RetrogeneDB ID:

retro_dnov_174

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:GeneScaffold_2332:17940..18954(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ZSCAN4
Ensembl ID:ENSDNOG00000011483
Aliases:None
Description:zinc finger and SCAN domain containing 4 [Source:HGNC Symbol;Acc:23709]


Retrocopy-Parental alignment summary:






>retro_dnov_174
ATGGCTTTAGATGTTAGAACCTCCTTTTGCCATGACCCATCCAGGAGTGATCATCCTGGGTCAGACAATCTAGAGTTTGA
ATCCCCCCAAGGACCTGATGTCCAGAGGAGAGAGGGTAACTCTAATTTCCAGGACCCTCAACTCAGCTTATATCAAACTA
ACAATGACTTATTTGCAAAGCAGGAACTAAAAAGACTCCGTAAGTTATTTCACTTGTGGCTGCATCCAGAAAAACACAGC
AAAGAAGAAATTATTTTTCAATTGGTCCTGAAACAGCTTATGATGAATGGATACTGCAGGAACAAGTCCACTTTGAGAGA
GAAATGGGATTCAAGTAGAAGAAACCTGGAGAAACTCATGGAAGAGCTGACTGATGAATGCGTGAAGTCACCTGGTTTTG
TCCATGCCCTCATGCAGGGACAGGAAGCCCTCTTCTCTGAGAATATACCTTAAGAGAAGTCATTCATCTCCTGAAACAAC
TGCCAGCAGGAATCCCAAGAGGCGAGAGCATGAGGACACCCTTCCAAGGTTCCCAAGGTATTATTCTCCTTCAAACAGGA
CATGGAGATGAACAGAAAGACAGCAGGAACATGTCTATGAAAAGCAATCAAGTAAATGACAGTATTACTAGTTGAGGGAA
GAAAGTATCTTCCCTGGTTTTTATTCAGGAAGATGATAGCCCTAAGCCGGAAGAGGGGAATAGTTCTTGGGAGAACCTTT
GCAACTCTAGAAGAGCAGAGCTTGACTCCTCCACATCCAGGAAGGATCCCTAGAAGAATCCTCTTCTCAAGATATCCCTA
TGGAAGTAGAACCACATTTTTTCCCAGGACAGATCAAGCCAAGCATAAGCCTACCAACTAAAGCATTGATGGAACATCCA
GATGTGGGATAAACGAAGAAAGAGTCCATAGTCCCCCAAAATCATACAGGTGTGAGAACTGTCCCAGGATCTTTAGGTAT
CTCTCTCAGCGAGATGCCCACCAGAGAAGACACAGGAGTGAGAGACCATTTGTT

ORF - retro_dnov_174 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.71 %
Parental protein coverage: 78.52 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMALDLRTSFRHDPSRSGHPGSHNLELEPTQGCDLQRREGNSKFQGPQLSLYQTSNGSFAKQELKRLRKVF
MALD.RTSF.HDPSRS.HPGS.NLE.E..QG.D.QRREGNS.FQ.PQLSLYQT.N..FAKQELKRLRK.F
RetrocopyMALDVRTSFCHDPSRSDHPGSDNLEFESPQGPDVQRREGNSNFQDPQLSLYQTNNDLFAKQELKRLRKLF
ParentalHLWLQPEKHSKEEIISQLILEQLVMNGYCRNRSILKEKWDSSGRNLEKLVGELNDDCMKSPDFVHVHMQG
HLWL.PEKHSKEEII.QL.L.QL.MNGYCRN.S.L.EKWDSS.RNLEKL..EL.D.C.KSP.FVH..MQG
RetrocopyHLWLHPEKHSKEEIIFQLVLKQLMMNGYCRNKSTLREKWDSSRRNLEKLMEELTDECVKSPGFVHALMQG
ParentalQEALFSENMP-LREVIYLMEQMPAGTPRGESMRTPFQGPQN-IPLQTGHGDEYKDDSNIFVKRNQINVNI
QEALFSEN.P.LREVI.L..Q.PAG.PRGESMRTPFQG.Q..I.LQTGHGDE.KD..N...K.NQ.N..I
RetrocopyQEALFSENIP<LREVIHLLKQLPAGIPRGESMRTPFQGSQGIILLQTGHGDEQKDSRNMSMKSNQVNDSI
ParentalTSQGNQVPYVVIIQEDDSPKPEEGSGSWKNLHNFRRAELGSPTS-QEGSLGESSSQDVPMEVE-TQFLPR
TS.G..V...V.IQEDDSPKPEEG..SW.NL.N.RRAEL.S.TS.QEGSL.ESSSQD.PMEVE.T.F.PR
RetrocopyTS*GKKVSSLVFIQEDDSPKPEEGNSSWENLCNSRRAELDSSTS<QEGSLEESSSQDIPMEVE<TTFFPR
ParentalTDQASPKPALTNQSSDGTSRCGINQERVHSPPKSYKCEDCPRIFRFPSQLEAHQRRHRNERPFV
TDQA..KP..TN.S.DGTSRCGIN.ERVHSPPKSY.CE.CPRIFR..SQ..AHQRRHR.ERPFV
RetrocopyTDQAKHKP--TN*SIDGTSRCGINEERVHSPPKSYRCENCPRIFRYLSQRDAHQRRHRSERPFV

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 0 .00 RPM 0 .00 RPM
SRP012922_cerebellum 0 .00 RPM 0 .14 RPM
SRP012922_heart 0 .00 RPM 0 .00 RPM
SRP012922_kidney 0 .00 RPM 0 .00 RPM
SRP012922_liver 0 .00 RPM 0 .00 RPM
SRP012922_lung 0 .00 RPM 0 .00 RPM
SRP012922_quadricep_muscle 0 .00 RPM 0 .00 RPM
SRP012922_spleen 0 .00 RPM 0 .00 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_174 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 5 parental genes, and 16 retrocopies.

Species Parental gene accession Retrocopies number
Cavia porcellus ENSCPOG000000054192 retrocopies
Dasypus novemcinctus ENSDNOG00000011483 11 retrocopies
Equus caballus ENSECAG000000152001 retrocopy
Loxodonta africana ENSLAFG000000032571 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000237791 retrocopy



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