RetrogeneDB ID:

retro_hsap_673

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:10:51785414..51786651(-)
Located in intron of:ENSG00000235618
Retrocopy
information
Ensembl ID:ENSG00000226631
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SLC9A3
Ensembl ID:ENSG00000066230
Aliases:SLC9A3, NHE3
Description:solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3 [Source:HGNC Symbol;Acc:11073]


Retrocopy-Parental alignment summary:






>retro_hsap_673
CTTCAGGGAGTTGCTACTGAATGACTGTACAATGTGTTTCAATCTTTTGTGACACTGGATGATGAGAACATGATCAGCGT
GGACCATGCCAAAAGTGTAGTGTCCTTTGTGGTGAGCCTGGGGGGCATGACTGTGGGGTGGTCTTTGCCTTCCTGCTGTC
ACTGGTGACCCACTTCACCAAGCATGTGCACATCATCTAGCCTGGTTTTGTGTTAGTCATCTCCTACCCGTCCATAGGAC
GTCTGAGAAGCTGTTGCTGTTGGCCATCCTGGCCATTATCTTCTGTGGCATCTGCTGTCATAAGTACATGAAGGCCAACA
TCTTGGAGCAGTCGGCCAACACCATGCACTACACCGTGAAGATGCTGGCCAGTGGTGTCAATACAATCTTCATATCCCTG
GGCATCTCGGTCATGAACCTGCTCATCTGGACGTGGAACATGGCCTTCATCCTCCTGCACTGGCCTACACCTTCATGTAC
CGAGCCATGGTGTCATCCAGTCCTGACTCCTGTAGTGCTATTGGATGATGCAGCTGGAGATCATAGACCAGGTGGTCATG
TCCTATAGAGGCCTGCATGGGGCCATGGCCTTCATCCTGGTCATGCTTCCGGACAGAAACAAGGTCAAGGAGAAGAACCT
GTTTGTCAGCACCACCGTCATCATCTTCTTCACAGTCATTTTCCAGGGGCTGACCATCAAGTCCCTGGTGCAGTGGCTGA
AGGTGAAGAGGAGTGAGCACCAGGAGCCCAAGCTCCATGAGAAGCTGCACCACCATGCTTTCAACCACATCCTCTTGGCC
ATCAAGGACATATCCCGGCATATCAGGCACAACTATCTCAGAGAGATGTGGTCCCACTTTGACAGGAAGTTCCTCAGTGG
GGTTCTCATGAGAATGCTGGCCCAGAAGTCTCCATATGGGATCCTCAATGTCTTCCATGAGCTGAACCTGAAGGATGCCA
TCAGCTAAGCCACCAAAGGAGAGTGCCTAAGGTCCGTGGCCTTCATCAGCTCCCCAAGTACTGATAACGTCGTCAACATG
GACTTCACGGCACGATTGTCCACCATGGTGGCCTCTGTCTCCTACCTTCTGAGGGAGAACATCAGTGCCGTCTGTCTGGA
CGTTCAGTCCCTGGAGCAGTGTGGCAGAGCATTCCGTATGGGGAGGACCCCGTCACGCACCACACGCTGCAGCAGTACCT
GTGCAAGCCGGGGAAGGAGTACATGCATCGCTACAGC

