RetrogeneDB ID:

retro_mdom_793

Retrocopy
location
Organism:Opossum (Monodelphis domestica)
Coordinates:2:522264099..522266499(+)
Located in intron of:ENSMODG00000023141
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CUL4B
Ensembl ID:ENSMODG00000010345
Aliases:None
Description:cullin 4B [Source:HGNC Symbol;Acc:2555]


Retrocopy-Parental alignment summary:






>retro_mdom_793
CCTAGCCATCACCACCTCCAGAAGAAGCTGGCTTTTGAGAACTCCTCAGATTGCACAGGACTGGATGTGAGGATGGCTGA
CCAATCGGCATCTTCATCACCTGATTTTGCTGAACCTCAGGAGCAGCAGCAGCCACTTAAAAGCTTATTCATCTCCTCTG
TGGCTGAAGAGCATCATATAAATGGGCTGACCAAAGCCCCTACTACCATCCCTAGCTTCACCAACAGCAAATCAAATGCA
GCCAAGAAACTGGTGATCAAGAACTTTAAAGACAAATATAAATTGCAGGAAAACTACATAGATGAAACATGGTGGAAACT
GAAAGAAGCCGTAGAAGCCATTCAGAACAATACTTCAATTCAATACAATTTAGAAGAACTCTATCAGGCTGTTGAAAACC
TCTGTTCCTACAGCATCTCTGCAAACTTGTACAGACAGCTGAGACAGATATGTGAGGAGCACATCAGATACCAAATTCTC
CAGTTCCAAGAAGATTCGCTGGATAGTGTTCTGTTTCTAAAGAAAATAGATAAATGCTGGCAAAATCACTGCAGACAAAT
GGTCATGATTAGGAGCATTTTTTTATTCCTGGACAGAACATATATTCTTCAGAATTCAATGCTGCCTTCTATTTGGGACA
TGGGTCTAGAGTTATTTAGGACCCACATAATTAGTGATCAGAAAGTCCAAAACAAGACTATCGAAGGCATTCTGCTTTTG
ATTGCAAAGGAAAGGAATGGTGAAGCAATCGATAGAAGTTTGCTTCGAAGTCTTCTGAGTATGCTTTCAGATTTGCAGAT
TTATCAAGATTCCTTTGAACAAAAATTTTTGGAAGAAACCAACCTGTTATATGCTGCAGAAGGCGAGTGTTTAATGCAAG
AAAAAGAGGTTCCTGAATACTTTCATCATGTCAACAAACGTCTAGAAGAAGAAACAGACAGACTGATCACCTATCTAGAT
ATGAGTACTCAGAAGCCACTAATTGCTACTGTAGAAAAGCAACTTCTCGGTGAACACTTAACAGCCATTCTTCAGAAGGG
TTTAAATCACCTTCTTGATGAAAATAGGACTCAAGATTTGTCTCTCCTCTATCAGCTGTTTAGTAGGGTACACAGTGGAG
TTCAGGTCCTCTTGCAGCACTGGATTGAATACATCAAAGCATTTGGGAGCACCATTGTCAATAATCCTGAAAAAGATAAG
ACCATGGTACAAGAATTGCTGGATTTTAAAGATAAAGTTGACCATATTATTGATATCTGCTTTATGAAAAATGAGAAGTT
TGTCAATGCAATGAAAGAAGCATTTGAAACCTTCATTAACAAAAGACCAAACAAGCCGGCTGAACTCCTAGCAAAGTATG
TGGATTCAAAGCTCCGAGCAGGTAACAGAGAAACCACCGATGAAGAACTTGAGAAAATGTTGGACAAGATCATGATTATA
TTTCGGTTCATTTACGGGAAAGATGTCTTTGAAGCCTTTTACAAAAAGGACTTGGTCAAAAGACTGTTAGTTGGAAAGAG
TGCATCAGTGGATGCTGAGAAATCAATGCTTTCCAAACTCAAGCATGAATGCGGGGCTGAGTTCACCAGAAACTTGGAAG
GGATGTTCAAAGACATGGAGGTGTCAAAAGACATCATGGTTCAGTTCAAACAATACACACAAAACCAAAATTTTCCTGGG
AGCATTGAACTAACTGTGAACACCTTGACAATGGGTTATTGGCCAACCTATGTGCCTATGGAGGTTCACTTGCCAGCTGA
GATGGTAAGACTTCAGGAGGTTTTTGTGACTTTTTACTTGAGTAAACACAGTGGAAGGAAACTTCAGTGGCAATCTAGTC
TAGGACATTGTGTACTGAAAGCAGAATTTAAAGAGGAGAAAAAGGAACTCCAGGTCTCTCTTTTTCAAACACTGGTGCTA
CTAATGTTTAATGAAGGTGAAGAATTCAGTTTAGAGGACATCAGGCAAGCTACAGGAATAGAGGATGGAGAATTAAGGAG
AACCCTCCAGTCATTAGCCTGTGGCAAAGCTAGAGTTCTGATTAAAGATTCGAAGGGCAAAGATGTGGAAGATGGTGATA
AATTTACTTGCAATGATGACTTCAGACACAAGCTCTTCCGGATAAAAATTAACCAGATCCAAATGAAAGAAACGGTAGAG
GAGCAAATAAGCACTACAGAAAAAGTCTTTCAAGACCGACAGTATCAAATTGATGCTGCCATTGTGAGAATCATGAAGAT
AAGAAAGGCCCTTGACCACAATCTGCTTGTTTCAGAAGTGTATAACCAGCTGAAGTTCCCAGTTAAACCTACTGATCTCA
AGAAGCGTATAGAATCTTTAATCGACATGGACTACATAGAAAGAGATAAAGAGAACCCCAACCGATACAACTATATTGCC

