RetrogeneDB ID:

retro_amel_31

Retrocopy
location
Organism:Panda (Ailuropoda melanoleuca)
Coordinates:GL194402.1:154403..156236(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSAMEG00000019953
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:DDX43
Ensembl ID:ENSAMEG00000007851
Aliases:None
Description:DEAD (Asp-Glu-Ala-Asp) box polypeptide 43 [Source:HGNC Symbol;Acc:18677]


Retrocopy-Parental alignment summary:






>retro_amel_31
GGCGGCGGCAGCAGCAGAAGGGGCGGAAGCGGCAGAGGCTGGAGCGCTCCCTCCGGCTCCATGGAGCTTAGAGCCTCAGG
CCCCAGAGAACCACCTCTCTGCTTTAGACTGAGGAGCAATATGATTGGTGTGGTGATTGGTCGTGGTGGATCAAAGATAA
AAGACATCCAGGCTATGACAAACACCAAAATACAGATCATAAAAGGTGATTCTGAAGCAGAGGTAAAAATTTTTGGCGCC
ACGGACATGAAAGCAAAGGCCAAAGCAGCTATAGATGCTCTTGTTAAAAAACAAGAACGAGGCCACCATTCAGAGTCCCG
TGTGGATAGTGCCACACCTCAGGCCTCTGCTGGAAGAGAGTTTCGCCCAGATAACACTGGCGGTAGGCAAGTTCAGTCAC
TGATAGATTGGGATCAAATTAGGGCAGAAGTTGTAGAGTGGGAAAAAAGAAAATGGGCATATTTACCACCAATTAAGAAA
AACTTTTACGTAGAATCTGAAGCAACCAGCTCATTGTCTCAAGTTCAGGTAGACATGTGGAGAAAGGAAAATTTTGACCT
AATATGTGACGACTTGAAAGATGGTGAAAAGCGCCCCATCCCCAATCCTACTCGTCTGTTTGAGGATGCTTTCCATCCTT
ATCCTGAACTTATTGAAAGCATTAAAAGAGCAGGTTTTCAAAAGCCAACGCCAATTCAGTCACAGGCGTGGCCAATTATT
CTACAAGGAATAGATCTTATAGGAGTTGCGCAAACCGGAACGGGCAAAACTTTGTCCTATTTAATGCCTGGGTTTATCCA
CCTCAATAATCAACCAATATCCAGAGAGGAAAGGAATGGACCTGGCATGCTAGTCCTTACACCCACTAGAGAATTAGCTC
TTCAGGTGGAAGCTGAATGTTCTAAGTATTCATATAAAGGTCTTAAAAGTATTTGTATATTTGGTGGCAGAAATAGAGAA
CAACAAATACGAGACATTACCAAAGGCATAGATATCATTATTGCAACTCCTGGACGACTAAATTATCTGCAAATGAATAA
CTTTGTCAACTTACAAAGCATAACCTACTTAGTCTTAGATGAAGCAGATAAAATGCTAGATCTGGGGTTTGAACACCAGA
TAATGAAGATTTTATTAGATGTGCGCCCAGACCGCCAGACTGTTATGATAAGTGCAACTTGGTCAGATACCATTCATCAG
CTTGGTCAGTCTTATTTGAAAGAGCCTATGATTGTTTATGTTGGTACTCTGGATCTAGTTGCTGTTAATACTGTGACGCA
AAATGTGATCATTACCACACAAGAAGAAAAACGATCTCTTCTCCAAGAATTCCTGCAGAACCGTTCACCCCAAGACAAAG
TCATCGTGTTTGTCAGAAGAAGACTTGTTGCTGATGACTTATCAAGTGATTTGAGCATCCAAGGCATAACAGTGCAGTCA
CTACATGGCGACAGAGACCAGCATGATCGTGAACGAGCATTGGAGGACTTCAGAAGTGGAAAAGTGAAAGTACTGATTGC
TACTGATTTAGCATCCAGAGGTCTTGATGTTAATGATATCACACACGTATATAATTACGACTTCCCGCGCAATATTGAAG
AATATGTACACAGAGTGGGGCGAACTGGAAGAGCAGGGAAGACTGGTTTATCAATTACCCTCATGACTCAAAATGATTGG
AAGATCGCCACTGAATTGATTAAAATTCTGAAACGAGCAAATCAGAGTGTCCCTGAAGATCTTCTAACAATGGCCGAGCA
ATACAAATTGCATAAACAAAAAAAGGACACAGGAAAAAGAAAATCTCAAGGAAAATCCAGGGAGTTTTATTGA

