RetrogeneDB ID:

retro_mdom_124

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:2:156554425..156556111(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMODG00000024606
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSMODG00000002756
Aliases:None
Description:Glutamate dehydrogenase [Source:UniProtKB/TrEMBL;Acc:F6YHB4]


Retrocopy-Parental alignment summary:






>retro_mdom_124
ATGTTCCGATGCCTCAGGGAAGTGCTGCAGTTGTTCCCGGCCTCGGCCACCAACGCCTGGGCCTCAGCCTTGGTCACTGC
TGCCCCGGTGTACCCTGCTGCTTCCACTCCGATCTTGCGGGACTGGGGTCAGCCTGCAGTCTCACCACCCACCTCTTGGC
GCCACTTTAGCAAGGAGGCCAGATCCCAGGACGACAATCCCAACTTCTTCAAGATGGTGGAGGGCTTCTTCGACCGCGGT
GCCAGCATCATGGAGGACAAGTTGGTGGAGGACTTGAAGACTCAGGAGAGTGAAGATCAGAAGCGCAACCGGGTTCGAGG
AATCCTGCGCATCATCAAACCCTGCAACCATGTGTTGAGCGTCACCTTCCCCATCAAGAGGGATGACGGCTCCTGGGAGG
TAATAGAAGGCTACCGGGCACAGCACAGCCAGCACCGCACCCCCTGCAAGGGAGGTATCCGTTACAGTACAGATGTTTGC
GTGGATGAAATAAAGGCTCTGGCATCTCTGATGACTTACAAATGTGCTGTGGTTGATGTGCCATTTGGAGGAGCCAAAGC
TGGTGTTAAAATCAATCCCAGGCATTATACAGACAATGAGTTGGAAAAGATTACAAGAAGGTTCACCATAGAGCTAGCAA
AAAAGGGCTTTATTGGACCTGGTATTGATGTCCCTGCTCCTGACATGAGCACAGGTGAAAGAGAGATGTCTTGGATTGCA
GATACCTACGCCAGTACCATAGGGCACTACGACATTAATGCATATGCCTGTGTCACGGGGAAACCCATCAGTCAAGGTGG
TATCCATGGGCGTATCTCTGCCACTGGTCGAGGTATCTTCCATGGAATTGAAAACTTCATCAATGAGGCTTCTTACACAG
ACCTTTTGGGAATGACTACAGGATTTGGAGATAAAACCTTTGTTGTTCAGGGATTTGGTAATGTTGGCTTTCACTCAATG
AGATATTTACATCGTTTTGGTGCTAAATGTGTTGGTGTTGGTGAAATCAATGGAAGCATCTGGAATTCAGATGGCATTGA
CCCGAAGGATCTAGTGAATTATAAATTGCAACATGGAACAATTGTTGGCTTCCCCAAGGCAAAGCCCTATGAAGGAAATA
TTTTGGAAGCTGATTGTGACATACTTATCCCTGCTGCTGGTGAGAAACAGTTGACGAAGTTCAATGCTTCCAGAATCAAA
GCAAAGATTATTGCAGAAGGTGCCAACGGACCCACAACCCCAGAGGCTGACAAGATTTTCCTGGAGAAGAATATCCTGGT
TTTGCCTGATCTCTATTTGAATGCTGGAGGTGTGACAGTGTCTTACTTTGAGTGGCTGAAAAATCTCAACCATGTTAGCT
TTGGCCGACTGACATTCAAATATGAAAGGGATTCTAACTACCACTTGCTCATGTCTGTTCAAGAAAGTTTAGAAAGAATG
TTTGGCAAGCATGGTGGTGCTATCCCAGTTGTACCTACAGCAGAATTCCAAGACAGGATATCAGGAGCATCTGAGAAGGA
CATCGTACACTCCGGGTTAGCATATACTATGGAGCGTTCTGCCCGGCAAATTATGCGCACTGCTATGAAGTATAACCTGG
GGCTGGACTTAAGAACTGCTGCCTATGTCAATGCAATCGAGAAAATCTTCAAAGTGTATAACGAAGCTGGGGTAGCCTTC
ACCTAG

