RetrogeneDB ID:

retro_dord_650

Retrocopy
location
Organism:Kangaroo rat (Dipodomys ordii)
Coordinates:scaffold_4809:71128..71547(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Rps4x
Ensembl ID:ENSDORG00000008571
Aliases:None
Description:ribosomal protein S4, X-linked [Source:MGI Symbol;Acc:MGI:98158]


Retrocopy-Parental alignment summary:






>retro_dord_650
ATGGCTTGTGGTCCCAAGAAACATCTGAAGGGGTAGCTGCTCCCAAGCATTGGATGTTGGACAAACTGACTGGTGTGTTT
GCTCTTTGTCCATCCATTGGTCCCCACAAGCTGAGAGAATGTCTACCTTTCATCATTTTCCTAAGGAGCAAGCTTAAGTA
TGCCTTGCTAGGAGATGAAGTCAAGAAAATCCACATGCAGTATTTCATTAAGATTGATGGAAAAGTCAGAACTGATATCA
CTTACCCAGCTGGTTTTATGGATGTCATCAGCATCGACAAGACTGGGGAGAAATTCCATCTATTCTATGGCACCAAGGGT
CACTTTGCTGTTTATTGCATTACACCAGAGGAAGCCAAGTACAAATTGTGCCAAGTGAGAAAGATCTTTGTCGGCACAAA
AGGGATCCCTCATCTGCTC

ORF - retro_dord_650 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.11 %
Parental protein coverage: 53.23 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMARGPKKHLKR-VAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDEVKKICMQRF
MA.GPKKHLK..VAAPKHWMLDKLTGVFA..PS.GPHKLRECLP.IIFLR..LKYAL.GDEVKKI.MQ.F
RetrocopyMACGPKKHLKG<VAAPKHWMLDKLTGVFALCPSIGPHKLRECLPFIIFLRSKLKYALLGDEVKKIHMQYF
ParentalIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAKYKLCKVRKIFVGTKGIPHL
IKIDGKVRTDITYPAGFMDVISIDKTGE.F.L.Y.TKG.FAV..ITPEEAKYKLC.VRKIFVGTKGIPHL
RetrocopyIKIDGKVRTDITYPAGFMDVISIDKTGEKFHLFYGTKGHFAVYCITPEEAKYKLCQVRKIFVGTKGIPHL
ParentalV
.
RetrocopyL

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_650 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 64 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000146011 retrocopy
Bos taurus ENSBTAG000000188005 retrocopies
Canis familiaris ENSCAFG000000171512 retrocopies
Cavia porcellus ENSCPOG000000063373 retrocopies
Dipodomys ordii ENSDORG00000008571 4 retrocopies
Equus caballus ENSECAG000000108526 retrocopies
Homo sapiens ENSG000001298241 retrocopy
Meleagris gallopavo ENSMGAG000000096711 retrocopy
Myotis lucifugus ENSMLUG000000116855 retrocopies
Monodelphis domestica ENSMODG000000110701 retrocopy
Mustela putorius furoENSMPUG0000000529411 retrocopies
Otolemur garnettii ENSOGAG000000118082 retrocopies
Pan troglodytes ENSPTRG000000224701 retrocopy
Rattus norvegicus ENSRNOG000000032011 retrocopy
Tarsius syrichta ENSTSYG0000000313716 retrocopies
Vicugna pacos ENSVPAG000000109524 retrocopies



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