RetrogeneDB ID:

retro_shar_682

Retrocopy
location
Organism:Tasmanian devil (Sarcophilus harrisii)
Coordinates:GL857011.1:67639..70108(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSHAG00000003574
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CUL4B
Ensembl ID:ENSSHAG00000011426
Aliases:None
Description:cullin 4B [Source:HGNC Symbol;Acc:2555]


Retrocopy-Parental alignment summary:






>retro_shar_682
CCCAAGAATTCCTCTCCCACCTCTTCCACCACTTTTACAGCTTCTTGCCCCGGGATTTCAGTTGCTATCCTCAAGTATCA
CTACCTCCAGAAGAAACTGCACCTGGAAGACTCCTTGGATTTTATTGGACTTAATGTGAAGATGGCTGAGGAATCCACAT
CTTCTTCTTCACCTGAACTTGCTGCAGATCAGCAGCAAGAACTTAAAAACAAAAATTTATTTCCCCCCTCTGTGACTAAA
GGGCAGCATGCAAGTGAGCTTCTCAGAGCCTCCTCTATTACCTCTAGCTTTACCACCAGTAAACCAGGCTCAGCCAAGAA
ATTGGTGATCAAGAACTTTAAAGAGAAACCTCTTCCAGAAAACTACACAGAGAAATTATGGCAGAAACTGAAGGAAGCAG
TAGAAGCCATTCAGAACAGTACTTCGATTACATACAATTTAGAAGAACTCTATCAGGCTGTTGAAAACCTCTGTTCCTAC
AGGATCTCTGCAAAATTATACAAACAGCTGAGACAAATTTGTGAAGAACACATCAGAACCCAAATTCACCAATTCCGAGA
GGATTCATTGGACAGTGTTCTCTTTCTAAAGAAGATAGATAAGTGCTGGCATAATCACTGCAGACAAATGTCCATGATTA
GGAGCATTTTTTTGTATTTGGATAGAACGTACGTTCTTCAGAATTCAATGCTGCCTTCCATTTGGGACATGGGTCTAGAA
TTATTTAGGACCCATATAATTAACGATCAGACAGTCCAGAACAGGACTATTGAAGGCATTCTCCTTTTGATTGACAGGGA
AAGGAACGGTGAAGCAATTGACAGGAGTCTGCTTAGAAGCCTCCTGAGTATGCTTTCAGACTTGCAGATTTATCAAGATT
CTTTTGAACAAAGATTTTTGGAAGAAACCAACCAGCTGTATGCGGCCGAGGGTCAGCGTTTGATGCAAGAAAGAGAGGTT
TCTGAATACTTTCATCATGTCAACAGACGTCTAGAAGAAGAAGAAGATAGGCTGATCACTTATCTAGATCTGAGTACTCA
GAAGCCACTAATTGCAACTGTAGAAAAGCAACTTCTAGGTGAACATTTAACAGCCATCCTTCAGAAAGGTTTAAGTCACC
TTCTCGATGAAAATCGGACTCAAGATTTGTCTCTACTCTATCAGCTATTTAGTAGGGTATGCAATGGAGTTCAGGTTCTC
TTGCAATACTGGACTGAATACATCAAGGCATTTGGCAGCGCTATTGTCATCAATCCCGAAAAAGATAAGACCATGGTACA
GGAATTGCTGGATTTTAAAGATAAAGTTGACTATATTACGGAAATCAGTTTTATGAAAAACGAAAGGTTTGTCAATGCCA
CGAAGGAAGCATTTGAAACCTTCATTAACAAAAGACCAAATAAGCCTGCTGAGCTCATAGCAAAGTACGTGGATTCGAAG
CTCCGTGCAGGTAATAGGGAAGCTACAGATGAAGAACTTGAGAAAATGTTGGATAAGATCATGATCATATTTCGGTTCAT
TTATGGGAAAGATGTCTTTGAAGCCTTTTATAAGAAGGACTTAGTCAAAAGGCTCTTGGTTGGAAAGAGTGCATCGACAG
ATGCTGAAAAGTCGATGCTTTCCAAACTCAAGCACGAATGTGGACCTGTGTTCACCAGCAAACTAGAAGGGATGTTCAAA
GACATAGAGCTGTCCAAAGATATCATGGTTCAATTCAAACAGTATGTGCAAAACCAAAACTCTCCTGTTAGCATTGAACT
AACCGTGAATATCCTGACAACGGGTCACTGGCCGACCTATGTGCCCATGGAGGTTCACTTACCGGCTGAGATGGTAAGAC
TCCAGGAGACTTTCAAGACTTTTTACTTAGGTAAACACAGTGGGAGGAAGCTTCAGTGGCAATCAACGCTAGGACACTGT
GTACTAAAAGCAGAATTTAAAGAGGGCAAAAAGGAGCTTCAGGTCTCTCTTTTCCAAACACTGGTGTTGCTAATGTTTAA
TGATGGCAAAGAATTTAGTGTAGAAGATATCAAGCAAGCTACAGGAATAGAGGATGGAGAATTAAGAAGATCACTCCAGT
CCTTAGCCTGTGGCAAAGCTAGAGTTCTGATGAAAAATCCCAAGGGCAAAGATGTGGAAGATGGTGATAAATTTACTTGC
AACGATGACTTCAGACACAAACTCTTCAGGATAAAAATCAATCAAATCCAGATGAAAGAAACAGTAGAGGAACAAGCAAG
CACTACTGAAAAAGTCTTTCAGGACCGACAGTATCACATTGATGCTGCAATTGTGAGAATCATGAAGATAAGAAAGGCTC
TAGACCACAATCAGCTTATTTCAGAAGCCTATAATCAACTGAGGTTCCCAGTTAAGCCTGCTGATCTCAAGAAGAGAATA
GAATCCTTAATTGACAGGGACTACATGGAAAGAGACAAAGAAAACCCAAACCAGTACAATTACGTTGCC

