RetrogeneDB ID:

retro_cfam_960

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:20:31992315..31993653(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TUBA1C
Ensembl ID:ENSCAFG00000008661
Aliases:None
Description:tubulin, alpha 1c [Source:HGNC Symbol;Acc:20768]


Retrocopy-Parental alignment summary:






>retro_cfam_960
GAGTGTATCTCCATCCACATTAGACAGGTTGGTGTCTAGATCAGCAATGCCTGCTGGGAGCTCTGTTGCCTAGAACATGG
CATTCAGCCCAATGGCCAGATGCCAAGTGACAAAACCATTGGGGGAGGAGATGACTCCTTCAACACCTTCTTCAGTGAGA
CAGGGGCTGGCAAGCATGTGCCCAGGGAAGGGTTTGTAGACCTGGAACCCACGGTCATTGATGAAGTTTGCACTGGCACC
TACTCAGGCTCTTCCACCCTGAGTAGCTCATCACAAGCAAGGAAGATACTGCCAATAACTATGCCCAAGGGCATTACACC
ATTGACAAGATCATTGATCTTGTCTTGGGCCAAATTAGGAAGCTTGGTTGACCAGCACTTGGTTCTTCAAGGCTTTTTGG
TTTTCCACAGCTTTTGGAGTGGGAACTGGTCCCAGGCTTAACACCCTGCTGATGGAACATCTCTCTGTCAAACATGGCAA
GAAGTCCAAGCTGGAGTTCTCCATTTAGCCAGGCCCCCAGATTTCTATAGCTGGATTCGAGCCCTACAACTCCATCCTCA
CTACCCACACACCCTGGAGCACTCTGACTGTGCCTTCACAATAGACAACAAGGCTATCCATGACATCTGTCATAGAAACG
TCACTATTGAACACCCAACCTGCACCAACCTTAACTACCTTATTAGCCAGACTGTGTTTTCCATCACTGCTTCCCTCAGA
TTTGACGGAGCCCTGAATATTGCTCTGATGGAATTCCACATGAAACTGGTGCCCTATCCCTGCATCCACTTTCCTCTGGC
CACATATGCCCCTGTCATCTCTGCTGAGAAAGCCTACCATGAACAGCTTACTGTAGCAGAGATCACCAATGCGTGCTTTG
AACCAGCCAACCAGATGGTGAAGTGTGACCCTTGTCATGGTAAATATATGGCCTGCTGCCTGTTGTACCATGGCAACATG
GTTCCCAAAGATGTCGATGCTGCCATTGTCACCATCAAGACCAAGTGTACCATCCAGTTTGTGGACTGGTGTCCCACTGG
CTTAAAAGTGGGCATTAATTGCCAGTCTTCCACTGTGGTACCTGGTGAAGACCTGGCCAAAGTACAGAGAGTTGTGTGCA
TGCTGAGCAACACCACAGCCATTGCTGAGGCCTGGGATTGCCTGGACCACAAGTTTGACCTAATGTGTGCCGAGCATGCC
TTTGTTCACTAGTATGTGGATAACAGCATGGAGGAAGGAGAGTTTTCTGAGGCCTGTGAGGACACAGCTGCCTTAGAGAA
GGATTATGAAGAGTTTGGATCAGATAGTGCTGAGGGAGAGGATGAGGGTAAAGAGTAT

ORF - retro_cfam_960 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.04 %
Parental protein coverage: 87.48 %
Number of stop codons detected: 4
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEP
ECISIH..Q.GV.I.NACWEL.CLEHGIQP.GQMPSDKTIGGGDDSFNTFFSETGAGKHVPR..FVDLEP
RetrocopyECISIHIRQVGV*ISNACWELCCLEHGIQPNGQMPSDKTIGGGDDSFNTFFSETGAGKHVPREGFVDLEP
ParentalTVIDEVRTGTYR-QLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLA-DQCTGLQGFLVFHS
TVIDEV.TGTY...LFHPE.LIT.KED.ANNYA.GHYTI.K.IIDLVL..IRKL..DQ...LQGFLVFHS
RetrocopyTVIDEVCTGTYS<RLFHPE*LITSKEDTANNYAQGHYTIDK-IIDLVLGQIRKLG>DQHLVLQGFLVFHS
ParentalF-GGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHT-TLEHSDCAFMVDNEA
F.G.GTG.....LLME.LSV..GKKSKLEFSI.P.PQ.S.A..EPYNSILTTHT.TLEHSDCAF..DN.A
RetrocopyF>GVGTGPRLNTLLMEHLSVKHGKKSKLEFSI*PGPQISIAGFEPYNSILTTHT<TLEHSDCAFTIDNKA
ParentalIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISA
I.DIC.RN..IE.PT.TNLN.LISQ.V.SITASLRFDGALN..L.EF...LVPYP.IHFPLATYAPVISA
RetrocopyIHDICHRNVTIEHPTCTNLNYLISQTVFSITASLRFDGALNIALMEFHMKLVPYPCIHFPLATYAPVISA
ParentalEKAYHEQLTVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCP
EKAYHEQLTVAEITNACFEPANQMVKCDP.HGKYMACCLLY.G..VPKDV.AAI.TIKTK..IQFVDWCP
RetrocopyEKAYHEQLTVAEITNACFEPANQMVKCDPCHGKYMACCLLYHGNMVPKDVDAAIVTIKTKCTIQFVDWCP
ParentalTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEF
TG.KVGIN.Q..TVVPG.DLAKVQR.VCMLSNTTAIAEAW..LDHKFDLM.A..AFVH.YV...MEEGEF
RetrocopyTGLKVGINCQSSTVVPGEDLAKVQRVVCMLSNTTAIAEAWDCLDHKFDLMCAEHAFVH*YVDNSMEEGEF
ParentalSEAREDMAALEKDYEEVGADSAEGEDEGEEY
SEA.ED.AALEKDYEE.G.DSAEGEDEG.EY
RetrocopySEACEDTAALEKDYEEFGSDSAEGEDEGKEY

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
SRP012049_cerebellum 0 .00 RPM 45 .95 RPM
SRP017611_brain 0 .00 RPM 6 .27 RPM
SRP017611_kidney 0 .00 RPM 120 .19 RPM
SRP017611_liver 0 .00 RPM 19 .00 RPM
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_960 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_960 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_960 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 12 parental genes, and 24 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000399921 retrocopy
Canis familiaris ENSCAFG000000052481 retrocopy
Canis familiaris ENSCAFG000000086408 retrocopies
Canis familiaris ENSCAFG00000008661 2 retrocopies
retro_cfam_960 , retro_cfam_978,
Canis familiaris ENSCAFG000000104121 retrocopy
Choloepus hoffmanni ENSCHOG000000084442 retrocopies
Erinaceus europaeus ENSEEUG000000040681 retrocopy
Felis catus ENSFCAG000000248521 retrocopy
Felis catus ENSFCAG000000286893 retrocopies
Macropus eugenii ENSMEUG000000107792 retrocopies
Oryctolagus cuniculus ENSOCUG000000280321 retrocopy
Otolemur garnettii ENSOGAG000000094351 retrocopy



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