ORF - retro_mdom_124 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.28 %
Parental protein coverage: 71.92 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMFRYLGEALQLSRAGASASAAA----AASVDPAASALLLRARGQPAAAPPAPRRLYSEAAGSREDDPNFF
MFR.L.E.LQL..A.A....A.....AA.V.PAAS...LR..GQPA..PP...R..S..A.S..D.PNFF
RetrocopyMFRCLREVLQLFPASATNAWASALVTAAPVYPAASTPILRDWGQPAVSPPTSWRHFSKEARSQDDNPNFF
ParentalNMVEGFFDRGASIVEDKLVEDLKTRESEDQKRNRVRGILRIIKPCNHVLSVTFPIKRDDGSWEVIEGYRA
.MVEGFFDRGASI.EDKLVEDLKT.ESEDQKRNRVRGILRIIKPCNHVLSVTFPIKRDDGSWEVIEGYRA
RetrocopyKMVEGFFDRGASIMEDKLVEDLKTQESEDQKRNRVRGILRIIKPCNHVLSVTFPIKRDDGSWEVIEGYRA
ParentalQHSQHRTPCKGGIRYSTDVCVDEVKALASLMTYKCAVVDVPFGGAKAGVKINPRHYTDNELEKITRRFTM
QHSQHRTPCKGGIRYSTDVCVDE.KALASLMTYKCAVVDVPFGGAKAGVKINPRHYTDNELEKITRRFT.
RetrocopyQHSQHRTPCKGGIRYSTDVCVDEIKALASLMTYKCAVVDVPFGGAKAGVKINPRHYTDNELEKITRRFTI
ParentalELAKKGFIGPGIDVPAPDMSTGEREMSWIADTYASTIGHYDINAHACVTGKPISQGGIHGRISATGRGVF
ELAKKGFIGPGIDVPAPDMSTGEREMSWIADTYASTIGHYDINA.ACVTGKPISQGGIHGRISATGRG.F
RetrocopyELAKKGFIGPGIDVPAPDMSTGEREMSWIADTYASTIGHYDINAYACVTGKPISQGGIHGRISATGRGIF
ParentalHGIENFINEASYMGLLGMTPGFGDKTFVVQGFGNVGLHSMRYLHRFGAKCVGVGEIDGSIWNSDGIDPKE
HGIENFINEASY..LLGMT.GFGDKTFVVQGFGNVG.HSMRYLHRFGAKCVGVGEI.GSIWNSDGIDPK.
RetrocopyHGIENFINEASYTDLLGMTTGFGDKTFVVQGFGNVGFHSMRYLHRFGAKCVGVGEINGSIWNSDGIDPKD
ParentalLEDYKLQHGSIVGFPKAKPYEGSILEADCDILIPAAGEKQLTKSNASRIKAKIIAEGANGPTTPEADKIF
L..YKLQHG.IVGFPKAKPYEG.ILEADCDILIPAAGEKQLTK.NASRIKAKIIAEGANGPTTPEADKIF
RetrocopyLVNYKLQHGTIVGFPKAKPYEGNILEADCDILIPAAGEKQLTKFNASRIKAKIIAEGANGPTTPEADKIF
ParentalLEKNILVVPDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFKYERDSNYHLLMSVQESLERKFGKHGGAIPV
LEKNILV.PDLYLNAGGVTVSYFEWLKNLNHVS.GRLTFKYERDSNYHLLMSVQESLER.FGKHGGAIPV
RetrocopyLEKNILVLPDLYLNAGGVTVSYFEWLKNLNHVSFGRLTFKYERDSNYHLLMSVQESLERMFGKHGGAIPV
ParentalVPTAEFQDRISGASEKDIVHSGLAYTMERSARVRMQKSV
VPTAEFQDRISGASEKDIVHSGLAYTMERSAR..M....
RetrocopyVPTAEFQDRISGASEKDIVHSGLAYTMERSARQIMRTAM

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






RNA-Seq - click to see more details

(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 624 .59 RPM
SRP007412_cerebellum 0 .00 RPM 876 .20 RPM
SRP007412_heart 0 .00 RPM 487 .81 RPM
SRP007412_kidney 0 .00 RPM 1095 .60 RPM
SRP007412_liver 0 .00 RPM 1916 .78 RPM
SRP007412_testis 0 .00 RPM 132 .40 RPM

ChIP-Seq - click to see more details

Monodelphis domestica was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_mdom_124 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_124 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 20 parental genes, and 28 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000075402 retrocopies
retro_btau_1413, retro_btau_1741,
Canis familiaris ENSCAFG000000160951 retrocopy
retro_cfam_747,
Choloepus hoffmanni ENSCHOG000000011011 retrocopy
retro_chof_2002,
Callithrix jacchus ENSCJAG000000116331 retrocopy
retro_cjac_2830,
Dipodomys ordii ENSDORG000000097671 retrocopy
retro_dord_400,
Equus caballus ENSECAG000000073712 retrocopies
retro_ecab_886, retro_ecab_919,
Echinops telfairi ENSETEG000000196382 retrocopies
retro_etel_141, retro_etel_2024,
Homo sapiens ENSG000001486721 retrocopy
retro_hsap_31,
Gorilla gorilla ENSGGOG000000157701 retrocopy
retro_ggor_2954,
Loxodonta africana ENSLAFG000000120591 retrocopy
retro_lafr_504,
Microcebus murinus ENSMICG000000165261 retrocopy
retro_mmur_524,
Monodelphis domestica ENSMODG00000002756 1 retrocopy
retro_mdom_124 ,
Nomascus leucogenys ENSNLEG000000116581 retrocopy
retro_nleu_36,
Otolemur garnettii ENSOGAG000000036411 retrocopy
retro_ogar_2757,
Procavia capensis ENSPCAG000000086621 retrocopy
retro_pcap_11,
Pongo abelii ENSPPYG000000028273 retrocopies
retro_pabe_3109, retro_pabe_3213, retro_pabe_79,
Pan troglodytes ENSPTRG000000027114 retrocopies
retro_ptro_3162, retro_ptro_3283, retro_ptro_3285, retro_ptro_3290,
Ictidomys tridecemlineatus ENSSTOG000000128431 retrocopy
retro_itri_737,
Tarsius syrichta ENSTSYG000000015781 retrocopy
retro_tsyr_313,
Tursiops truncatus ENSTTRG000000081451 retrocopy
retro_ttru_950,


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