ORF - retro_shar_682 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.5 %
Parental protein coverage: 88.49 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalPKNSSTSSSASSTASCPGISIAAPNHHHLQKKLRFEDSLDFLGLDVKMAEESASSSSPGLGVSQQQ-LKN
PKNSS..SS...TASCPGIS.A....H.LQKKL..EDSLDF.GL.VKMAEES.SSSSP.L...QQQ.LKN
RetrocopyPKNSSPTSSTTFTASCPGISVAILKYHYLQKKLHLEDSLDFIGLNVKMAEESTSSSSPELAADQQQELKN
ParentalKSLLISSVATGHHANGLTKAPSSISSFTNSKPGSAKKLVIKNFKEKPKLPENYTDETWQKLKDAVEAIQN
K.L...SV..G.HA..L..A.S..SSFT.SKPGSAKKLVIKNFKEKP.LPENYT...WQKLK.AVEAIQN
RetrocopyKNLFPPSVTKGQHASELLRASSITSSFTTSKPGSAKKLVIKNFKEKP-LPENYTEKLWQKLKEAVEAIQN
ParentalSTSIKYNLEELYQAVENLCSYKISANLYKQLRQICEEHIKSQIHQFREDSLDSVLFLKKIDKCWQNHCRQ
STSI.YNLEELYQAVENLCSY.ISA.LYKQLRQICEEHI..QIHQFREDSLDSVLFLKKIDKCW.NHCRQ
RetrocopySTSITYNLEELYQAVENLCSYRISAKLYKQLRQICEEHIRTQIHQFREDSLDSVLFLKKIDKCWHNHCRQ
ParentalMIMIRSIFLFLDRTYVLQNSMLPSIWDMGLELFRTHIISDQKVQNKTIEGILLLIERERSGEAIDRSLLR
M.MIRSIFL.LDRTYVLQNSMLPSIWDMGLELFRTHII.DQ.VQN.TIEGILLLI.RER.GEAIDRSLLR
RetrocopyMSMIRSIFLYLDRTYVLQNSMLPSIWDMGLELFRTHIINDQTVQNRTIEGILLLIDRERNGEAIDRSLLR
ParentalSLLSMLSDLQIYQDSFEQKFLEETNRLYSAEGQRLMQEREVPEYLHHVNKRLEEEADRLITYLDLSTQKP
SLLSMLSDLQIYQDSFEQ.FLEETN.LY.AEGQRLMQEREV.EY.HHVN.RLEEE.DRLITYLDLSTQKP
RetrocopySLLSMLSDLQIYQDSFEQRFLEETNQLYAAEGQRLMQEREVSEYFHHVNRRLEEEEDRLITYLDLSTQKP
ParentalLIATVEKQLLGEHLTAILQKGLNHLLDENRIQDLSLLYQLFSRVRSGVQVLLQHWIEYIKAFGSTIVINP
LIATVEKQLLGEHLTAILQKGL.HLLDENR.QDLSLLYQLFSRV..GVQVLLQ.W.EYIKAFGS.IVINP
RetrocopyLIATVEKQLLGEHLTAILQKGLSHLLDENRTQDLSLLYQLFSRVCNGVQVLLQYWTEYIKAFGSAIVINP
ParentalEKDKTMVQELLDFKDKVDHIIDVCFMKNEKFVNAMKEAFETFINKRPNKPAELIAKYVDSKLRAGNKEAT
EKDKTMVQELLDFKDKVD.I....FMKNE.FVNA.KEAFETFINKRPNKPAELIAKYVDSKLRAGN.EAT
RetrocopyEKDKTMVQELLDFKDKVDYITEISFMKNERFVNATKEAFETFINKRPNKPAELIAKYVDSKLRAGNREAT
ParentalDEELEKMLDKIMIIFRFIYGKDVFEAFYKKDLAKRLLVGKSASVDAEKSMLSKLKHECGAAFTSKLEGMF
DEELEKMLDKIMIIFRFIYGKDVFEAFYKKDL.KRLLVGKSAS.DAEKSMLSKLKHECG..FTSKLEGMF
