RetrogeneDB ID:

retro_mmus_1562

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:17:30177607..30178788(+)
Located in intron of:ENSMUSG00000044477
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Tuba1b
Ensembl ID:ENSMUSG00000023004
Aliases:Tuba1b, Tuba2
Description:tubulin, alpha 1B [Source:MGI Symbol;Acc:MGI:107804]


Retrocopy-Parental alignment summary:






>retro_mmus_1562
GACAAGACCATTGGACGAAGAGAGGACTCCTTCATCACCTTCCTCAGTGAGACGGGCACTGGCAAGCATGTGCCTTGGGC
AGTTTTTGTTGCCCTGGAAGCCACAGTTATTGATGAAGTTCACACTAGTCTCTACCACCAGCTCTTCCACCCTAAGCAGC
TCATCACAGGCCAAGAGGATGCTGCCAGTAAATATGCCCGCGGCCACTACACCACTGCAAGGAGCTCATTGGCCTTGTCT
TGGACAGAATTTGCAAACTGGCTAATCATTGCATAGGTCTTTGGGGCTTCTTGGTTTCCTACAGCTTTGGCAAGGGAACT
GGCTCTGGAATGGAGAGGGTCTCTGTTGATTACCAAAAGAAATCCGAGCTGGAGCTCTCCATTAACCTGTCCCCTAGGTT
TCCACTGCTATGATTGAGCTCTACACCTCCATGCTCATCACCCACACCACCTTGGAGTTCTCTGATTGTGCCTTCATGAT
AGACAGTGAAGTCATCTATAACACGTCTAGAAACCTCAATACTGAGTGCCCGACTTAGACTAACCTTTATCGCATTATTA
GCCTGATTAGTGTCTTCCAACACTGCTTCCCTCAGCTTTGATGGAGCCCTGAATGTTGATCTGACAGAATTCCAGACCAG
CCTGGTGCTCTACCCTCACATCCACTTCCCTCTCGCCACTTATGCTCCTGTCATCTCTGCTGAGAAAGCCTACCAGGAGC
AGCTTTCTATAGAAAAGATTACTAGTGCCTGCTTTGAGCCAGCCAACCAGAAGGTGAAATGTGATTCTTGTCATGGTAAA
TACATGGCTTGCTGCCTATTGTACCACAGTGGTATGATTCCCAAAGATATCCATGCTGCTATTGCCACCACCAAGACCAG
GTGCAGCATCCAGCTTGTGGACTGGTACCCCACTGGCTTCAAGGTTGGCATTAATTACCAGCCTCACTGTGGTCCCTGGA
GCAACCTGGCCAAGGTCCAGAGAGCTGTGTGCATGCTGAGCAACACCACAGCCATTGCTGAGGCCTGGGCTCCTGTAGAC
CACAAGTTTGATCTGTTGCATGCCAAGCGTGCCTTTGTGCACTGGTGTGTGGGTGAGGACATGGCTGCCCTAGAGAAGGG
TTATGAGGAGGTTGGTATGGGTTCTGTTGAAGCTGAGGGTGAGGAGGAGGACAGGGATACT

ORF - retro_mmus_1562 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.56 %
Parental protein coverage: 88.91 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHY
DKTIG...DSF.TF.SETG.GKHVP.AVFV.LE.TVIDEV.T..Y.QLFHP.QLITG.EDAA..YARGHY
RetrocopyDKTIGRREDSFITFLSETGTGKHVPWAVFVALEATVIDEVHTSLYHQLFHPKQLITGQEDAASKYARGHY
ParentalTIG-KEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIY-PAPQ
T...KE.I.LVLDRI.KLA..C.GL.GFLV..S...G.G...T...MER.SVDY.KKS.LE.SI..P.P.
RetrocopyTTA<KELIGLVLDRICKLANHCIGLWGFLV--SYSFGKG---TGSGMERVSVDYQKKSELELSIN<PVP*
ParentalVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQI-VSSITASLRFD
VSTA..E.Y.S.L.THTTLE.SDCAFM.D.E.IY...R.NL..E.PT.TNL.R.IS.I.VSS.TASL.FD
RetrocopyVSTAMIELYTSMLITHTTLEFSDCAFMIDSEVIYNTSR-NLNTECPT*TNLYRIISLI>VSSNTASLSFD
ParentalGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMAC
GALNVDLTEFQT.LV.YP.IHFPLATYAPVISAEKAY.EQLS...IT.ACFEPANQ.VKCD..HGKYMAC
RetrocopyGALNVDLTEFQTSLVLYPHIHFPLATYAPVISAEKAYQEQLSIEKITSACFEPANQKVKCDSCHGKYMAC
ParentalCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIA
CLLY.....PKD..AAIAT.KT..SIQ.VDW.PTGFKVGINYQ.P...P...LAKVQRAVCMLSNTTAIA
RetrocopyCLLYHSGMIPKDIHAAIATTKTRCSIQLVDWYPTGFKVGINYQ-PHCGPWSNLAKVQRAVCMLSNTTAIA
ParentalEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDS
EAWA..DHKFDL..AKRAFVHW.VGE.M...E.......M...E...EE...D.
RetrocopyEAWAPVDHKFDLLHAKRAFVHWCVGEDMAALEKGYEEVGMGSVEAEGEEEDRDT

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain 0 .14 RPM 77 .45 RPM
SRP007412_cerebellum 0 .09 RPM 63 .92 RPM
SRP007412_heart 0 .03 RPM 36 .14 RPM
SRP007412_kidney 0 .10 RPM 16 .90 RPM
SRP007412_liver 0 .08 RPM 8 .82 RPM
SRP007412_testis 0 .46 RPM 8 .14 RPM
RNA Polymerase II actvity near the 5' end of retro_mmus_1562 was not detected
No EST(s) were mapped for retro_mmus_1562 retrocopy.
No TSS is located nearby retro_mmus_1562 retrocopy 5' end.
retro_mmus_1562 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_1562 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 14 parental genes, and 29 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000122441 retrocopy
Choloepus hoffmanni ENSCHOG000000084442 retrocopies
Callithrix jacchus ENSCJAG000000208742 retrocopies
Felis catus ENSFCAG000000286893 retrocopies
Homo sapiens ENSG000001234161 retrocopy
Macropus eugenii ENSMEUG000000107792 retrocopies
Macropus eugenii ENSMEUG000000111674 retrocopies
Monodelphis domestica ENSMODG000000152062 retrocopies
Mus musculus ENSMUSG00000023004 6 retrocopies
Mus musculus ENSMUSG000000430911 retrocopy
Mus musculus ENSMUSG000000673381 retrocopy
Otolemur garnettii ENSOGAG000000094351 retrocopy
Pan troglodytes ENSPTRG000000129501 retrocopy
Sus scrofa ENSSSCG000000001902 retrocopies



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