RetrogeneDB ID:

retro_dord_693

Retrocopy
location
Organism:Kangaroo rat (Dipodomys ordii)
Coordinates:scaffold_5656:51322..52926(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Snw1
Ensembl ID:ENSDORG00000012380
Aliases:None
Description:SNW domain containing 1 [Source:MGI Symbol;Acc:MGI:1913604]


Retrocopy-Parental alignment summary:






>retro_dord_693
ATGGCGCTCACCAGCTTTTTACCCGCACCTACTCAGCTATCCCAGGACCAACTTGAAGCAGAAGAGAAGGCAAGATCTCA
CAGTTCTTGGCAGACCTGCCTGGCCTCCTCACACAGAGAAGCTCCCCCGTATGGGTGCCGAAAAGGTTGGAATCCTCGCT
CGCTAGAAGATTTTGGAGATGGAGGTGCTTTTCCAGAGATCCATGTGGCCCAGTATCCACTGGATATGGGAGGACAACAA
ACCAGGTCCAATGCGCTGGCCATTCAGGTCGATCTGAAGGAAGAATTCGGTACGATGCAGTTGCTCGACAAGGTCAATCA
AAAGACAAGGTCATTTACAGCAAATATACTGACCTGGTGCCACAGGAGGGGATGAATGCCGGTGATCCAGACCCACAGAG
ACCCGGCGAAGAAGCTATTCAAGAGATCACAGCAAAGACAAGGGTAGCCTTAGAGAAGTGTGTGCAGCAGAAGGTTGCCT
CAGCCATGCCAGTTGGGGCAGCTGATCAATCGGCTCCTGCTCAGTATCTGCGATACACACCATCTCAGCAAGGAGTGGCA
TTGAACTCTGGAGCTACACAGATGCTCATTTGCATGGTAGAGATGCAGACAGATCCAATGGAGCCTCCTAGGTTCCGGAT
CAACCAGAAGATTCCCCAGGGACCACCTTCTCCTCCTGCACCTGTCATGCACTCTCCAAGCCAAAAGATGACTGCCAAGG
AGCAACAAGAGTGGAAGATTCCTCCTTGCATCTCCAACTGGAAAAATGCAAAGGGGTATACAATTCCCTTAGACAAGCGA
CTGGCCGCCGATGGAAGAGGACTTCAGATGGTACACATCAATGAGAACTTTGCCAAACTGGCCGAAGCTCTCTACATTGC
CGATCGGAAGGCTCGGGAGGCTGTGGAAACACGGGCCCAAGTGGAGAGAAAAAGGGCTCAGAAAGCAAAAGAGAAGCATG
AAGAGAAACTTAGAGTGATGGCCCAAAAAGCCAGGAAGAGGAGAGCTGGCATCAAAACCCGTGTGGACAGAGAAGATGGG
GAGGCACGTGGGAGGGAGGAGATCCGGCACGAGAGGCAAAAAGAGAGACAGCACAACCACAATCTTTCCAGGACAGCTGC
TGAGAAGAGATGGAAACCGCAGAGGAAGGAACATCGAGATATCACTGAAGTCATTGCTCTGGGTGTCCCCAATCCTGGAA
TCTCCAAGGACGTTTGGTACGACCAGAGGCTCTTCAACCAGTCCAAAGGTATGGACAGCGGATTTGCAGGTGGAGAAGAT
GACATTTACAGCATTTATGATCTCAGCTGGAGAGGTGATAAAGACATGGCCCAGACCATCTATAGGCCCAGGACAAATCT
GGACAAGGACATGTATGGTGATGACCTAAAAATCAAAATCCAGACCAACAGCTTTCTTCCAGTTAAAGAGTTTTCCGGTT
CAGAACATAGGCAGACCGCACGAGAAGGGCCAGTTCAGTTTGAGGAGGATCCTTTTGGTTTGGACAAGTTTCTGCAAGAA
GCTAAACAGCACAGTGGCTCCAAAAGACTTGCAGAAAGCAGCCGACCAGAGGAGCATGAGCATGAAGGCAAGAAGAGGAG
GAAG

