RetrogeneDB ID:

retro_dnov_1442

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_20541:6314..7725(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSDNOG00000011371
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TRIM24
Ensembl ID:ENSDNOG00000006533
Aliases:None
Description:tripartite motif containing 24 [Source:HGNC Symbol;Acc:11812]


Retrocopy-Parental alignment summary:






>retro_dnov_1442
ACTGCCAACAGCACATCCTCTACTCCTTCCAGTCCCACCATTACTAGTGCAGCAGGATATGATGGAAAGACTTTTGGTTC
ACCTATGATTGATTTGAGCTCACCAGTGGGGGGGTTCTTATAATCTTCCTTCTCTTCCAGATATTGATTGTTCAAGTACT
ATTATGCTGGACAATATTGTGAGGAAGGATACTAGCTTAGATCATGGCCAGTCAAGACCACCCTCAAACAGAACTGTCCA
GTCACCAAATTCATCAGTGCCATCTCCAGGCTTTGCAGGACCTGTGACTCTGACTAGTGTACATCCCCCAATACGTTCAC
CTAGTGCCTCCAGCGTTGGGAGCCGAGGAAGCTCTGGCTCTTCTAGCAAACCAACAGGGGCTGATTCTACACACAAAGTC
CCAGTGGTCATGTTGGAACCCATCCGAATAAAACAAGAAAACAGTGGACCACCAGAAAATTATGATTTTCCTGTTGTTAT
AGTGAAACAAGAATCAGATGAAGAATCTAGACCTCAAAATACGAATTATCCAAGAAGCATACTCACTTCCCTGCTCTTAA
ATAGCAATCAGGGCTCTACTTCTGAGGAGACTGTGTTAAGATCAGATGCTCCAGACAGCACAGGCGATCAACCTGGACTT
CACCAGGAAAATTCCTCAAATGGAAAGTCTGAGTGGCTAGATGCTTCCCAGAAGTCACCACTTCATGTTGGAGACACAAG
AAAAGAGGATGACCCCAATGAAGACTGGTGTGCAGTTTGTCAGAATGGAGGGGAACTCTTGTGCTGTGAAAAATGTCCCA
AAGTATTCCATCTTTCTTGTCATGTGCCCACATTGACAAATTTTCCAAGTGGAGAATGGATTTGCACTTTCTGCCGAGAC
TTATCTAAACCAGAAGTTGAATATGATTGTGATGCTCCCACTCACGACTCAGAAAAAAAGAAAACTGAAGGCCTTTTTAA
ATTAACACCAGTAGATAAAAGGTGTGAACGGCTACTTTTATTTCTTTATTGCCATGAAATGAGCCTGGCTTTTCAAGACC
CAGTTCCTCTAACTGTGCCTGATTATTACAAAATAATTAAAAATCCAATGGACTTGTCAACCATCAAGAAAAGACTACAA
GAAGATTATTCCATGTATACAAAGCCTGAAGACTTTGTAGCTGATTTTAGATTGATCTTTCAAAATTGTGCTGAATTCAA
TGAGCCTGATTCAGAAGTAGCCAATGCTGGTATAAAACTTGAAAACTATTTTGAAGAACTTCTAAAGAATCTTTATCTAG
AAAAAAGGTTTCCTAAACTAGAATTCAGGAATGAATCAGAAGATAATAAATTTAGTGACGATTCAGATGATGACTTTGTA
CAGCCCCCGAAGAAACGTGTCAAAAGCATTGAGGAACGCCAGCTGCTTAAA

