RetrogeneDB ID:

retro_hsap_419

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:92000224..92001163(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000241318
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:WDR82
Ensembl ID:ENSG00000164091
Aliases:WDR82, MST107, MSTP107, PRO2730, PRO34047, SWD2, TMEM113, WDR82A
Description:WD repeat domain 82 [Source:HGNC Symbol;Acc:28826]


Retrocopy-Parental alignment summary:






>retro_hsap_419
ATGAAGCTGACCCACCGCATGCTGCTTCGAAGCTTCTGTATCGCCAACGTGTTCTGCGAAAACTCGGGACAAGATTAACT
GCTTCGATTTCAGCCCTAAAAGCGAGGTGATCACCTTGAGCAGCAACGACGACTCCATCGTGCTCTCTGACTGCCAGGAG
GGCAAACCAAAACCCTGTTCAGTAAGAAATACGGTGTGGCCTCATCAGATAAACTCCTGCGGCAAACACAGTTGTTTACA
GCTGTAACAAAATAGACGATACTATTCGTTACTTGTCCTTGCATGACAACAAATACATCAGATACTTTCCTGGACATAGC
AAAAGGGTGGTGGTCTTGTCCATGTCACCTGTGGATGACACTTTCATTTTTGGGTCTCTTGAATAAGACCATTCGACTCT
GGGATCTCCGGTCTCCCAACTGCCAGGGCCTCATGCACATAAAGGGGAATCCAGTTTGTTCTTTTGATCCAGAAGGGTGA
ATTTTTGCTGCTGGTGTCAACTCTGAAATGGTCAAACTTTATGACCTTCGTTCTTTTGATAAGGGGCCATTTGCTACCTT
TAAGATGCAGTATGATCGAACTTGTGAGTGGACAGCACTTAAAATCAGCAACGGTGGCAAGCTCATCCTCATTTCCACCA
ATGTCAGCTTCATTCGTCTCATTGGTGCATTCAAAGGAGTGGTGATACACACATTTGGCAGTTATGCCAACAGCGAAGCT
GTCACACTGGAGGCTTCATTTACTGCAGACTCTCAGTTTGTTATGATTGGTTCAGAGGATGGCAAGATCCATGTCTGGAA
TGAAGAGAGTGGTATAAAAGTAGCTGGGTTGGATGGTAAACACACAGGCCCAATTACCTGTTTGCAATTCAACCCCAAGT
TTGTGACTTTTGCCAGCGGGTGTACCAACATGGCCTTCTGGTTGCCCACCATTGATGAC

ORF - retro_hsap_419 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.28 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMKLTDSVL-RSFRVAKVFRENS-DKINCFDFSPNGETVISSSDDDSIVLYDCQE-GKPKRTLYSKKYGV-
MKLT...L.RSF..A.VF.ENS.DKINCFDFSP..E....SS.DDSIVL.DCQE.G..K.TL.SKKYGV.
RetrocopyMKLTHRMLLRSFCIANVFCENS>DKINCFDFSPKSEVITLSSNDDSIVLSDCQE<GQTK-TLFSKKYGV<
ParentalDLIRYTHAANTVVYSSNKIDDTIRYLSLHDNKYIRYFPGHSKRVVALSMSPVDDTFISGSLD-KTIRLWD
.LIR.T.AANTVVYS.NKIDDTIRYLSLHDNKYIRYFPGHSKRVV.LSMSPVDDTFI.GSL..KTIRLWD
RetrocopyGLIR*TPAANTVVYSCNKIDDTIRYLSLHDNKYIRYFPGHSKRVVVLSMSPVDDTFIFGSLE>KTIRLWD
ParentalLRSPNCQGLMHLQGKPVCSFDPEGLIFAAGVNSEMVKLYDLRSFDKGPFATFKMQYDRTCEWTGLKFSND
LRSPNCQGLMH..G.PVCSFDPEG.IFAAGVNSEMVKLYDLRSFDKGPFATFKMQYDRTCEWT.LK.SN.
RetrocopyLRSPNCQGLMHIKGNPVCSFDPEG*IFAAGVNSEMVKLYDLRSFDKGPFATFKMQYDRTCEWTALKISNG
ParentalGKLILISTNGSFIRLIDAFKGVVMHTFGGYANSKAVTLEASFTPDSQFIMIGSEDGKIHVWNGESGIKVA
GKLILISTN.SFIRLI.AFKGVV.HTFG.YANS.AVTLEASFT.DSQF.MIGSEDGKIHVWN.ESGIKVA
RetrocopyGKLILISTNVSFIRLIGAFKGVVIHTFGSYANSEAVTLEASFTADSQFVMIGSEDGKIHVWNEESGIKVA
ParentalVLDGKHTGPITCLQFNPKFMTFASACSNMAFWLPTIDD
.LDGKHTGPITCLQFNPKF.TFAS.C.NMAFWLPTIDD
RetrocopyGLDGKHTGPITCLQFNPKFVTFASGCTNMAFWLPTIDD

