RetrogeneDB ID:

retro_dnov_43

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_74747:5903..7250(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSDNOG00000016491
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:TUBA1A
Ensembl ID:ENSDNOG00000004121
Aliases:None
Description:tubulin, alpha 1a [Source:HGNC Symbol;Acc:20766]


Retrocopy-Parental alignment summary:






>retro_dnov_43
CGTGAGTGCATCTCCATCCACGTCGGCCAGGCTGGTGTCCAGATTGGCAATGCCTGCTGGGAGCTCTACTGCCTGGAACA
CGGCATCCAGCCCGATGGCCAGATGCCAAGTGACAAGACCATTGGGGGAGGAGATGACTCCTTCAACACCTTCTTCAGTG
AGACTGGCGCTGGCAAGCATGTGCCCAGGGCAGTGTTTGTAGACCTGGAACCCACAGTCATTGATGAAGTTCGCACTGGC
ACCTACCGCCAGCTCTTCCACCCTGAGCAGCTCATCACAGGCAAGGAAGATGCTGCCAATAACTATGCCCGTGGGCATTA
CACCATCGGCAAGGAGATCATCGACCTGGTTCTGGACAGAATTCGCAAACTGGCCGACCAGTGCACAGGGCTTCAGGGCT
TCTTGGTTTTCCACAGCTTTGGTGGGGGAACGGGTTCCGGGTTCACCTCCCTGCTGATGGAACGCCTTTCTGTTGATTAC
GGCAAGAAGTCCAAGCTGGAGTTCTCCATTTACCCAGCCCCCCAGGTCTCCACAGCTGTGGTCGAGCCCTACAACTCCAT
CCTCACCACCCACACCACCCTGGAGCACTCAGATTGTGCCTTCATGGTAGACAATGAGGCCATCTATGACATCTGTCGCA
GAAATCTTGATATTGAGCGCCCAACCTACACCAACCTTAACCACCTTATTAGCCAGATTGTGTCCTCCATCACAGCCTCC
CTCAGGTTTGATGGTGCCCTGAATGTAGATCTGACAGAATTCCAGACCAACCTGGTGCCCTATCCCCGCATCCACTTTCC
TCTGGCCACATCCGCCCCTGTCATCTCTGCTGAGAAAGCCTACCATGAGCAGCTTTCTGTAGCAGAGATTACCAATGCTT
GCTTTGAGCCGGCCAACCAGATGGTGAAATGCGACCCTAACCACGGTAAATACATGGCCTGCTGCCTGTTGTACCGGGGC
GACGTGGTTCCCAAAGACGTCAATGCTGCCATTGCCACCATCAAGACCAAGCGCACCATCCAGTTTGTGGACTGGTGTCC
CACTGGCTTCAAGGTCAGCATTAATTACCAGCCTCCCACTGTGGTTCCTGGTGGCGACCTGGCCAAGGTCCAGCGAGCTG
TGTGCATGCTGAGCAACACCACAGCCGTGGCCGAGGCCTGGGCTCGCCTGGACCACAAGTTTGACCTGATGTACGCCAAG
CGTGCCTTTGTCCACTGGTACGTGGGGGAGGGAATGGAGGAAGGAGAGTTCTCTGAGGCCCGTGAGGACATGGCTGCCCT
CGAGAAGGATTATGAGGAGGTTGGGGCAGATAGTGGCGAGGGAGAGAATGAGGGTGAGGAGTATTAG

ORF - retro_dnov_43 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94. %
Parental protein coverage: 99.56 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLE
RECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLE
RetrocopyRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLE
ParentalPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSF
PTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSF
RetrocopyPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSF
ParentalGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYD
GGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYD
RetrocopyGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYD
ParentalICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVDQTEFPTKLVPYPHIHFPLATYAPIISVEKA
ICRRNLDIERPTYTNLN.LI.QIVSSITASLRFDGALNVD.TEF.T.LVPYP.IHFPLAT.AP.IS.EKA
RetrocopyICRRNLDIERPTYTNLNHLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATSAPVISAEKA
ParentalYHEQLSVAEITSVCFELANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGF
YHEQLSVAEIT..CFE.ANQMVKCDP.HGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGF
RetrocopyYHEQLSVAEITNACFEPANQMVKCDPNHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGF
ParentalKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKHAFVHCYMREGMEEGEFSEA
KV.INYQPPTVVPGGDLAKVQRAVCMLSNTTA.AEAWARLDHKFDLMYAK.AFVH.Y..EGMEEGEFSEA
RetrocopyKVSINYQPPTVVPGGDLAKVQRAVCMLSNTTAVAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEA
ParentalHENMAALKKDYEEVGVDSVEGEGEEEGEDY
.E.MAAL.KDYEEVG.DS..GEGE.EGE.Y
RetrocopyREDMAALEKDYEEVGADS--GEGENEGEEY

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
SRP012922_ascending_colon 11 .67 RPM 26 .64 RPM
SRP012922_cerebellum 19 .52 RPM 155 .89 RPM
SRP012922_heart 4 .41 RPM 18 .56 RPM
SRP012922_kidney 9 .86 RPM 14 .51 RPM
SRP012922_liver 2 .94 RPM 6 .50 RPM
SRP012922_lung 7 .18 RPM 53 .00 RPM
SRP012922_quadricep_muscle 3 .63 RPM 11 .94 RPM
SRP012922_spleen 12 .71 RPM 47 .27 RPM
Dasypus novemcinctus was not studied using ChIP-Seq data.
Dasypus novemcinctus was not studied using EST data.
Dasypus novemcinctus was not studied using FANTOM5 data.
retro_dnov_43 was not experimentally validated.

Retrocopy orthology:
Dasypus novemcinctus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

Parental genes homology:
Parental genes homology involve 10 parental genes, and 20 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000014893 retrocopies
Callithrix jacchus ENSCJAG000000208942 retrocopies
Dasypus novemcinctus ENSDNOG00000004121 1 retrocopy
retro_dnov_43 ,
Equus caballus ENSECAG000000137981 retrocopy
Homo sapiens ENSG000001675521 retrocopy
Nomascus leucogenys ENSNLEG000000178362 retrocopies
Oryctolagus cuniculus ENSOCUG000000278121 retrocopy
Pteropus vampyrus ENSPVAG000000046452 retrocopies
Rattus norvegicus ENSRNOG000000045593 retrocopies
Vicugna pacos ENSVPAG000000057494 retrocopies



Copyright © RetrogeneDB 2014-2017