RetrogeneDB ID:

retro_dord_408

Retrocopy
location
Organism:Kangaroo rat (Dipodomys ordii)
Coordinates:scaffold_17192:19449..19755(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Ube2d4
Ensembl ID:ENSDORG00000006888
Aliases:None
Description:ubiquitin-conjugating enzyme E2D 4 [Source:MGI Symbol;Acc:MGI:3644823]


Retrocopy-Parental alignment summary:






>retro_dord_408
ATGGCTCTGAAGAGAATCCAAAAGGAATTGAATGACCTGGCACGGGATCCCCCAGCACAATGTTCAGCCGGCCCTGTTGG
AGATGACATGTTTCATTGGCAAGCTATTATAAGGGGACCAAATGACAGTCCCTATCAGGGTGGAGTATTTTTCTTGACAA
TTCATTTCCCAACTGATTACCCCTTCAAACCACCTAAGGTTGCAGTTACAACAAGAATTTATCATCCAAATATTAGCAGT
AATGGGAGCATTTGTCTTGATAGTCTACGGTCACAGTGGTCTCCAGCACTAACTATTTCAAAAGTC

ORF - retro_dord_408 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.22 %
Parental protein coverage: 69.39 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMALKRIQKELTDLQRDPPAQCSAGPVGDDLFHWQATIMGPNESPYQGGVFFLTIHFPTDYPFKPPKVAFT
MALKRIQKEL.DL.RDPPAQCSAGPVGDD.FHWQA.I.GPN.SPYQGGVFFLTIHFPTDYPFKPPKVA.T
RetrocopyMALKRIQKELNDLARDPPAQCSAGPVGDDMFHWQAIIRGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAVT
ParentalTKIYHPNINSNGSICLDILRSQWSPALTVSKV
T.IYHPNI.SNGSICLD.LRSQWSPALT.SKV
RetrocopyTRIYHPNISSNGSICLDSLRSQWSPALTISKV

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_408 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 16 parental genes, and 57 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000039971 retrocopy
Callithrix jacchus ENSCJAG000000078754 retrocopies
Dipodomys ordii ENSDORG000000067622 retrocopies
Dipodomys ordii ENSDORG00000006888 5 retrocopies
Dipodomys ordii ENSDORG000000114061 retrocopy
Dipodomys ordii ENSDORG000000154411 retrocopy
Homo sapiens ENSG000000789672 retrocopies
Gorilla gorilla ENSGGOG000000033783 retrocopies
Myotis lucifugus ENSMLUG000000119193 retrocopies
Macaca mulatta ENSMMUG000000024105 retrocopies
Nomascus leucogenys ENSNLEG000000033643 retrocopies
Oryctolagus cuniculus ENSOCUG000000089001 retrocopy
Pongo abelii ENSPPYG000000297271 retrocopy
Sus scrofa ENSSSCG000000167222 retrocopies
Tupaia belangeri ENSTBEG000000036919 retrocopies
Tarsius syrichta ENSTSYG0000000059514 retrocopies



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