAGGCGGAGAGCAACATGAACGACCTGGTA

Alignment

ORF - retro_mmus_1109 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.26 %
• Parental protein coverage: 86.47 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IDCAGSYCGTSALQLERISVYYNEAYGKKYVPRAVLVDLEPGTMDSIRSSRLGVLFQPDSFVHGNSGAGN
          ID..GSY.G.S.LQLERI.VYYNEA.G.KYVP.A.LVDLEPGTMDS.RS...G..F..D.FV.G.S.AGN
Retrocopy IDPTGSYHGDSDLQLERINVYYNEAAGNKYVPWAILVDLEPGTMDSVRSGPFGQIFRSDNFVLGQSDAGN

Parental  NWAKGHYTEGAELIENVMDVVRRESESCDCLQGFQIVHSLGGGTGSGMGTLLMNKIREEYPDRILNSFSV
          NWAKGHY..GAEL...V.DVVR.ESESCDCLQGFQ..H.LGGGTGSGMGTLL..KIREEYPDRI...FSV
Retrocopy NWAKGHYRKGAELVDSVLDVVRKESESCDCLQGFQLTHLLGGGTGSGMGTLLISKIREEYPDRIMKTFSV

Parental  MPSPKVSDTVVEPYNAVLSIHQLIENTDACFCIDNEALYDICFRTLRLTTPTYGDLNHLVSLTMSGITTS
          MPSPKVSDTVVEPYN..L..HQL.ENTD....IDN.AL.DICFRTL.LTTPTYGDLNHLVS.TMS..TT.
Retrocopy MPSPKVSDTVVEPYNVTL*VHQLVENTDET*SIDN*AL*DICFRTLKLTTPTYGDLNHLVSATMSEVTTC

Parental  LRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTAQGSQQYRALSVAELTQQMFDARNIMAACDPRRGR
          LRFPGQLNADL.KLAVNMVPFPRLHFFMPGFAPLT.QGSQQYRAL.V.ELTQ.MF...N.MA.CDPR.GR
Retrocopy LRFPGQLNADLHKLAVNMVPFPRLHFFMPGFAPLTSQGSQQYRALTVPELTQPMFNSKNMMAVCDPRHGR

Parental  YLTVACIFRGKMSTKEVDQQLLSIQ-TR-NSNCFVEWIPNNVKVAVCDIPPRGLNMAATFLGNNTAIQEL
          YLT.A.IFRG.MS.KEVD.Q.L..Q.TR.NS..FVEWIPNNVK.AVCDIPPRGL.M.ATF.GN..AIQEL
Retrocopy YLTMA-IFRGRMSMKEVDEQMLNVQ>TRTNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSIAIQEL

Parental  FTRVSEHFSAMFRRRAFVHWYTSEGMDISEFGEAESDIHDLV
          F.R.SE.F.AMF.R.AF.H.YT.EGMD..EF.EAES...DLV
Retrocopy FKRISEQFTAMFQRKAFLH*YTGEGMDEMEFTEAESNMNDLV

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	0.14 RPM	0.00 RPM
SRP007412_cerebellum	0.04 RPM	0.09 RPM
SRP007412_heart	0.03 RPM	6.10 RPM
SRP007412_kidney	0.04 RPM	0.33 RPM
SRP007412_liver	0.03 RPM	0.38 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1109 was not detected

EST

No EST(s) were mapped for retro_mmus_1109 retrocopy.

TSS

No TSS is located nearby retro_mmus_1109 retrocopy 5' end.

Lab

retro_mmus_1109 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1109 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010101	1 retrocopy	retro_cjac_800,
Callithrix jacchus	ENSCJAG00000011697	1 retrocopy	retro_cjac_3284,
Dipodomys ordii	ENSDORG00000015889	1 retrocopy	retro_dord_254,
Homo sapiens	ENSG00000173213	1 retrocopy	retro_hsap_3733,
Homo sapiens	ENSG00000173876	1 retrocopy	retro_hsap_3944,
Mus musculus	ENSMUSG00000016255	1 retrocopy	retro_mmus_1109 ,
Mus musculus	ENSMUSG00000036752	2 retrocopies	retro_mmus_158, retro_mmus_422,
Pongo abelii	ENSPPYG00000011180	1 retrocopy	retro_pabe_3250,