RetrogeneDB ID:

retro_dnov_932

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_12312:49134..50318(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PLEKHM3
Ensembl ID:ENSDNOG00000004208
Aliases:None
Description:pleckstrin homology domain containing, family M, member 3 [Source:HGNC Symbol;Acc:34006]


Retrocopy-Parental alignment summary:






>retro_dnov_932
TCTTTTCATGTCTCTCACTTCACTAGACCATCTTTTCTGTCACCATCATCAAATAATGTAGAAGATGCTCAAGGAAATAC
TGAACACAAGCAGACATTCCCAAACATTCTGAAGAAGGGTTACCTGGAGTTTAGGAAGGACCATGATAGTTATTGGCAAA
GCTGTTATGCAGAACTATCACCCTACAACTTAAACTACTTTAATCTCTACAGCAGGGCAAATCAAAACCTCTGTGCCACA
TATCAACTTTCACACTTTCAGACCATACCTGTTTTGGGCAACCTTGAGGCCAGAATAGTGGATACCATCTTGTATGAAAA
CATTCAGCTACAGCTCAAGGCAGAGTCACCATGGGAGGCTTTGGACTGGGGCTAGAAGCTTTGGGAAGGTGTGCATACTG
CTGTGCTTGGTTACATGGGACAGGAGGATAAGCTGGCAAACTCACCAGACCTTGGTCCTAATGCTGACCGTACACAGAAT
CATTGTTTACAGAAGAAATCCAGAGGGTTGCTGCCATCATCGCCTGCCTCAGATAGCCCCAAACAGTACCAAAACATCCT
CAAATCAGGGACGCTCTGCAGGCTAACTGTCCAAAACAACTGGAAGGCATTTATGTTTGTGCTGAGCACAGCCTGCCTTA
CGGATTTTCAGCCTGGCAAGCTAGACGAGGGTCTCCTGCTGAGCTACAATGTGGATGTGTGTCTGGCTGTCCAGATAGAC
AACCTGGATGATTGTGACTCTTTCAAGTCATTTTTCCACAAGATATCCTCTATCTCCATGCTGAGACCTGACAAAGAGCT
CAGGAATGGATGGAGGCTCTGAAAAGAAGCTACCAACACTGCAAGGAGTTCAGAGCAAAATCTGCAAGTGACACTGAGGA
ACAAATCCAAGGATCAGATTGGTGGGCACAAACTCAGGAAGAACAAACATCAGTCCATGACCACCAGCTTCCTGAGCATT
CTGACAACTTTGTCTCTAGAATGAAGACTTACTGCTCAGAGTTTCAAATGTGAAGGAAGCCAGTGATGCACAGGTCTTTC
CAATGAGAAAGCCAAGGTGTGTGATTACAGTGGGTGCTATTACTGAAGCGGCTGCCATGTGGACGACAGTTTTCTTATCC
CAGCATACATTGTCCACAACTGGGACACTTCTAAATATAAGTGTCTAAGCAGGCCAAAGAGTTT

ORF - retro_dnov_932 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.21 %
Parental protein coverage: 52.04 %
Number of stop codons detected: 5
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalSLHGPHFTRPSFLLPSSNKVEDAQGNTENKQTFPNILKKGYLEIRKDHDSYWQSCYAELSPYNLNFFNLD
S.H..HFTRPSFL.PSSN.VEDAQGNTE.KQTFPNILKKGYLE.RKDHDSYWQSCYAELSPYNLN.FNL.
RetrocopySFHVSHFTRPSFLSPSSNNVEDAQGNTEHKQTFPNILKKGYLEFRKDHDSYWQSCYAELSPYNLNYFNLY
ParentalSSANQNLCATYQLTHFQSISVLGNLEARIVDTVLYDNTQLQLKAESPWEALDWGQKLWEVVHMAVPGYMG
S.ANQNLCATYQL.HFQ.I.VLGNLEARIVDT.LY.N.QLQLKAESPWEALDWG.KLWE.VH.AV.GYMG
RetrocopySRANQNLCATYQLSHFQTIPVLGNLEARIVDTILYENIQLQLKAESPWEALDWG*KLWEGVHTAVLGYMG
ParentalRQDKLANSSDLGLNADCTQNHCLQKKSRGLLPSSPVLDSPKQYQNILKSGTLYRLTVQNNWKAFTFVLSR
..DKLANS.DLG.NAD.TQNHCLQKKSRGLLPSSP..DSPKQYQNILKSGTL.RLTVQNNWKAF.FVLS.
RetrocopyQEDKLANSPDLGPNADRTQNHCLQKKSRGLLPSSPASDSPKQYQNILKSGTLCRLTVQNNWKAFMFVLST
ParentalACLMAFQPGKLDEDPLLSYNVDVCLAVQIDNLDDCDSCFQVIF-PQDILRLRAETRQRAQEWMEAL-KTA
ACL..FQPGKLDE..LLSYNVDVCLAVQIDNLDDCDS.F...F.PQDIL.L.AET.QRAQEWMEAL.K.A
RetrocopyACLTDFQPGKLDEGLLLSYNVDVCLAVQIDNLDDCDS-FKSFF<PQDILYLHAET*QRAQEWMEAL>KEA
ParentalANTARSSEQNLQVTLRNKSKDQMGAHELRKNKRQSVTTSFLSILTTLSLERGLTAQSFKCAGCQRCIGLS
.NTARSSEQNLQVTLRNKSKDQ.G.H.LRKNK.QS.TTSFLSILTTLSLE..LTAQSFKC.G.Q.C.GLS
RetrocopyTNTARSSEQNLQVTLRNKSKDQIGGHKLRKNKHQSMTTSFLSILTTLSLE*RLTAQSFKCEGSQ*CTGLS
ParentalNGKAKVCNYSGWYYCSSCHVDDSFLIPARIVHNWDTSKYK-VSKQAKEF
N.KAKVC.YSG.YY.S.CHVDDSFLIPA.IVHNWDTSKYK.VSKQAKEF
RetrocopyNEKAKVCDYSGCYY*SGCHVDDSFLIPAYIVHNWDTSKYK<VSKQAKEF

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 0 .00 RPM 5 .25 RPM
SRP012922_cerebellum 0 .00 RPM 8 .80 RPM
SRP012922_heart 0 .00 RPM 2 .32 RPM
SRP012922_kidney 0 .00 RPM 0 .55 RPM
SRP012922_liver 0 .00 RPM 1 .55 RPM
SRP012922_lung 0 .00 RPM 4 .73 RPM
SRP012922_quadricep_muscle 0 .00 RPM 1 .73 RPM
SRP012922_spleen 0 .00 RPM 5 .61 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_932 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 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG00000004208 1 retrocopy
retro_dnov_932 ,




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