RetrogeneDB ID:

retro_mdom_1520

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:5:101310412..101311621(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:DDX5
Ensembl ID:ENSMODG00000003743
Aliases:None
Description:DEAD (Asp-Glu-Ala-Asp) box helicase 5 [Source:HGNC Symbol;Acc:2746]


Retrocopy-Parental alignment summary:






>retro_mdom_1520
TATCGAAGAAGCAAAGAAATTACAGTTCGAGGTCACAAGGGCCCAAAACCAATTCTAAACTTCTATGAAGCCAACTTTCC
TGCAAACGTCATGGATGTAATTGCAAGACAGAACTTTGCCCAACCTACTGCTATCCAAGCCCAGGGGTGGCCTGTTGCTC
TAAGAGGGCTGCATCTGGTGGGAGTAGCACAGACTGGATCAGGGAAAAGGCTGTCTTATTTGCTGCCTGCTATCGTGCAC
GTAAATCATCAGCCATTCCTAGAGAGAGGTGATGGGCCTATTTGTTTGGTGCTGGCGCCAACTCGTGAACTGGCCCAACA
GGTCTAAGGAGTAGCTGCTGCATACAGTAGAGCCTGTGTTCTAAAATCCACCTGCATTTATGGTGGTGCTCCAAAGGGAC
CACAAAGAGGGGACCTGGAAAGAGGGGCAGAAATGTGCATGGCCACACCTGGAAGACTGATAGACTCTTTAGAGTGCAGG
AAAACAAATTTGAGAAGAACTACTTACCTTGTACTTGATGAAGCAGACAGGATGCTTGATATGGGCTTTGAGCTTCAAAT
CAGGAAAATTGTGGGTCAGATAAGACCTGATAGACAAACCCTACTGTGGAGTGCTTCGTGGCCAAAAGAAGTGAGGCAGC
TTGCTGAAGACTTTTTGAAAGATTATATTCATATCAACATTGGTGCCCTGGAACTGAGTGCAAAAAACAGTATTCTTCAG
ATTGTGGATGTCTGTCATGATAGAGAAAAGGATGAGAAACTTATCCCATTGATGGAGGAGATCATGAGTGAAGGGGAAAA
TAAGAGGATTGTTTTTGTGGAAACCAAAAGAAGATGTGATGAACTTACCACAAAAATGAGGAGAGATGGGTGGCCTGCAA
TGGGTGTCCATGGTGCCAAGAGTCAGGAGGAGGGAGACTGGGTTCTAAATGAATTCAAAGATGGAAAAGCTCCTATCCTG
ATTGCCACAGATGTTGCATCTAGAGGGCTAGATGTGGAAGATGTGAAATTTGTCATCAATGATGACTACCCCAACTCTTC
AGAGGATTATATCCACTGAATTGGAGGAACTGCACCTTGGACCAAAACAGGCACAGCATAGACATTCCTTACACCTAATA
ACATAAAACAAGTAGGTGACCTCATCTCTGTGCTTCAGGAGGCTAATCAAGCAATCAATCCCAAATTGCTTCAGTTGATT
GAAGACAGG

ORF - retro_mdom_1520 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.59 %
Parental protein coverage: 59. %
Number of stop codons detected: 3
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalYRRSKEITVRGHNCPKPILNFYEANFPANVMDVIARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKT
YRRSKEITVRGH..PKPILNFYEANFPANVMDVIARQNF..PTAIQAQGWPVAL.GL..VGVAQTGSGK.
RetrocopyYRRSKEITVRGHKGPKPILNFYEANFPANVMDVIARQNFAQPTAIQAQGWPVALRGLHLVGVAQTGSGKR
ParentalLSYLLPAIVHINHQPFLERGDGPICLVLAPTRELAQQVQQVAAEYSRACRLKSTCIYGGAPKGPQIRDLE
LSYLLPAIVH.NHQPFLERGDGPICLVLAPTRELAQQV..VAA.YSRAC.LKSTCIYGGAPKGPQ..DLE
RetrocopyLSYLLPAIVHVNHQPFLERGDGPICLVLAPTRELAQQV*GVAAAYSRACVLKSTCIYGGAPKGPQRGDLE
ParentalRGVEICIATPGRLIDFLECGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKE
RG.E.C.ATPGRLID.LEC.KTNLRRTTYLVLDEADRMLDMGFE.QIRKIV.QIRPDRQTL.WSA.WPKE
RetrocopyRGAEMCMATPGRLIDSLECRKTNLRRTTYLVLDEADRMLDMGFELQIRKIVGQIRPDRQTLLWSASWPKE
ParentalVRQLAEDFLKDYIHINIGALELSANHNILQIVDVCHDVEKDEKLIRLMEEIMSEKENKTIVFVETKRRCD
VRQLAEDFLKDYIHINIGALELSA...ILQIVDVCHD.EKDEKLI.LMEEIMSE.ENK.IVFVETKRRCD
RetrocopyVRQLAEDFLKDYIHINIGALELSAKNSILQIVDVCHDREKDEKLIPLMEEIMSEGENKRIVFVETKRRCD
ParentalELTRKMRRDGWPAMGIHGDKSQQERDWVLNEFKHGKAPILIATDVASRGLDVEDVKFVINYDYPNSSEDY
ELT.KMRRDGWPAMG.HG.KSQ.E.DWVLNEFK.GKAPILIATDVASRGLDVEDVKFVIN.DYPNSSEDY
RetrocopyELTTKMRRDGWPAMGVHGAKSQEEGDWVLNEFKDGKAPILIATDVASRGLDVEDVKFVINDDYPNSSEDY
ParentalIHRIGRTARSTKTGTAYTFFTPNNIKQVSDLISVLREANQAINPKLLQLIEDR
IH.IG.TA..TKTGTA.TF.TPNNIKQV.DLISVL.EANQAINPKLLQLIEDR
RetrocopyIH*IGGTAPWTKTGTA*TFLTPNNIKQVGDLISVLQEANQAINPKLLQLIEDR

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 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

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_1520 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_1520 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 11 parental genes, and 17 retrocopies.

Species Parental gene accession Retrocopies number
Echinops telfairi ENSETEG000000199501 retrocopy
retro_etel_1009,
Felis catus ENSFCAG000000035121 retrocopy
retro_fcat_172,
Myotis lucifugus ENSMLUG000000094964 retrocopies
retro_mluc_1136, retro_mluc_1499, retro_mluc_1845, retro_mluc_2208,
Monodelphis domestica ENSMODG00000003743 4 retrocopies
retro_mdom_1519, retro_mdom_1520 , retro_mdom_1955, retro_mdom_1956,
Monodelphis domestica ENSMODG000000185461 retrocopy
retro_mdom_14,
Mus musculus ENSMUSG000000207191 retrocopy
retro_mmus_788,
Pteropus vampyrus ENSPVAG000000019321 retrocopy
retro_pvam_1267,
Rattus norvegicus ENSRNOG000000306801 retrocopy
retro_rnor_1277,
Tupaia belangeri ENSTBEG000000094901 retrocopy
retro_tbel_4260,
Tarsius syrichta ENSTSYG000000121491 retrocopy
retro_tsyr_1269,
Tursiops truncatus ENSTTRG000000087931 retrocopy
retro_ttru_1662,


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