ORF - retro_mdom_793 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.03 %
Parental protein coverage: 87.46 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalPNHHHLQKKLRFEDSLDFIGLDVKMAEESASSSSPGLAVSQQQQQFKNKSLLISTVAAGHHANGLTKAPT
P.HHHLQKKL.FE.S.D..GLDV.MA..SASSS.P..A..Q.QQQ...KSL.IS.VA..HH.NGLTKAPT
RetrocopyPSHHHLQKKLAFENSSDCTGLDVRMADQSASSS-PDFAEPQEQQQ-PLKSLFISSVAEEHHINGLTKAPT
ParentalTISSFTNSKPGSAKKLVIKNFKEKPKLPENYTDETWQKLKEAVEAIQKSTSIKYNLEELYQAVENLCSYK
TI.SFTNSK...AKKLVIKNFK.K.KL.ENY.DETW.KLKEAVEAIQ..TSI.YNLEELYQAVENLCSY.
RetrocopyTIPSFTNSKSNAAKKLVIKNFKDKYKLQENYIDETWWKLKEAVEAIQNNTSIQYNLEELYQAVENLCSYS
ParentalISANLYKQLRQICEEHIRFQIFQFREGSLDSVLFLKKIDKCWQNHCRQMIMIRSIFLFLDRTYVLQNSML
ISANLY.QLRQICEEHIR.QI.QF.E.SLDSVLFLKKIDKCWQNHCRQM.MIRSIFLFLDRTY.LQNSML
RetrocopyISANLYRQLRQICEEHIRYQILQFQEDSLDSVLFLKKIDKCWQNHCRQMVMIRSIFLFLDRTYILQNSML
ParentalPSIWDMGLELFRTHIISDQKVQNKTIEGILLLIERERTGEAIDRSLLRSLLSMLSDLQIYQDSFEQKFLE
PSIWDMGLELFRTHIISDQKVQNKTIEGILLLI..ER.GEAIDRSLLRSLLSMLSDLQIYQDSFEQKFLE
RetrocopyPSIWDMGLELFRTHIISDQKVQNKTIEGILLLIAKERNGEAIDRSLLRSLLSMLSDLQIYQDSFEQKFLE
ParentalETNRLYSAEGQRLMQEREVPEYLHHVNRRLEEEADRLITYLDLSTQKPLIATVEKQLLGEHLTAILQKGL
ETN.LY.AEG..LMQE.EVPEY.HHVN.RLEEE.DRLITYLD.STQKPLIATVEKQLLGEHLTAILQKGL
RetrocopyETNLLYAAEGECLMQEKEVPEYFHHVNKRLEEETDRLITYLDMSTQKPLIATVEKQLLGEHLTAILQKGL
ParentalNHLLDENRIQDLSLLYQLFTRVRSGVQVLLQHWIEYIKAFGSTIVINPEKDKTMVQELLDFKDKVDHIID
NHLLDENR.QDLSLLYQLF.RV.SGVQVLLQHWIEYIKAFGSTIV.NPEKDKTMVQELLDFKDKVDHIID
RetrocopyNHLLDENRTQDLSLLYQLFSRVHSGVQVLLQHWIEYIKAFGSTIVNNPEKDKTMVQELLDFKDKVDHIID
ParentalICFMKNEKFVNAMKEAFETFINKRPNKPAELIAKYVDSKLRAGNKEATDEELEKMLDKIMIIFRFIYGKD
ICFMKNEKFVNAMKEAFETFINKRPNKPAEL.AKYVDSKLRAGN.E.TDEELEKMLDKIMIIFRFIYGKD