ORF - retro_dord_693 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.72 %
Parental protein coverage: 99.81 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMALTSFLPAPTQLSQDQLEAEEKARSQRSRQTSLVSSRREPPPYGYRKGWIPRLLEDFGDGGAFPEIHVA
MALTSFLPAPTQLSQDQLEAEEKARS..S.QT.L.SS.RE.PPYG.RKGW.PR.LEDFGDGGAFPEIHVA
RetrocopyMALTSFLPAPTQLSQDQLEAEEKARSHSSWQTCLASSHREAPPYGCRKGWNPRSLEDFGDGGAFPEIHVA
ParentalQYPLDMGRKKKMSNALAIQVD-PEGKIKYDAIARQGQSKDKVIYSKYTDLVPKEVMNADDPDLQRPDEEA
QYPLDMG.....SNALAIQVD..EG.I.YDA.ARQGQSKDKVIYSKYTDLVP.E.MNA.DPD.QRP.EEA
RetrocopyQYPLDMGGQQTRSNALAIQVD<SEGRIRYDAVARQGQSKDKVIYSKYTDLVPQEGMNAGDPDPQRPGEEA
ParentalIKEITEKTRVALEKSVSQKVAAAMPVRAADKLAPAQYIRYTPSQQGVAFNSGAKQRVIRMVEMQKDPMEP
I.EIT.KTRVALEK.V.QKVA.AMPV.AAD..APAQY.RYTPSQQGVA.NSGA.Q..I.MVEMQ.DPMEP
RetrocopyIQEITAKTRVALEKCVQQKVASAMPVGAADQSAPAQYLRYTPSQQGVALNSGATQMLICMVEMQTDPMEP
ParentalPRFKINKKIPRGPPSPPAPVMHSPSRKMTVKEQQEWKIPPCISNWKNAKGYTIPLDKRLAADGRGLQTVH
PRF.IN.KIP.GPPSPPAPVMHSPS.KMT.KEQQEWKIPPCISNWKNAKGYTIPLDKRLAADGRGLQ.VH
RetrocopyPRFRINQKIPQGPPSPPAPVMHSPSQKMTAKEQQEWKIPPCISNWKNAKGYTIPLDKRLAADGRGLQMVH
ParentalINENFAKLAEALYIADRKAREAVETRAQVERKMAQKEKEKHEEKLREMAQKARERRAGIKTHVEKEDGEA
INENFAKLAEALYIADRKAREAVETRAQVERK.AQK.KEKHEEKLR.MAQKAR.RRAGIKT.V..EDGEA
RetrocopyINENFAKLAEALYIADRKAREAVETRAQVERKRAQKAKEKHEEKLRVMAQKARKRRAGIKTRVDREDGEA
ParentalRERDEIRHDRRKERQHDRNLSRAAPDKRSKLQRNENRDISEVIALGVPNPRTSNEVQYDQRLFNQSKGMD
R.R.EIRH.R.KERQH..NLSR.A..KR.K.QR.E.RDI.EVIALGVPNP..S..V.YDQRLFNQSKGMD
RetrocopyRGREEIRHERQKERQHNHNLSRTAAEKRWKPQRKEHRDITEVIALGVPNPGISKDVWYDQRLFNQSKGMD
ParentalSGFAGGEDEIYNVYDQAWRGGKDMAQSIYRPSKNLDKDMYGDDLEARIKTNRFVPDKEFSGSDRRQRGRE
SGFAGGED.IY..YD..WRG.KDMAQ.IYRP..NLDKDMYGDDL...I.TN.F.P.KEFSGS..RQ..RE
RetrocopySGFAGGEDDIYSIYDLSWRGDKDMAQTIYRPRTNLDKDMYGDDLKIKIQTNSFLPVKEFSGSEHRQTARE
ParentalGPVQFEEDPFGLDKFLEEAKQHGGSKRPSDSSRPKEHEHEGKKRRK
GPVQFEEDPFGLDKFL.EAKQH.GSKR...SSRP.EHEHEGKKRRK
RetrocopyGPVQFEEDPFGLDKFLQEAKQHSGSKRLAESSRPEEHEHEGKKRRK

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






RNA-Seq - click to see more details

Dipodomys ordii was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Dipodomys ordii was not studied using ChIP-Seq data.

EST - click to see more details

Dipodomys ordii was not studied using EST data.

TSS - click to see more details

Dipodomys ordii was not studied using FANTOM5 data.

Lab - click to see more details

retro_dord_693 was not experimentally validated.

Retrocopy orthology:
Dipodomys ordii 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 19 parental genes, and 29 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000039762 retrocopies
retro_amel_163, retro_amel_912,
Canis familiaris ENSCAFG000000304091 retrocopy
retro_cfam_195,
Callithrix jacchus ENSCJAG000000169472 retrocopies
retro_cjac_2932, retro_cjac_576,
Dipodomys ordii ENSDORG00000012380 3 retrocopies
retro_dord_693 , retro_dord_781, retro_dord_782,
Felis catus ENSFCAG000000016371 retrocopy
retro_fcat_635,
Homo sapiens ENSG000001006031 retrocopy
retro_hsap_174,
Gorilla gorilla ENSGGOG000000260161 retrocopy
retro_ggor_257,
Loxodonta africana ENSLAFG000000034822 retrocopies
retro_lafr_474, retro_lafr_787,
Myotis lucifugus ENSMLUG000000052282 retrocopies
retro_mluc_387, retro_mluc_805,
Monodelphis domestica ENSMODG000000052521 retrocopy
retro_mdom_1841,
Mustela putorius furoENSMPUG000000087241 retrocopy
retro_mputfur_551,
Mus musculus ENSMUSG000000210392 retrocopies
retro_mmus_1022, retro_mmus_387,
Nomascus leucogenys ENSNLEG000000167711 retrocopy
retro_nleu_982,
Ochotona princeps ENSOPRG000000075681 retrocopy
retro_opri_737,
Pongo abelii ENSPPYG000000060311 retrocopy
retro_pabe_454,
Pan troglodytes ENSPTRG000000065871 retrocopy
retro_ptro_165,
Sorex araneus ENSSARG000000022793 retrocopies
retro_sara_403, retro_sara_568, retro_sara_727,
Taeniopygia guttata ENSTGUG000000123402 retrocopies
retro_tgut_15, retro_tgut_30,
Tarsius syrichta ENSTSYG000000109511 retrocopy
retro_tsyr_1871,


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