RetrogeneDB ID:

retro_mdom_487

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:1:721972664..721972975(+)
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:ENSMODG00000006616
Aliases:None
Description:SSU72 RNA polymerase II CTD phosphatase homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:25016]


Retrocopy-Parental alignment summary:






>retro_mdom_487
GTTGTTTGTTCCAGTAACCAGAACTGTATCAGAGGGGCCCACTACACTGTCAGCATCCAAGGATTCTGTGTCAGATCCTT
TGGAACAGGAAGCTACACTCTCAGGATTATCAGCATACAAGCCCAATGTTTATTATTTCAAAACAACCTATGAGAAGATC
TATAATGATTACAGAAAGATAGGGCATTCAGTACACTGAATAGGATTTTGCACATGTTGAGCAGAAATAAAAGAATTAAT
CTGGTACTAAATAGATTCCTGAATTGTCAAGATCACTTGATCTCATCCTTACCTGTGAAGAGAGAGTCTAT

ORF - retro_mdom_487 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 59.09 %
Parental protein coverage: 55.15 %
Number of stop codons detected: 0
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalVVCSSNQNRSMEAHNILSKRGFSVRSFGTGT-HVKLPGPAPDKPNVYDFKTTYDQMYNDLLRK-DKELYT
VVCSSNQN....AH...S..GF.VRSF..GT....L.G....KPNVY.FKTTY...YND..RK.D....T
RetrocopyVVCSSNQNCIRGAHYTVSIQGFCVRSF--GT>EATLSGLSAYKPNVYYFKTTYEKIYND-YRK<DRAFST
ParentalQNGILHMLDRNKRIKPRPERFQNCKD-LFDLILTCEERVY
.N.ILHML.RNKRI.....RF.NC.D...DLILTCEERVY
RetrocopyLNRILHMLSRNKRINLVLNRFLNCQD<SLDLILTCEERVY

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






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain 0 .00 RPM 0 .00 RPM
SRP007412_cerebellum 0 .00 RPM 0 .00 RPM
SRP007412_heart 0 .00 RPM 0 .00 RPM
SRP007412_kidney 0 .00 RPM 0 .00 RPM
SRP007412_liver 0 .00 RPM 0 .00 RPM
SRP007412_testis 0 .00 RPM 0 .00 RPM
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_487 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_487 was not experimentally validated.

Retrocopy orthology:
Monodelphis domestica 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 22 parental genes, and 67 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000137363 retrocopies
Canis familiaris ENSCAFG000000192542 retrocopies
Callithrix jacchus ENSCJAG000000109573 retrocopies
Cavia porcellus ENSCPOG000000022382 retrocopies
Dipodomys ordii ENSDORG000000117141 retrocopy
Homo sapiens ENSG000001600758 retrocopies
Gorilla gorilla ENSGGOG000000044211 retrocopy
Loxodonta africana ENSLAFG000000020764 retrocopies
Macropus eugenii ENSMEUG000000151701 retrocopy
Myotis lucifugus ENSMLUG000000165172 retrocopies
Macaca mulatta ENSMMUG000000015511 retrocopy
Monodelphis domestica ENSMODG00000006616 3 retrocopies
retro_mdom_16, retro_mdom_1997, retro_mdom_487 ,
Mustela putorius furoENSMPUG000000143942 retrocopies
Mus musculus ENSMUSG000000290381 retrocopy
Otolemur garnettii ENSOGAG000000244302 retrocopies
Pongo abelii ENSPPYG000000020001 retrocopy
Pan troglodytes ENSPTRG0000000003416 retrocopies
Pteropus vampyrus ENSPVAG000000176954 retrocopies
Rattus norvegicus ENSRNOG000000178292 retrocopies
Sus scrofa ENSSSCG000000033482 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000029604 retrocopies
Tursiops truncatus ENSTTRG000000170512 retrocopies



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