RetrogeneDB ID:

retro_dord_700

Retrocopy
location
Organism:Kangaroo rat (Dipodomys ordii)
Coordinates:scaffold_58074:3485..3757(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Cbx3
Ensembl ID:ENSDORG00000005487
Aliases:None
Description:chromobox 3 [Source:MGI Symbol;Acc:MGI:108515]


Retrocopy-Parental alignment summary:






>retro_dord_700
CAAAAAGCTGGTTTATCTGACAATGAATTTGATGATAGCACATCAGAGAATAAAAGCGATGCTGGTGACAACCCAAGGGG
CTTTGCTAGAGGTCTTGAGCCTGAATGAATAATTGCTGTTACAGAAAACAGTAGGGGACTGATGTTCCTCACGAAGTGGA
AAGATTAGAGGAAGCTGAGTTGGTGCCAGGAAAAGAGGTAAATATGTAATGTCCTCAGACTGTAATTGCTTTTTATGAAA
AGAGAATCCTTTGGGATTCAGAAGATGAAGCT

ORF - retro_dord_700 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 60.64 %
Parental protein coverage: 50.82 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalKRKSLSDSESDDSKSKKKRDTADKPRGFARGLDPERIIGATDSSGELMFLMKWKD-SDEADLVLAKEANM
....LSD.E.DDS.S..K.D..D.PRGFARGL.PE.II..T..S..LMFL.KWKD...EA.LV..KE.NM
RetrocopyQKAGLSDNEFDDSTSENKSDAGDNPRGFARGLEPE*IIAVTENSRGLMFLTKWKD<LEEAELVPGKEVNM
ParentalKCPQIVIAFYEERLTWHSCPEDEA
.CPQ.VIAFYE.R..W.S..EDEA
Retrocopy*CPQTVIAFYEKRILWDS--EDEA

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_700 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 13 parental genes, and 65 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG0000000289711 retrocopies
Callithrix jacchus ENSCJAG000000079528 retrocopies
Dipodomys ordii ENSDORG000000007162 retrocopies
Dipodomys ordii ENSDORG00000005487 11 retrocopies
Loxodonta africana ENSLAFG000000069073 retrocopies
Myotis lucifugus ENSMLUG000000075912 retrocopies
Mus musculus ENSMUSG000000298361 retrocopy
Otolemur garnettii ENSOGAG000000165831 retrocopy
Ochotona princeps ENSOPRG000000117139 retrocopies
Pongo abelii ENSPPYG0000001771410 retrocopies
Rattus norvegicus ENSRNOG000000118142 retrocopies
Sarcophilus harrisii ENSSHAG000000179131 retrocopy
Sus scrofa ENSSSCG000000167114 retrocopies



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