RetrogeneDB ID:

retro_hsap_89

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:13336985..13338053(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000123594
Aliases:ATXN3L, MJDL
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:ATXN3
Ensembl ID:ENSG00000066427
Aliases:ATXN3, AT3, ATX3, JOS, MJD, MJD1, SCA3
Description:ataxin 3 [Source:HGNC Symbol;Acc:7106]


Retrocopy-Parental alignment summary:






>retro_hsap_89
ATGGATTTCATCTTTCATGAGAAACAGGAAGGTTTCCTGTGTGCTCAGCACTGTCTGAACAATCTATTGCAAGGAGAATA
TTTTAGCCCTGTGGAATTAGCCTCAATTGCACATCAGCTAGATGAAGAAGAGAGGATGAGAATGGCAGAAGGAGGAGTCA
CCAGTGAAGAGTATCTTGCATTTTTACAGCAGCCTTCAGAAAACATGGATGATACCGGTTTCTTCTCCATTCAGGTAATA
AGCAATGCCTTGAAGTTCTGGGGTTTAGAGATCATCCATTTCAATAATCCTGAATATCAGAAGCTCGGCATTGATCCTAT
AAATGAAAGATCTTTTATATGTAATTATAAACAACACTGGTTTACTATTAGAAAATTTGGAAAACACTGGTTTAACTTGA
ATTCTCTCTTGGCGGGTCCAGAATTAATATCAGATACATGCCTTGCAAATTTCTTGGCTCGATTACAACAACAAGCATAT
TCTGTATTTGTTGTCAAGGGTGATCTGCCAGACTGTGAAGCTGACCAACTCCTGCAGATCATCAGTGTCGAAGAGATGGA
TACACCAAAACTTAATGGAAAAAAATTAGTAAAACAAAAAGAGCATAGAGTCTATAAAACAGTCCTTGAAAAAGTATCAG
AAGAAAGTGATGAGTCTGGAACATCAGACCAAGATGAGGAGGATTTTCAGAGGGCCCTTGAACTAAGCCGCCAAGAAACC
AATAGAGAAGATGAACATCTCCGCAGTACTATTGAGTTAAGCATGCAAGGTAGTTCCGGAAACACATCGCAAGATCTTCC
AAAGACATCATGTGTAACTCCTGCTTCAGAACAGCCGAAGAAAATAAAAGAAGACTATTTTGAAAAGCATCAGCAGGAAC
AGAAGCAGCAGCAACAACAGTCAGATCTGCCGGGCCACAGTTCATACCTACACGAAAGGCCAACAACAAGTTCGAGAGCA
ATTGAGAGTGATCTCAGTGATGACATCAGTGAAGGCACAGTACAGGCCGCTGTCGACACCATTTTAGAAATTATGAGAAA
GAATTTGAAAATCAAAGGGGAAAAATAA