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
bodymap2_adipose 0 .02 RPM 160 .67 RPM
bodymap2_adrenal 0 .00 RPM 172 .93 RPM
bodymap2_brain 0 .00 RPM 165 .93 RPM
bodymap2_breast 0 .06 RPM 108 .21 RPM
bodymap2_colon 0 .15 RPM 153 .86 RPM
bodymap2_heart 0 .02 RPM 86 .16 RPM
bodymap2_kidney 0 .00 RPM 104 .71 RPM
bodymap2_liver 0 .00 RPM 42 .56 RPM
bodymap2_lung 0 .07 RPM 132 .14 RPM
bodymap2_lymph_node 0 .00 RPM 162 .69 RPM
bodymap2_ovary 0 .02 RPM 241 .85 RPM
bodymap2_prostate 0 .07 RPM 168 .40 RPM
bodymap2_skeletal_muscle 0 .00 RPM 143 .39 RPM
bodymap2_testis 0 .11 RPM 199 .47 RPM
bodymap2_thyroid 0 .00 RPM 190 .57 RPM
bodymap2_white_blood_cells 0 .00 RPM 412 .56 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_419 was not detected

EST - click to see more details

1 EST(s) were mapped to retro_hsap_419 retrocopy
EST ID Start End Identity Match Mis-match Score
W95028 92000522 92000645 96.8 119 4 115

TSS - click to see more details

No TSS is located nearby retro_hsap_419 retrocopy 5' end.

Lab - click to see more details

retro_hsap_419 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_419 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pongo abelii retro_pabe_300
Macaca mulatta retro_mmul_511
Callithrix jacchus retro_cjac_3022
Parental genes homology:
Parental genes homology involve 11 parental genes, and 20 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000007741 retrocopy
retro_chof_2299,
Callithrix jacchus ENSCJAG000000061141 retrocopy
retro_cjac_3022,
Homo sapiens ENSG00000164091 2 retrocopies
retro_hsap_2816, retro_hsap_419 ,
Loxodonta africana ENSLAFG000000283091 retrocopy
retro_lafr_639,
Macropus eugenii ENSMEUG000000092801 retrocopy
retro_meug_1207,
Macaca mulatta ENSMMUG000000082342 retrocopies
retro_mmul_339, retro_mmul_511,
Monodelphis domestica ENSMODG000000116144 retrocopies
retro_mdom_1259, retro_mdom_144, retro_mdom_219, retro_mdom_398,
Nomascus leucogenys ENSNLEG000000071042 retrocopies
retro_nleu_1016, retro_nleu_1195,
Otolemur garnettii ENSOGAG000000160321 retrocopy
retro_ogar_1314,
Pongo abelii ENSPPYG000000138122 retrocopies
retro_pabe_185, retro_pabe_300,
Rattus norvegicus ENSRNOG000000484413 retrocopies
retro_rnor_1003, retro_rnor_1109, retro_rnor_1152,

Expression level across human populations :
image/svg+xml GBR_HG00142 GBR_HG00099 GBR_HG00114 GBR_HG00143 GBR_HG00131 GBR_HG00137 GBR_HG00133 GBR_HG00119 GBR_HG00111 GBR_HG00134 FIN_HG00378 FIN_HG00338 FIN_HG00349 FIN_HG00375 FIN_HG00315 FIN_HG00277 FIN_HG00328 FIN_HG00321 FIN_HG00377 FIN_HG00183 TSI_NA20756 TSI_NA20538 TSI_NA20798 TSI_NA20532 TSI_NA20765 TSI_NA20518 TSI_NA20513 TSI_NA20512 TSI_NA20771 TSI_NA20786 YRI_NA19114 YRI_NA19099 YRI_NA18870 YRI_NA18907 YRI_NA19223 YRI_NA19214 YRI_NA18916 YRI_NA19093 YRI_NA19118 YRI_NA19213 Toscaniin Italia: Finnish inFinland: British in England and Scotland: Utah Residents (CEPH) with Northernand Western European Ancestry: Yoruba in Ibadan, Nigeria: CEU_NA12760 CEU_NA12827 CEU_NA12872 CEU_NA12751 CEU_NA12873 CEU_NA12400 CEU_NA11930 CEU_NA12004 CEU_NA11831 CEU_NA11843 No expression ( = 0 RPM ) > 0 RPM = 0.1 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .09 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .10 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .02 RPM
YRI_NA19223 0 .02 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).



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