RetrocopyDEELEKMLDKIMIIFRFIYGKDVFEAFYKKDLVKRLLVGKSASTDAEKSMLSKLKHECGPVFTSKLEGMF
ParentalKDMELSKDIMVQFKQYIQNQNFPGNIELTVNILTMGYWPTYVPMEVHLPAEMVRLQEIFKTFYLGKHSGR
KD.ELSKDIMVQFKQY.QNQN.P..IELTVNILT.G.WPTYVPMEVHLPAEMVRLQE.FKTFYLGKHSGR
RetrocopyKDIELSKDIMVQFKQYVQNQNSPVSIELTVNILTTGHWPTYVPMEVHLPAEMVRLQETFKTFYLGKHSGR
ParentalKLQWQSTLGHCVLKAEFKEGRKELQVSLFQTLVLLMFNEGEEFSLEDIKQATGIEDGELRRTLQSLACGK
KLQWQSTLGHCVLKAEFKEG.KELQVSLFQTLVLLMFN.G.EFS.EDIKQATGIEDGELRR.LQSLACGK
RetrocopyKLQWQSTLGHCVLKAEFKEGKKELQVSLFQTLVLLMFNDGKEFSVEDIKQATGIEDGELRRSLQSLACGK
ParentalARVLTKNPKGKDVEDGDKFTCNDDFRHKLFRIKINQIQMKETVEEQASTTERVFQDRQYQIDAAIVRIMK
ARVL.KNPKGKDVEDGDKFTCNDDFRHKLFRIKINQIQMKETVEEQASTTE.VFQDRQY.IDAAIVRIMK
RetrocopyARVLMKNPKGKDVEDGDKFTCNDDFRHKLFRIKINQIQMKETVEEQASTTEKVFQDRQYHIDAAIVRIMK
ParentalMRKALGHNLLVSEVYNQLKFPVKPADLKKRIESLIDRDYMERDKENPNQYNYIA
.RKAL.HN.L.SE.YNQL.FPVKPADLKKRIESLIDRDYMERDKENPNQYNY.A
RetrocopyIRKALDHNQLISEAYNQLRFPVKPADLKKRIESLIDRDYMERDKENPNQYNYVA

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






RNA-Seq - click to see more details

Sarcophilus harrisii was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Sarcophilus harrisii was not studied using ChIP-Seq data.

EST - click to see more details

Sarcophilus harrisii was not studied using EST data.

TSS - click to see more details

Sarcophilus harrisii was not studied using FANTOM5 data.

Lab - click to see more details

retro_shar_682 was not experimentally validated.

Retrocopy orthology:
Sarcophilus harrisii 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 ENSMODG000000103451 retrocopy
retro_mdom_793,
Oryctolagus cuniculus ENSOCUG000000156331 retrocopy
retro_ocun_349,
Otolemur garnettii ENSOGAG000000012822 retrocopies
retro_ogar_2069, retro_ogar_2642,
Sarcophilus harrisii ENSSHAG00000011426 1 retrocopy
retro_shar_682 ,


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