ORF - retro_hsap_89 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.81 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMESIFHEKQEGSLCAQHCLNNLLQGEYFSPVELSSIAHQLDEEERMRMAEGGVTSEDYRTFLQQPSGNMD
M..IFHEKQEG.LCAQHCLNNLLQGEYFSPVEL.SIAHQLDEEERMRMAEGGVTSE.Y..FLQQPS.NMD
RetrocopyMDFIFHEKQEGFLCAQHCLNNLLQGEYFSPVELASIAHQLDEEERMRMAEGGVTSEEYLAFLQQPSENMD
ParentalDSGFFSIQVISNALKVWGLELILFNSPEYQRLRIDPINERSFICNYKEHWFTVRKLGKQWFNLNSLLTGP
D.GFFSIQVISNALK.WGLE.I.FN.PEYQ.L.IDPINERSFICNYK.HWFT.RK.GK.WFNLNSLL.GP
RetrocopyDTGFFSIQVISNALKFWGLEIIHFNNPEYQKLGIDPINERSFICNYKQHWFTIRKFGKHWFNLNSLLAGP
ParentalELISDTYLALFLAQLQQEGYSIFVVKGDLPDCEADQLLQMIRVQQMHRPKLIGEELAQLKEQRVHKTDLE
ELISDT.LA.FLA.LQQ..YS.FVVKGDLPDCEADQLLQ.I.V..M..PKL.G..L...KE.RV.KT.LE
RetrocopyELISDTCLANFLARLQQQAYSVFVVKGDLPDCEADQLLQIISVEEMDTPKLNGKKLVKQKEHRVYKTVLE
ParentalRVLEANDGSGMLDEDEEDLQRALALSRQEIDMEDEEADLRRAIQLSMQGSSRNISQDMTQTSGTNLTSEE
.V.E..D.SG..D.DEED.QRAL.LSRQE...EDE...LR..I.LSMQGSS.N.SQD...TS.....SE.
RetrocopyKVSEESDESGTSDQDEEDFQRALELSRQETNREDEH--LRSTIELSMQGSSGNTSQDLPKTSCVTPASEQ
ParentalLRKRREAYFEKQQQKQQQQQQQQQQGDLSGQSSHPCERPATSSGALGSDLGDAMSEEDMLQAAVTMSLET
..K..E.YFEK.QQ.Q.QQQQQ....DL.G.SS...ERP.TSS.A..SDL.D..S.E...QAAV...LE.
RetrocopyPKKIKEDYFEKHQQEQKQQQQQ---SDLPGHSSYLHERPTTSSRAIESDLSDDIS-EGTVQAAVDTILEI
ParentalVRNDLKTEGKK
.R..LK..G.K
RetrocopyMRKNLKIKGEK

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 .00 RPM 18 .33 RPM
bodymap2_adrenal 0 .00 RPM 28 .94 RPM
bodymap2_brain 0 .00 RPM 16 .71 RPM
bodymap2_breast 0 .00 RPM 39 .61 RPM
bodymap2_colon 0 .00 RPM 21 .98 RPM
bodymap2_heart 0 .00 RPM 13 .00 RPM
bodymap2_kidney 0 .00 RPM 21 .61 RPM
bodymap2_liver 0 .00 RPM 6 .67 RPM
bodymap2_lung 0 .00 RPM 17 .95 RPM
bodymap2_lymph_node 0 .00 RPM 29 .16 RPM
bodymap2_ovary 0 .00 RPM 27 .22 RPM
bodymap2_prostate 0 .00 RPM 28 .23 RPM
bodymap2_skeletal_muscle 0 .00 RPM 5 .35 RPM
bodymap2_testis 2 .85 RPM 35 .63 RPM
bodymap2_thyroid 0 .00 RPM 20 .34 RPM
bodymap2_white_blood_cells 0 .00 RPM 42 .25 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_89 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_89 retrocopy.

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_1973011826 libraries2 libraries1 library0 libraries0 libraries

The graphical summary, for retro_hsap_89 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_89 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_89 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 10 parental genes, and 15 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000057862 retrocopies
retro_btau_1652, retro_btau_330,
Choloepus hoffmanni ENSCHOG000000053021 retrocopy
retro_chof_2238,
Callithrix jacchus ENSCJAG000000180252 retrocopies
retro_cjac_1724, retro_cjac_375,
Cavia porcellus ENSCPOG000000108871 retrocopy
retro_cpor_1460,
Homo sapiens ENSG00000066427 1 retrocopy
retro_hsap_89 ,
Macaca mulatta ENSMMUG000000207511 retrocopy
retro_mmul_298,
Monodelphis domestica ENSMODG000000020062 retrocopies
retro_mdom_1498, retro_mdom_1573,
Nomascus leucogenys ENSNLEG000000171261 retrocopy
retro_nleu_66,
Pongo abelii ENSPPYG000000060751 retrocopy
retro_pabe_9,
Tupaia belangeri ENSTBEG000000080993 retrocopies
retro_tbel_102, retro_tbel_2635, retro_tbel_3925,

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 = 0.07 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .05 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 .06 RPM
FIN_HG00321 0 .06 RPM
FIN_HG00328 0 .05 RPM
FIN_HG00338 0 .04 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 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 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 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 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .04 RPM
YRI_NA19093 0 .05 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .06 RPM
YRI_NA19213 0 .07 RPM
YRI_NA19214 0 .02 RPM
YRI_NA19223 0 .00 RPM

Indel association:

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



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