RetrogeneDB ID:

retro_ptro_18

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:3:125782366..125783359(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPTRG00000030152
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:WDR5
Ensembl ID:ENSPTRG00000023653
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_18
ATGGCAACCAAGGACTCAAGAGACGCCAAAGCACAGTTGGCCCTCTCCTCATCGGCCAATCAGAGCAAGGAAGTGCCTGA
AAACCCAAACTATGCTCTCAAATGTACTCTTGTGGGACACACGGAAGCAGTGTCATCAGTTAAGTTTAGTCCTAATGGAG
AATGGCTAGCAAGTTCTTCTGCTGATAGGCTAATCATAATTTGGGGAGCATATGATGGAAAATATGAGAAAACACTCTAT
GGTCATAATTTGGAAATATCGGATGTTGCCTGGTCATCAGATTCCAGTCGTCTTGTTTCTGCCTCAGATGATAAAACTCT
AAAATTATGGGATGTGAGATCTGGAAAATGTTTGAAAACACTGAAGGGGCACAGTAATTATGTCTTTTGTTGTAACTTCA
ATCCGCCATCCAACCTTATAATCTCGGGATCTTTTGATGAGACTGTAAAAATATGGGAGGTGAAAACAGGAAAGTGTCTC
AAGACTTTGTCTGCTCATTCTGACCCAGTTTCTGCTGTTCATTTTAATTGTAGTGGGTCCTTGATAGTGTCAGGTAGCTA
TGATGGCCTCTGTAGAATCTGGGATGCTGCATCAGGTCAGTGTTTAAAAACGCTCGTTGATGACGATAACCCTCCTGTCT
CTTTTGTAAAGTTTTCTCCAAATGGTAAATACATTCTCACTGCAACTTTGGACAACACTCTTAAACTATGGGATTATAGC
AGAGGCAGGTGCCTGAAAACATACACTGGTCATAAGAATGAGAAATATTGCATATTTGCCAATTTTTCAGTTACTGGTGG
AAAGTGGATTGTGTCTGGTTCCGAGGATAACCTGGTTTACATTTGGAACCTTCAGACTAAAGAGATTGTGCAGAAATTAC
AAGGCCATACAGATGTTGTGATCTCAGCAGCTTGTCATCCTACAGAAAACCTCATCGCATCAGCAGCATTAGAAAATGAC
AAAACAATTAAACTGTGGATGAGTAACCACTAA

ORF - retro_ptro_18 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.15 %
Parental protein coverage: 97.31 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalETEAARAQPTPSSSATQSKPTPVKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGK
....A.AQ...SSSA.QSK..P..PNYALK.TL.GHT.AVSSVKFSPNGEWLASSSAD.LI.IWGAYDGK
RetrocopyDSRDAKAQLALSSSANQSKEVPENPNYALKCTLVGHTEAVSSVKFSPNGEWLASSSADRLIIIWGAYDGK
ParentalFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQSNLIVSGS
.EKT..GH.L.ISDVAWSSDS..LVSASDDKTLK.WDV.SGKCLKTLKGHSNYVFCCNFNP.SNLI.SGS
RetrocopyYEKTLYGHNLEISDVAWSSDSSRLVSASDDKTLKLWDVRSGKCLKTLKGHSNYVFCCNFNPPSNLIISGS
ParentalFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVS
FDE.V.IW.VKTGKCLKTL.AHSDPVSAVHFN..GSLIVS.SYDGLCRIWD.ASGQCLKTL.DDDNPPVS
RetrocopyFDETVKIWEVKTGKCLKTLSAHSDPVSAVHFNCSGSLIVSGSYDGLCRIWDAASGQCLKTLVDDDNPPVS
ParentalFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNL
FVKFSPNGKYIL.ATLDNTLKLWDYS.G.CLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNL
RetrocopyFVKFSPNGKYILTATLDNTLKLWDYSRGRCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNL
ParentalQTKEIVQKLQGHTDVVISTACHPTENIIASAALENDKTIKLWKSD
QTKEIVQKLQGHTDVVIS.ACHPTEN.IASAALENDKTIKLW.S.
RetrocopyQTKEIVQKLQGHTDVVISAACHPTENLIASAALENDKTIKLWMSN

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_prefrontal_cortex 0 .75 RPM 34 .02 RPM
SRP007412_cerebellum 1 .22 RPM 45 .78 RPM
SRP007412_heart 0 .67 RPM 12 .12 RPM
SRP007412_kidney 2 .28 RPM 39 .10 RPM
SRP007412_liver 1 .51 RPM 54 .63 RPM
SRP007412_testis 5 .16 RPM 93 .16 RPM

ChIP-Seq - click to see more details

Pan troglodytes was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ptro_18 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_18 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_18 has 10 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_11
Gorilla gorilla retro_ggor_171
Macaca mulatta retro_mmul_190
Callithrix jacchus retro_cjac_1
Mus musculus retro_mmus_132
Rattus norvegicus retro_rnor_258
Bos taurus retro_btau_299
Sus scrofa retro_sscr_1
Canis familiaris retro_cfam_128
Equus caballus retro_ecab_82
Parental genes homology:
Parental genes homology involve 27 parental genes, and 29 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000111791 retrocopy
retro_amel_29,
Bos taurus ENSBTAG000000470311 retrocopy
retro_btau_299,
Canis familiaris ENSCAFG000000198301 retrocopy
retro_cfam_128,
Callithrix jacchus ENSCJAG000000101231 retrocopy
retro_cjac_1,
Cavia porcellus ENSCPOG000000147901 retrocopy
retro_cpor_12,
Dipodomys ordii ENSDORG000000150101 retrocopy
retro_dord_7,
Equus caballus ENSECAG000000173891 retrocopy
retro_ecab_82,
Echinops telfairi ENSETEG000000157311 retrocopy
retro_etel_15,
Felis catus ENSFCAG000000057121 retrocopy
retro_fcat_119,
Homo sapiens ENSG000001963631 retrocopy
retro_hsap_11,
Gorilla gorilla ENSGGOG000000049972 retrocopies
retro_ggor_171, retro_ggor_2023,
Loxodonta africana ENSLAFG000000111921 retrocopy
retro_lafr_55,
Microcebus murinus ENSMICG000000080851 retrocopy
retro_mmur_34,
Myotis lucifugus ENSMLUG000000022361 retrocopy
retro_mluc_11,
Macaca mulatta ENSMMUG000000141591 retrocopy
retro_mmul_190,
Mustela putorius furoENSMPUG000000121841 retrocopy
retro_mputfur_2,
Mus musculus ENSMUSG000000269171 retrocopy
retro_mmus_132,
Otolemur garnettii ENSOGAG000000089601 retrocopy
retro_ogar_86,
Procavia capensis ENSPCAG000000134761 retrocopy
retro_pcap_43,
Pan troglodytes ENSPTRG000000085511 retrocopy
retro_ptro_1569,
Pan troglodytes ENSPTRG000000208531 retrocopy
retro_ptro_344,
Pan troglodytes ENSPTRG00000023653 2 retrocopies
retro_ptro_18 , retro_ptro_1975,
Pteropus vampyrus ENSPVAG000000016661 retrocopy
retro_pvam_112,
Rattus norvegicus ENSRNOG000000082121 retrocopy
retro_rnor_258,
Sus scrofa ENSSSCG000000249121 retrocopy
retro_sscr_1,
Ictidomys tridecemlineatus ENSSTOG000000158991 retrocopy
retro_itri_117,
Drosophila melanogaster FBgn00400661 retrocopy
retro_dmel_69,


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