ORF - retro_dnov_1442 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.86 %
Parental protein coverage: 51.77 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalTAPSTTSCPPILTITSMVRYD-KDFGSPMINLSSPVES-SYILSSLLDXXCSSTIMLDNIVRKDTSLDHG
TA.ST.S.P...TITS...YD.K.FGSPMI.LSSPV...SY.L.SL.D..CSSTIMLDNIVRKDTSLDHG
RetrocopyTANSTSSTPSSPTITSAAGYDGKTFGSPMIDLSSPVGG>SYNLPSLPDIDCSSTIMLDNIVRKDTSLDHG
ParentalQPRPPSNRTVQSPNSSVPSPGLAGPVTLTSVHPPIRSPSASSVGSRGSSGSSSKPTGADSTHKVPVVMLE
Q.RPPSNRTVQSPNSSVPSPG.AGPVTLTSVHPPIRSPSASSVGSRGSSGSSSKPTGADSTHKVPVVMLE
RetrocopyQSRPPSNRTVQSPNSSVPSPGFAGPVTLTSVHPPIRSPSASSVGSRGSSGSSSKPTGADSTHKVPVVMLE
ParentalPIRIKQENSGPPENYDFPVVIVKQESDEESRPQNTNYPRSILTSLLLNSNQGSTSEETVLRSDAPDSTGD
PIRIKQENSGPPENYDFPVVIVKQESDEESRPQNTNYPRSILTSLLLNSNQGSTSEETVLRSDAPDSTGD
RetrocopyPIRIKQENSGPPENYDFPVVIVKQESDEESRPQNTNYPRSILTSLLLNSNQGSTSEETVLRSDAPDSTGD
ParentalQPGLHQENSSNGKSEWLDASQKSPLHVGETRKEDDPNEDWCAVCQNGGELLCCEKCPKVFHLSCHVPTLT
QPGLHQENSSNGKSEWLDASQKSPLHVG.TRKEDDPNEDWCAVCQNGGELLCCEKCPKVFHLSCHVPTLT
RetrocopyQPGLHQENSSNGKSEWLDASQKSPLHVGDTRKEDDPNEDWCAVCQNGGELLCCEKCPKVFHLSCHVPTLT
ParentalNFPSGEWICTFCRDLSKPEVEYDCDAPTHNSEKKKTEGLFKLTPIDKRKCERLLLF-YCHEMSLAFQDPV
NFPSGEWICTFCRDLSKPEVEYDCDAPTH.SEKKKTEGLFKLTP.DKR.CERLLLF.YCHEMSLAFQDPV
RetrocopyNFPSGEWICTFCRDLSKPEVEYDCDAPTHDSEKKKTEGLFKLTPVDKR-CERLLLFLYCHEMSLAFQDPV
ParentalPLTVPDYYKIIKNPMDLSTIKKRLQEDYSMYTKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFE
PLTVPDYYKIIKNPMDLSTIKKRLQEDYSMYTKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFE
RetrocopyPLTVPDYYKIIKNPMDLSTIKKRLQEDYSMYTKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFE
ParentalELLKNLYPEKRFPKLEFRNESEDNKFSDDSDDDFVQPRKKRVKSIEERQLLK
ELLKNLY.EKRFPKLEFRNESEDNKFSDDSDDDFVQP.KKRVKSIEERQLLK
RetrocopyELLKNLYLEKRFPKLEFRNESEDNKFSDDSDDDFVQPPKKRVKSIEERQLLK

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






RNA-Seq - click to see more details

(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 4 .08 RPM 10 .31 RPM
SRP012922_cerebellum 1 .65 RPM 4 .54 RPM
SRP012922_heart 5 .10 RPM 15 .55 RPM
SRP012922_kidney 2 .19 RPM 7 .94 RPM
SRP012922_liver 3 .10 RPM 6 .81 RPM
SRP012922_lung 5 .19 RPM 15 .12 RPM
SRP012922_quadricep_muscle 3 .46 RPM 9 .87 RPM
SRP012922_spleen 10 .30 RPM 16 .71 RPM

ChIP-Seq - click to see more details

Dasypus novemcinctus was not studied using ChIP-Seq data.

EST - click to see more details

Dasypus novemcinctus was not studied using EST data.

TSS - click to see more details

Dasypus novemcinctus was not studied using FANTOM5 data.

Lab - click to see more details

retro_dnov_1442 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 2 parental genes, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000128851 retrocopy
retro_cjac_3923,
Dasypus novemcinctus ENSDNOG00000006533 1 retrocopy
retro_dnov_1442 ,


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