RetrogeneDB ID:

retro_dord_433

Retrocopy
location
Organism:Kangaroo rat (Dipodomys ordii)
Coordinates:scaffold_183663:276..633(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Ssu72
Ensembl ID:ENSDORG00000011714
Aliases:None
Description:Ssu72 RNA polymerase II CTD phosphatase homolog (yeast) [Source:MGI Symbol;Acc:MGI:1916241]


Retrocopy-Parental alignment summary:






>retro_dord_433
TATACCCATAATGGCATTTTGCATATGCTAAATCGAAATAAAAGAATCAAACCGGGCCCTGAAAGGTTTCAGAACTGTAA
AGATAGATTTGACCTGATACTTACATGCGAAGAGCGAGTCTATGACCTGGTGGTGGAAGACCTGAATTCCAGAGAGCAGG
AGACCTGCCAACTTGTCCATGTGGTCAACGTAGATATCCAGGACAACTATGAAGATGCCACCATTGGGTCGTTCCTCCTC
TGTGATCTCTGCCAGTGTATGCAGGAGACGGAAGACTTGGACAATGAGATTGAGGAGCTCCTTTTGGTGTTCGAGGAAAA
GACTGGCAAAGCTTTCCTGCACACCGTCTGCTTCTAT

ORF - retro_dord_433 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.35 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalYTQNGILHMLDRNKRIKPRPERFQNCKDLFDLILTCEERVYDQVVEDLNSREQETCQPVHVVNVDIQDNH
YT.NGILHML.RNKRIKP.PERFQNCKD.FDLILTCEERVYD.VVEDLNSREQETCQ.VHVVNVDIQDN.
RetrocopyYTHNGILHMLNRNKRIKPGPERFQNCKDRFDLILTCEERVYDLVVEDLNSREQETCQLVHVVNVDIQDNY
ParentalEEATLGAFLICELCQCIQHTEDMENEIDELLQEFEEKSGRAFLHTVCFY
E.AT.G.FL.C.LCQC.Q.TED..NEI.ELL..FEEK.G.AFLHTVCFY
RetrocopyEDATIGSFLLCDLCQCMQETEDLDNEIEELLLVFEEKTGKAFLHTVCFY

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






RNA-Seq - click to see more details

Dipodomys ordii was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Dipodomys ordii was not studied using ChIP-Seq data.

EST - click to see more details

Dipodomys ordii was not studied using EST data.

TSS - click to see more details

Dipodomys ordii was not studied using FANTOM5 data.

Lab - click to see more details

retro_dord_433 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 18 parental genes, and 39 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000137363 retrocopies
retro_amel_1930, retro_amel_292, retro_amel_84,
Canis familiaris ENSCAFG000000192542 retrocopies
retro_cfam_185, retro_cfam_42,
Callithrix jacchus ENSCJAG000000109573 retrocopies
retro_cjac_1640, retro_cjac_2335, retro_cjac_37,
Cavia porcellus ENSCPOG000000022382 retrocopies
retro_cpor_83, retro_cpor_909,
Dipodomys ordii ENSDORG00000011714 1 retrocopy
retro_dord_433 ,
Felis catus ENSFCAG000000033181 retrocopy
retro_fcat_54,
Gorilla gorilla ENSGGOG000000044211 retrocopy
retro_ggor_206,
Loxodonta africana ENSLAFG000000020764 retrocopies
retro_lafr_1153, retro_lafr_1154, retro_lafr_1155, retro_lafr_400,
Myotis lucifugus ENSMLUG000000165172 retrocopies
retro_mluc_292, retro_mluc_371,
Macaca mulatta ENSMMUG000000015511 retrocopy
retro_mmul_159,
Monodelphis domestica ENSMODG000000066163 retrocopies
retro_mdom_16, retro_mdom_1997, retro_mdom_487,
Mustela putorius furoENSMPUG000000143942 retrocopies
retro_mputfur_108, retro_mputfur_1408,
Otolemur garnettii ENSOGAG000000244302 retrocopies
retro_ogar_124, retro_ogar_13,
Pongo abelii ENSPPYG000000020001 retrocopy
retro_pabe_53,
Pteropus vampyrus ENSPVAG000000176954 retrocopies
retro_pvam_11, retro_pvam_1151, retro_pvam_272, retro_pvam_767,
Sarcophilus harrisii ENSSHAG000000097471 retrocopy
retro_shar_32,
Sus scrofa ENSSSCG000000033482 retrocopies
retro_sscr_1179, retro_sscr_38,
Ictidomys tridecemlineatus ENSSTOG000000029604 retrocopies
retro_itri_1055, retro_itri_1352, retro_itri_1496, retro_itri_99,


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