RetrocopyICFMKNEKFVNAMKEAFETFINKRPNKPAELLAKYVDSKLRAGNRETTDEELEKMLDKIMIIFRFIYGKD
ParentalVFEAFYKKDLAKRLLVGKSASVDAEKSMLSKLKHECGAAFTSKLEGMFKDMELSKDIMVQFKQYIQNQNF
VFEAFYKKDL.KRLLVGKSASVDAEKSMLSKLKHECGA.FT..LEGMFKDME.SKDIMVQFKQY.QNQNF
RetrocopyVFEAFYKKDLVKRLLVGKSASVDAEKSMLSKLKHECGAEFTRNLEGMFKDMEVSKDIMVQFKQYTQNQNF
ParentalPGSIELTVNILTMGYWPTYVPMEVHLPAEMVRLQEIFKTFYLGKHSGRKLQWQSTLGHCVLKAEFKEGKK
PGSIELTVN.LTMGYWPTYVPMEVHLPAEMVRLQE.F.TFYL.KHSGRKLQWQS.LGHCVLKAEFKE.KK
RetrocopyPGSIELTVNTLTMGYWPTYVPMEVHLPAEMVRLQEVFVTFYLSKHSGRKLQWQSSLGHCVLKAEFKEEKK
ParentalELQVSLFQTLVLLMFNENEEFSLEDIRHATGIEDGELRRTLQSLACGKARVLAKNPKGKDVEDGDKFICN
ELQVSLFQTLVLLMFNE.EEFSLEDIR.ATGIEDGELRRTLQSLACGKARVL.K..KGKDVEDGDKF.CN
RetrocopyELQVSLFQTLVLLMFNEGEEFSLEDIRQATGIEDGELRRTLQSLACGKARVLIKDSKGKDVEDGDKFTCN
ParentalDDFRHKLFRIKINQIQMKETVEEQASTTERVFQDRQYQIDAAIVRIMKMRKALGHNLLVSEVYNQLKFPV
DDFRHKLFRIKINQIQMKETVEEQ.STTE.VFQDRQYQIDAAIVRIMK.RKAL.HNLLVSEVYNQLKFPV
RetrocopyDDFRHKLFRIKINQIQMKETVEEQISTTEKVFQDRQYQIDAAIVRIMKIRKALDHNLLVSEVYNQLKFPV
ParentalKPADLKKRIESLIDRDYMERDKENPNQYNYIA
KP.DLKKRIESLID.DY.ERDKENPN.YNYIA
RetrocopyKPTDLKKRIESLIDMDYIERDKENPNRYNYIA

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_793 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_793 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 4 parental genes, and 5 retrocopies.

Species Parental gene accession Retrocopies number
Monodelphis domestica ENSMODG00000010345 1 retrocopy
retro_mdom_793 ,
Oryctolagus cuniculus ENSOCUG000000156331 retrocopy
retro_ocun_349,
Otolemur garnettii ENSOGAG000000012822 retrocopies
retro_ogar_2069, retro_ogar_2642,
Sarcophilus harrisii ENSSHAG000000114261 retrocopy
retro_shar_682,


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