RetrogeneDB ID:

retro_pvam_112

Retrocopy
location
Organism:Megabat (Pteropus vampyrus)
Coordinates:GeneScaffold_143:182964..183902(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPVAG00000012710
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:WDR5
Ensembl ID:ENSPVAG00000001666
Aliases:None
Description:WD repeat domain 5 [Source:HGNC Symbol;Acc:12757]


Retrocopy-Parental alignment summary:






>retro_pvam_112
TCATCAGCCAATGGAAGCAAGCAAGCATCTGAAAACCCAAACTATACTCTCAAATTTACTCTGGTGGGACATACGGAAGC
AGTGTCATCAGTTAAGTTTAGTCCTAATGGAGAATGGCTAGCAAGTCTTCTGCTGATAAAGTAATTATAATTTGGGGAGC
CTATGATGGAAAATATGAGAAAACACTTTATGGTCACAATTTGGAAATATCGGATGTTGATTGGTCATCAGATTCCAGTC
GTCTTGTTTCTGCCTCAGATGATAAAACTCTAAAGATTTGGGATGTGAGGTCTGGAAAATGTCTGAAAACGCTGAAAGGG
CACAGTAATTATGTTTTCTGCTGTAATTTCAATCCACTATCTAACCTTATAATTTCAGGCTCTTTTGATGAGAGTGTGAA
AATATGGGAGGTGAAAACGGGAAAGTGCCTCAAGACTCTATCTGCTCATTCTGATCCAGTTTCTGCTGTTCATTTTAATT
GTAGTGGGTCCTTGATAGTATCAGGTAGCTATGATGGTGTCTGTAGAATCTGGGATGCTGCATCAGGTCAGTGTTTAAAA
GCACTTGTTGATGATGATAACCCTCCTGTATCTTTTGTAAAATTTTCTCCAAATGGTAAATATATTCTGATGGCGACTTT
GGACAATACTCTTAAATTATGGGATTATAGCAGAGGCAGATGCCTGAAGACATACACTGGCCATAAGAATGAGAAATACT
GCATATTTGCCAATTTTTCGGTTACTGGTGGAAAGTGGATTGTGTCTGGTTCAGAGGATAACCTGATTTACATTTGGAAC
CTTCAGACAAAAGAGATTGTACAGAAATTACAAGGGCATACAGATGTTGTAATCTCAGCAGCTTGTCATCCTACAGAAAA
CATCATTGCATCAGCAGCATTAGAAAATGACAAAACAATTAAACTGTGGATGAGTAAC

ORF - retro_pvam_112 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.62 %
Parental protein coverage: 93.71 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalSSATQSKPAPVKPNYALKFTLAGHTKAVSSVKFSPNGEWLAS-SSADKLIKIWGAYDGKFEKTISGHKLG
SSA..SK.A...PNY.LKFTL.GHT.AVSSVKFSPNGEWLAS.SSADK.I.IWGAYDGK.EKT..GH.L.
RetrocopySSANGSKQASENPNYTLKFTLVGHTEAVSSVKFSPNGEWLAS<SSADKVIIIWGAYDGKYEKTLYGHNLE
ParentalISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQSNLIVSGSFDESVRIWDVK
ISDV.WSSDS..LVSASDDKTLKIWDV.SGKCLKTLKGHSNYVFCCNFNP.SNLI.SGSFDESV.IW.VK
RetrocopyISDVDWSSDSSRLVSASDDKTLKIWDVRSGKCLKTLKGHSNYVFCCNFNPLSNLIISGSFDESVKIWEVK
ParentalTGKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYI
TGKCLKTL.AHSDPVSAVHFN..GSLIVS.SYDG.CRIWD.ASGQCLK.L.DDDNPPVSFVKFSPNGKYI
RetrocopyTGKCLKTLSAHSDPVSAVHFNCSGSLIVSGSYDGVCRIWDAASGQCLKALVDDDNPPVSFVKFSPNGKYI
ParentalLAATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDSLVYIWNLQTKEVVQKLQG
L.ATLDNTLKLWDYS.G.CLKTYTGHKNEKYCIFANFSVTGGKWIVSGSED.L.YIWNLQTKE.VQKLQG
RetrocopyLMATLDNTLKLWDYSRGRCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLIYIWNLQTKEIVQKLQG
ParentalHTDVVISTACHPTENIIASAALENDKTIKLWKSD
HTDVVIS.ACHPTENIIASAALENDKTIKLW.S.
RetrocopyHTDVVISAACHPTENIIASAALENDKTIKLWMSN

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






RNA-Seq - click to see more details

Pteropus vampyrus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Pteropus vampyrus was not studied using ChIP-Seq data.

EST - click to see more details

Pteropus vampyrus was not studied using EST data.

TSS - click to see more details

Pteropus vampyrus was not studied using FANTOM5 data.

Lab - click to see more details

retro_pvam_112 was not experimentally validated.

Retrocopy orthology:
Pteropus vampyrus 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 26 parental genes, and 28 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,
Nomascus leucogenys ENSNLEG000000134721 retrocopy
retro_nleu_63,
Otolemur garnettii ENSOGAG000000089601 retrocopy
retro_ogar_86,
Procavia capensis ENSPCAG000000134761 retrocopy
retro_pcap_43,
Pan troglodytes ENSPTRG000000236532 retrocopies
retro_ptro_18, retro_ptro_1975,
Pteropus vampyrus ENSPVAG00000001666 1 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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