ORF - retro_amel_31 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.87 %
Parental protein coverage: 94.15 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalGQEARRGGRGGGWTNPSGLQQPVAPGLREPPLCFGLKNAWVGAVIEIGRGGSKIKDIQSTTNTKIQITKG
G...RRGG.G.GW..PSG.....A.G.REPPLCF.L.....G.VI..GRGGSKIKDIQ..TNTKIQI.KG
RetrocopyGGSSRRGGSGRGWSAPSGSMELRASGPREPPLCFRLRSNMIGVVI--GRGGSKIKDIQAMTNTKIQIIKG
ParentalHLEEAEVRIFGSKVMQAKAKTVIDNLVKKQEN-YSSKLRTDIGAFQPSVGRDVKTDNNVTEN-QPLIDWD
...EAEV.IFG...M.AKAK..ID.LVKKQE....S..R.D....Q.S.GR....DN......Q.LIDWD
RetrocopyD-SEAEVKIFGATDMKAKAKAAIDALVKKQERGHHSESRVDSATPQASAGREFRPDNTGGRQVQSLIDWD
ParentalQIREDALKWGKKKWEDLPPIKKNFYVESEATSTMSQVQVDNWRKENYNIMCDDLKENEKRSIPNPTCKFE
QIR.....W.K.KW..LPPIKKNFYVESEATS..SQVQVD.WRKEN....CDDLK..EKR.IPNPT..FE
RetrocopyQIRAEVVEWEKRKWAYLPPIKKNFYVESEATSSLSQVQVDMWRKENFDLICDDLKDGEKRPIPNPTRLFE
ParentalDAFQRYPEVMENIKKAGFQKPTPIQSQSWPIVLQGIDLIGVAQTGTGKTLSYLMPGFIHLDSQPVIRGQR
DAF..YPE..E.IK.AGFQKPTPIQSQ.WPI.LQGIDLIGVAQTGTGKTLSYLMPGFIHL..QP..R..R
RetrocopyDAFHPYPELIESIKRAGFQKPTPIQSQAWPIILQGIDLIGVAQTGTGKTLSYLMPGFIHLNNQPISREER
ParentalNGPGMLVLTPTRELALQVEAECSKYSYKGLKSVCIYGGGDRNGQIQDLKKGVDIIIATPGRLNDLQMNNF
NGPGMLVLTPTRELALQVEAECSKYSYKGLKS.CI.GG..R..QI.D..KG.DIIIATPGRLN.LQMNNF
RetrocopyNGPGMLVLTPTRELALQVEAECSKYSYKGLKSICIFGGRNREQQIRDITKGIDIIIATPGRLNYLQMNNF
ParentalVNLRSVTYLVLDEADKMLDMGFEPQIMKILLDVRPDRQTIMTSATWPYAVRRLAQSYLKEPMIVYVGTLD
VNL.S.TYLVLDEADKMLD.GFE.QIMKILLDVRPDRQT.M.SATW......L.QSYLKEPMIVYVGTLD
RetrocopyVNLQSITYLVLDEADKMLDLGFEHQIMKILLDVRPDRQTVMISATWSDTIHQLGQSYLKEPMIVYVGTLD
ParentalLMAVSTVKQNIIVTTEEEKCSHIQTFLESMSPKDKVIVFVSRKATADHLSSDLILRHVSVESLHGNREQS
L.AV.TV.QN.I.TT.EEK.S..Q.FL...SP.DKVIVFV.R...AD.LSSDL......V.SLHG.R.Q.
RetrocopyLVAVNTVTQNVIITTQEEKRSLLQEFLQNRSPQDKVIVFVRRRLVADDLSSDLSIQGITVQSLHGDRDQH
ParentalDRERALENFKTGKVRILIATDLASRGLDVLDITHVYNYDFPRNIEEYVHRVGRTGRAGRTGISITLLTRN
DRERALE.F..GKV..LIATDLASRGLDV.DITHVYNYDFPRNIEEYVHRVGRTGRAG.TG.SITL.T.N
RetrocopyDRERALEDFRSGKVKVLIATDLASRGLDVNDITHVYNYDFPRNIEEYVHRVGRTGRAGKTGLSITLMTQN
ParentalDWRVAGELINILERAQQSIPEDLVAMAKRYEANKLKKEMEEKLGKPQGKPQRFY
DW..A.ELI.IL.RA.QS.PEDL..MA..Y...K.KK.......K.QGK...FY
RetrocopyDWKIATELIKILKRANQSVPEDLLTMAEQYKLHKQKKDTGKR--KSQGKSREFY

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






RNA-Seq - click to see more details

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_amel_31 retrocopy.

TSS - click to see more details

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab - click to see more details

retro_amel_31 was not experimentally validated.

Retrocopy orthology:
Ailuropoda melanoleuca 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 15 parental genes, and 17 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG00000007851 1 retrocopy
retro_amel_31 ,
Callithrix jacchus ENSCJAG000000099662 retrocopies
retro_cjac_3639, retro_cjac_3640,
Equus caballus ENSECAG000000179711 retrocopy
retro_ecab_7,
Felis catus ENSFCAG000000316311 retrocopy
retro_fcat_583,
Homo sapiens ENSG000000800071 retrocopy
retro_hsap_76,
Gorilla gorilla ENSGGOG000000160921 retrocopy
retro_ggor_2889,
Microcebus murinus ENSMICG000000171451 retrocopy
retro_mmur_1603,
Monodelphis domestica ENSMODG000000185461 retrocopy
retro_mdom_14,
Mustela putorius furoENSMPUG000000043421 retrocopy
retro_mputfur_47,
Nomascus leucogenys ENSNLEG000000012091 retrocopy
retro_nleu_1094,
Oryctolagus cuniculus ENSOCUG000000063382 retrocopies
retro_ocun_1061, retro_ocun_227,
Otolemur garnettii ENSOGAG000000136601 retrocopy
retro_ogar_227,
Procavia capensis ENSPCAG000000059621 retrocopy
retro_pcap_151,
Pongo abelii ENSPPYG000000167741 retrocopy
retro_pabe_39,
Pan troglodytes ENSPTRG000000183441 retrocopy
retro_ptro_35,


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