ORF - retro_hsap_673 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.79 %
Parental protein coverage: 50.12 %
Number of stop codons detected: 5
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalLNDAVTVVLYNVFESFVALGGDNVTGVDCVKGIVSFFVVSLGGTLVG-VVFAFLLSLVTRFTKHVRIIEP
L....T..LYNVF.SFV.L...N...VD..K..VSF.VVSLGG..VG.VVFAFLLSLVT.FTKHV.II.P
RetrocopyLQGVATE*LYNVFQSFVTLDDENMISVDHAKSVVSF-VVSLGGMTVG<VVFAFLLSLVTHFTKHVHII*P
ParentalGFVFIISYLS-YLTSEMLSLSAILAITFCGICCQKYVKANISEQSATTVRYTMKMLASSAETIIFMFLGI
GFV..ISY.S...TSE.L.L.AILAI.FCGICC.KY.KANI.EQSA.T..YT.KMLAS...T.IF..LGI
RetrocopyGFVLVISYPS<HRTSEKLLLLAILAIIFCGICCHKYMKANILEQSANTMHYTVKMLASGVNT-IFISLGI
ParentalSAVNPFIWTWNTAFVLL-TLVFISVYRAI-GVVLQTWLLNRYRMVQLEPIDQVVLSYGGLRGAVAFALVV
S..N..IWTWN.AF.LL..L.....YRA..GV..Q..LL..Y.M.QLE.IDQVV.SY.GL.GA.AF.LV.
RetrocopySVMNLLIWTWNMAFILL<ALAYTFMYRAM<GVI-QS*LL*CYWMMQLEIIDQVVMSYRGLHGAMAFILVM
ParentalLLDGDKVKEKNLFVSTTIIVVFFTVIFQGLTIKPLVQWLKVKRSEHREPRLNEKLHGRAFDHILSAIEDI
L.D..KVKEKNLFVSTT.I..FFTVIFQGLTIK.LVQWLKVKRSEH.EP.L.EKLH..AF.HIL.AI.DI
RetrocopyLPDRNKVKEKNLFVSTTVI-IFFTVIFQGLTIKSLVQWLKVKRSEHQEPKLHEKLHHHAFNHILLAIKDI
ParentalSGQIGHNYLRDKWSHFDRKFLSRVLMRRSAQKSRDRILNVFHELNLKDAISYVAEGERRGSLAFIRSPST
S..I.HNYLR..WSHFDRKFLS.VLMR..AQKS...ILNVFHELNLKDAIS....GE...S.AFI.SPST
RetrocopySRHIRHNYLREMWSHFDRKFLSGVLMRMLAQKSPYGILNVFHELNLKDAIS*ATKGECLRSVAFISSPST
ParentalDNVVNVDFTPRSSTVEASVSYLLRENVSAVCLDMQSLEQRRR-SIRDAEDMVTHHTLQQYLYKPRQEYKH
DNVVN.DFT.R.ST..ASVSYLLREN.SAVCLD.QSLEQ..R.SI...ED.VTHHTLQQYL.KP..EY.H
RetrocopyDNVVNMDFTARLSTMVASVSYLLRENISAVCLDVQSLEQCGR<SIPYGEDPVTHHTLQQYLCKPGKEYMH
ParentalLYS
.YS
RetrocopyRYS

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 0 .28 RPM
bodymap2_adrenal 0 .00 RPM 0 .43 RPM
bodymap2_brain 0 .00 RPM 0 .23 RPM
bodymap2_breast 0 .00 RPM 0 .19 RPM
bodymap2_colon 0 .00 RPM 0 .21 RPM
bodymap2_heart 0 .02 RPM 0 .15 RPM
bodymap2_kidney 0 .00 RPM 25 .89 RPM
bodymap2_liver 0 .00 RPM 0 .08 RPM
bodymap2_lung 0 .00 RPM 0 .39 RPM
bodymap2_lymph_node 0 .00 RPM 0 .64 RPM
bodymap2_ovary 0 .00 RPM 0 .71 RPM
bodymap2_prostate 0 .00 RPM 0 .43 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .00 RPM
bodymap2_testis 0 .00 RPM 0 .72 RPM
bodymap2_thyroid 0 .00 RPM 0 .51 RPM
bodymap2_white_blood_cells 0 .00 RPM 0 .00 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_673 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_673 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_673 retrocopy 5' end.

Lab - click to see more details

retro_hsap_673 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_673 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000066230 2 retrocopies
retro_hsap_2546, retro_hsap_673 ,

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 .07 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .06 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .04 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .06 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 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 .03 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 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 .00 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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