RetrogeneDB ID:

retro_dord_528

Retrocopy
location
Organism:Kangaroo rat (Dipodomys ordii)
Coordinates:scaffold_27268:239..620(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Tvp23a
Ensembl ID:ENSDORG00000015782
Aliases:None
Description:trans-golgi network vesicle protein 23A [Source:MGI Symbol;Acc:MGI:3665441]


Retrocopy-Parental alignment summary:






>retro_dord_528
ATGGTGACAATTATCTTGTTGTCATGTGACTTTTGGGCTGTGAAGAATGTTACAGATAGACTAGTGGTCAGCCTCCATTG
GCGGAATCATATTGATGAGGATGGAAAAAGCCACTGGGTGTTTGAGTCCAGAGAGGCAACTCCTCAAGATAATAAAACTG
TTTCAGAAGCTGAATCAAGAATCTTTTGGTTGGGACTTACTGCCTTTTCAGTGCTGTGGGTGATATTTGCCTTCAGTGCT
CTCTTCTCCTTCAGAGTCAAGTGGTTGGCTGTGGTTATTATGGATGTGGTACTACAAGGTGCCAACCTGTATGGTTACAT
AAGGTGTAAAGTGGGCAGCAGGAAGAACTTAACTACCATGGCTACCTTGTATCTTGGAAAG

ORF - retro_dord_528 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 52.76 %
Parental protein coverage: 69.23 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalVTVLLLLAFDFWSVKNVTGRLLVGLRWWNQIDEDGRSHWVFEARKASPHHVAT-TEAEARIFWLGLIICP
.....LL..DFW.VKNVT.RL.V.L.W.N.IDEDG.SHWVFE.R.A.P....T..EAE.RIFWLGL....
RetrocopyMVTIILLSCDFWAVKNVTDRLVVSLHWRNHIDEDGKSHWVFESREATPQDNKTVSEAESRIFWLGLTAFS
ParentalLIWMVFFFTTLFSLKLKWLALVVAGISLQAANLYGYILCKMGGDSDLSKVAASFLSQ
..W..F.F..LFS...KWLA.V.....LQ.ANLYGYI.CK.G....L...A...L..
RetrocopyVLWVIFAFSALFSFRVKWLAVVIMDVVLQGANLYGYIRCKVGSRKNLTTMATLYLGK

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






Dipodomys ordii was not studied using RNA-Seq expression data.
Dipodomys ordii was not studied using ChIP-Seq data.
Dipodomys ordii was not studied using EST data.
Dipodomys ordii was not studied using FANTOM5 data.
retro_dord_528 was not experimentally validated.

Retrocopy orthology:
Dipodomys ordii 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 4 parental genes, and 5 retrocopies.

Species Parental gene accession Retrocopies number
Dipodomys ordii ENSDORG00000015782 2 retrocopies
retro_dord_528 , retro_dord_565,
Nomascus leucogenys ENSNLEG000000101371 retrocopy
Pongo abelii ENSPPYG000000070941 retrocopy
Tursiops truncatus ENSTTRG000000156411 retrocopy



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