RetrogeneDB ID:

retro_mdom_69

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:4:416244677..416245304(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMODG00000018250
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:HMGB2
Ensembl ID:ENSMODG00000003527
Aliases:None
Description:high mobility group box 2 [Source:HGNC Symbol;Acc:5000]


Retrocopy-Parental alignment summary:






>retro_mdom_69
ATGGGCAAGGTTCATATTAAGCCCAAAGTGAATCTGTCTTCATATGTCCACTTTTTATTAAACTGCAGGAACAAGCACAA
GGAACAACAGCCAAATGCTTACATCAATTTCAAAGAGTTCTCCAAAAAGTGCTCAGAAAAGTGGAAGACAATCTCTAAGC
ATGAAAAGTCCAAGTATGAAGCTATAGCCAAACTTGACAAAGCACGCTACCAGAAAGAAATGAAAAACTATGTTCCCCCT
GCAGGAATGAAGAGGAAGAAAAGAAGGAAGAAGGACCCCAAAGCTCCCAAGAGACCACCCTCATCTTTTATACTCTTCAG
TAGAGAGAATTATACAAAAATCAAGGGTGACAATCCACACTGGTCTGTAATAGAAGTGGCAAAATTCCTGGGGGAGATGT
GGTCCAAAAAGTCAGAGCAGGAGAAGCAACCTTATGAAGAGAAGGCAGCTAGACTGAGAACCAAGTACCACCAAGAACTC
ACAGCCTACCGAGTCAATTATGGTCAGGGATGTTCAAGAAAGAAAGGACCAGGGCCTTCTGGCCAGTATCAGAACAGAAA
GAAATCCAAGTCAGACAAGAAGTGTGAAAAATATGATGAATCTGATTCAGAAGGGGAGCTGGATTAG

ORF - retro_mdom_69 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 52.22 %
Parental protein coverage: 95.17 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalKPRGKMSSYAFFVQTCREEHKKKHPDSPVNFAEFSKKCSERWKTMSAKEKSKFEDLAKGDKARYDREMKN
KP....SSY..F...CR..HK...P....NF.EFSKKCSE.WKT.S..EKSK.E..AK.DKARY..EMKN
RetrocopyKPKVNLSSYVHFLLNCRNKHKEQQPNAYINFKEFSKKCSEKWKTISKHEKSKYEAIAKLDKARYQKEMKN
ParentalYVPPKG--DKKGKKKDPNAPKRPPSAFFLFCAEHRPKIKSEHPGLSIGDTAKKLGELWSEQSAKDKLPYE
YVPP.G...KK..KKDP.APKRPPS.F.LF..E...KIK...P..S....AK.LGE.WS..S...K.PYE
RetrocopyYVPPAGMKRKKRRKKDPKAPKRPPSSFILFSRENYTKIKGDNPHWSVIEVAKFLGEMWSKKSEQEKQPYE
ParentalQKVAKLKEKYEKDIAAYRAK-GKGDAGKKGPGRPTG---SKKKNEPDEEEEDEDEEDEDEEDD
.K.A.L..KY.....AYR...G.G...KKGPG.P.G.....KK...D...E..DE.D...E.D
RetrocopyEKAARLRTKYHQELTAYRVNYGQGCSRKKGPG-PSGQYQNRKKSKSDKKCEKYDESDSEGELD

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_69 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_69 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 27 parental genes, and 112 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000151011 retrocopy
Callithrix jacchus ENSCJAG000000051122 retrocopies
Cavia porcellus ENSCPOG000000035524 retrocopies
Dasypus novemcinctus ENSDNOG000000194404 retrocopies
Erinaceus europaeus ENSEEUG000000122388 retrocopies
Echinops telfairi ENSETEG000000103793 retrocopies
Echinops telfairi ENSETEG000000163791 retrocopy
Felis catus ENSFCAG000000042182 retrocopies
Homo sapiens ENSG000001641041 retrocopy
Gorilla gorilla ENSGGOG000000158821 retrocopy
Loxodonta africana ENSLAFG000000104173 retrocopies
Macropus eugenii ENSMEUG000000022563 retrocopies
Myotis lucifugus ENSMLUG000000263034 retrocopies
Monodelphis domestica ENSMODG00000003527 3 retrocopies
retro_mdom_1160, retro_mdom_1919, retro_mdom_69 ,
Monodelphis domestica ENSMODG000000057357 retrocopies
Monodelphis domestica ENSMODG0000000923814 retrocopies
Mustela putorius furoENSMPUG000000019199 retrocopies
Mus musculus ENSMUSG0000005471723 retrocopies
Nomascus leucogenys ENSNLEG000000066623 retrocopies
Oryctolagus cuniculus ENSOCUG000000000741 retrocopy
Otolemur garnettii ENSOGAG000000171493 retrocopies
Pongo abelii ENSPPYG000000152043 retrocopies
Pan troglodytes ENSPTRG000000165973 retrocopies
Pteropus vampyrus ENSPVAG000000146561 retrocopy
Rattus norvegicus ENSRNOG000000131672 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000239802 retrocopies
Tursiops truncatus ENSTTRG000000156501 retrocopy



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