RetrogeneDB ID:

retro_dnov_1573

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_23813:10538..11487(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RYK
Ensembl ID:ENSDNOG00000010657
Aliases:None
Description:receptor-like tyrosine kinase [Source:HGNC Symbol;Acc:10481]


Retrocopy-Parental alignment summary:






>retro_dnov_1573
CTCGTAGCAGTAATATTAGCTGTTTTTGCACCTTTATTGTATGAAAAAGATTGAACTGGATGACAGCATCAGTGCCAGCA
GTGTTCCCACGGGCTGTCTCAGCCATCCACCCAGATGACTCGTATCTGAGAGCTGACACGCCCAACAATGCAACTCCCGT
TACCAGCTCCCCACGTTATCCTACTTTGTGGATCGAGAAGAACCTGAGAAGTGTCACTCTTTTGGAGGCCAAGGCCAAGG
TGAAAGATATAGCAATAACCAGAGAGAGGATGACTCTAAAAGATGTACTCCAAGAAGGTACTTTTGGGCATATTTTCCAT
GAGACTTTAATAGATGAAAAGATCCAAATAAAGAAAAACAAGCATTTGTAAAAACAGTTAAAGATCAAGCTTCTTGAAAT
TCAGGTGACAATGATGCTCACTGAAGTTGTAAGCTACGATGTCTTCATCACAGAAATCTTCCTATTACTGGTGTGTGTAT
AGAAGAAGGAGAAAAGCCCATGCCTTACATGAATTGGCGGAATCTTAAATTGTTCTTAAGGCAGTGCAAATTAGTAGAGG
CCAACAGTCCTCAGGCAATTTCTCAATAGGACCTGGAACACATGGCCATTCAGAATGCCTGCAGAATGAGCTATCTGGCC
AGAAGGGAAGTCACCCCCAAAGATCTAGCTGCTAGGAATTGTGTAATTGATGATACGCTTCAAGTGCAGATCACAGACGC
CGCCCTCTCAAGAGACTTGTTCCCCGTGGACTATCACTGTCAAGGGGACAGTGAAAACAGGCCAGTTTGATGGATGGCTC
TTGAAAGTCTAGTTAATAATGCGTTTTCCAGCACCAGTGATGTGTGGGCCTTGGGAGTGACGCTGTGGGAGCTCATGACT
CTGGGCCAAACGCCATATGTGGATCCCTTTGAGATGGCCGCATACCTGAGAGATGGTTACTGGATAGCC

ORF - retro_dnov_1573 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.55 %
Parental protein coverage: 60.83 %
Number of stop codons detected: 2
Number of frameshifts detected 6


Retrocopy - Parental Gene Alignment:

ParentalLVAIILAG-LHLRSMKRIELDDSISASS-SSQGLSQPSTQTTQ-YLRADTPNNATPITSSSGYPTLRIEK
LVA.ILA..LHL..MK.IELDDSISASS..S.GLSQPSTQ.T..YLRADTPNNATP.TSS..YPTL.IEK
RetrocopyLVAVILAV>LHLYCMKKIELDDSISASS<CSHGLSQPSTQMTR<YLRADTPNNATPVTSSPRYPTLWIEK
ParentalNDLRSVTLLEAKAKVKDIAITRERITLKDVLQEGTFGRIFHGTL-DEK-DPNKEKQAFVKTVKDQAS-EI
N.LRSVTLLEAKAKVKDIAITRER.TLKDVLQEGTFG.IFH.TL.DEK.DPNKEKQAFVKTVKDQAS.EI
RetrocopyN-LRSVTLLEAKAKVKDIAITRERMTLKDVLQEGTFGHIFHETLIDEK<DPNKEKQAFVKTVKDQAS>EI
ParentalQVTMMLTE-SCKLRGLHHRNLLPITHVCIEEGEKPMVILPYMNWGNLKLFLRQCKLVEANNPQAISQQDL
QVTMMLTE.SCKLR.LHHRNL.PIT.VCIEEGEKPM...PYMNW.NLKLFLRQCKLVEAN.PQAISQ.DL
RetrocopyQVTMMLTE<SCKLRCLHHRNL-PITGVCIEEGEKPM---PYMNWRNLKLFLRQCKLVEANSPQAISQ*DL
ParentalVHMAIQIACGMSYLARREVIHKDLAARNCVIDDTLQVKITDNALSRDLFPMDYHCLGDNENRPVRWMALE
.HMAIQ.AC.MSYLARREV..KDLAARNCVIDDTLQV.ITD.ALSRDLFP.DYHC.GD.ENRPV.WMALE
RetrocopyEHMAIQNACRMSYLARREVTPKDLAARNCVIDDTLQVQITDAALSRDLFPVDYHCQGDSENRPV*WMALE
ParentalSLVNNEFSSASDVWAFGVTLWELMTLGQTPYVDIDPFEMAAYLKDGYRIA
SLVNN.FSS.SDVWA.GVTLWELMTLGQTPYVD..PFEMAAYL.DGY.IA
RetrocopySLVNNAFSSTSDVWALGVTLWELMTLGQTPYVD--PFEMAAYLRDGYWIA

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 .19 RPM 46 .09 RPM
SRP012922_cerebellum 0 .14 RPM 26 .39 RPM
SRP012922_heart 0 .00 RPM 19 .95 RPM
SRP012922_kidney 0 .00 RPM 23 .82 RPM
SRP012922_liver 0 .00 RPM 23 .22 RPM
SRP012922_lung 0 .15 RPM 63 .23 RPM
SRP012922_quadricep_muscle 0 .17 RPM 26 .48 RPM
SRP012922_spleen 0 .23 RPM 57 .23 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_1573 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 ENSDNOG00000010657 1 retrocopy
retro_dnov_1573 ,



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