RetrogeneDB ID:

retro_mdom_698

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:2:153432486..153432978(+)
Located in intron of:ENSMODG00000008061
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HMGB3
Ensembl ID:ENSMODG00000005735
Aliases:HMGB3, HmgB3x
Description:high mobility group protein B3 [Source:RefSeq peptide;Acc:NP_001157151]


Retrocopy-Parental alignment summary:






>retro_mdom_698
AAAGGTGATCCAAAGAAACCAAAAGGCAAAATGTCTGTTTATGCCTTTTATACAAATATGACATGAAGAACATGAAAGGA
AAAAATCCTTTTGTTCCTGTCAATATTGCAGAATTTTCAAAGTAGTATTCAGAAAGATGGATGTATCTGTCTGGAAAGGA
AAAACCCAAGTTTGATGAAATGGTAACAGTTGATATGTTGTAGTATGACAGAGAGATGAAGGACTATGTACATGGGATGG
AGGTGGGTAATGGGTGGGTGGGGGATCCTAATGCTCCCAAATGGCTCCCACCTGGATTCTCTCTGTTCTGTTCAGAATTT
TGCCCCAAGATAAAATCTACAAACCCTGAGACATCTGGGGATGTAGCCAAAAAAAAAAAAATTGGCAAGATGTAGAATAA
TCTGAATGATAATGAAAAGCAGTCATATGATAATAATTAGGCAGCAAAACTGAAGGAAAAAATGTGAAAGGGATGTTGCT
GATTCTAAGTCC

ORF - retro_mdom_698 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.67 %
Parental protein coverage: 85.11 %
Number of stop codons detected: 4
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalKGDPKKPKGKMSAYAFFVQTC-REEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRY
KGDPKKPKGKMS.YAF..........K.KNP.VPVN.AEFSK..SERW...SGKEK.KFDEM...D...Y
RetrocopyKGDPKKPKGKMSVYAFYTNMT<MKNMKGKNPFVPVNIAEFSK*YSERWMYLSGKEKPKFDEMVTVDML*Y
ParentalDREMKDY--GPAKGGKKKKDPNAPKRPPSGFFLFCSEFRPKIKSTNPGISIGDVA--KKLGEMWNNLSDN
DREMKDY..G...G.....DPNAPK..P.GF.LFCSEF.PKIKSTNP..S.GDVA.....G.M.NNL.DN
RetrocopyDREMKDYVHGMEVGNGWVGDPNAPKWLPPGFSLFCSEFCPKIKSTNPETS-GDVAXXXXXGKM*NNLNDN
ParentalEKQPY-NNKAAKLKEKY-EKDVADYKS
EKQ.Y.NN.AAKLKEK..E.DVAD.KS
RetrocopyEKQSYDNN*AAKLKEKM>ERDVADSKS

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_698 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_698 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 34 parental genes, and 223 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000051502 retrocopies
Canis familiaris ENSCAFG000000287151 retrocopy
Choloepus hoffmanni ENSCHOG000000050052 retrocopies
Callithrix jacchus ENSCJAG000000039369 retrocopies
Cavia porcellus ENSCPOG000000006012 retrocopies
Dipodomys ordii ENSDORG000000108264 retrocopies
Equus caballus ENSECAG000000205961 retrocopy
Echinops telfairi ENSETEG000000156894 retrocopies
Felis catus ENSFCAG000000246244 retrocopies
Homo sapiens ENSG000000299938 retrocopies
Gorilla gorilla ENSGGOG0000002716416 retrocopies
Loxodonta africana ENSLAFG000000258771 retrocopy
Microcebus murinus ENSMICG000000156684 retrocopies
Myotis lucifugus ENSMLUG000000109264 retrocopies
Macaca mulatta ENSMMUG0000000463320 retrocopies
Monodelphis domestica ENSMODG000000035273 retrocopies
Monodelphis domestica ENSMODG00000005735 7 retrocopies
Monodelphis domestica ENSMODG0000000923814 retrocopies
Mustela putorius furoENSMPUG000000116062 retrocopies
Mus musculus ENSMUSG000000152171 retrocopy
Oryctolagus cuniculus ENSOCUG000000059867 retrocopies
Otolemur garnettii ENSOGAG0000000177319 retrocopies
Procavia capensis ENSPCAG000000019451 retrocopy
Pongo abelii ENSPPYG0000002081822 retrocopies
Pan troglodytes ENSPTRG0000002237122 retrocopies
Pteropus vampyrus ENSPVAG000000002191 retrocopy
Rattus norvegicus ENSRNOG000000110964 retrocopies
Rattus norvegicus ENSRNOG000000509105 retrocopies
Sarcophilus harrisii ENSSHAG000000029162 retrocopies
Sus scrofa ENSSSCG000000127453 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000239086 retrocopies
Tupaia belangeri ENSTBEG0000000306818 retrocopies
Tursiops truncatus ENSTTRG000000002052 retrocopies
Vicugna pacos ENSVPAG000000000962 retrocopies



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