RetrogeneDB ID:

retro_hsap_2317

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:131935210..131936519(-)
Located in intron of:ENSG00000115762
Retrocopy
information
Ensembl ID:ENSG00000230450
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:NEK2
Ensembl ID:ENSG00000117650
Aliases:NEK2, HsPK21, NEK2A, NLK1, RP67
Description:NIMA-related kinase 2 [Source:HGNC Symbol;Acc:7745]


Retrocopy-Parental alignment summary:






>retro_hsap_2317
ATGCCGTCCCGGGCTGAGAACTATGAAGTGTTGTACACCATTGGCACAGGCTCCTGTGGCCGCTGCCAGAAGATCCAGAG
GAAGAGTGACGGCAAGATACTAGTTTGGAAAGAACTTCATTATGGCTCCATGACAGAAGCTGAGAAACAGATGCTTGTTT
CTGAAGTGAATTTGCTTTGTGAACTGAAAAATCCAAACATCGTTCATTACTATGATCGTATTATTGACCGGACCAACACA
ACACTGTACATTGTAATGGAATATTGTGAAGAAGGAGACCTGGCTAGTGTAATTACAAAGGGAACCAAGGAAAGGCAATA
CTTAGATGAAGAGTTTGTTCTTCGAGTGACGACTCAGTTGACTCTGGCCCTGAAGTAATGCCACAGACGAAGTGATGGTG
ATCATACTGTAGTGCGTCGGGATCTGAAACCAGCCAGTGTTTTCCTGGATGGCAAGCAAAACGTCAAGCTTGGAGATTTG
GGGCTAGCCAGAATATTAAACCACGACACGAGTTTTGCAAAAACATTTGTTGGCACACCTTATTACATGTCTCCTGAACA
AACGAATCACATGTCCTACAATGAGAAACCAGATATCTGGTCATTGGGCCGTTTGCTGTATGAGTTAGGTGCATTAATGC
CTCCATTTACAGCTTTTAGCCAGAAAGAACTTGCTGGGAAAATCAGAGAAGGCAAATTCAGGCAAATTCTATACCGTGAC
TCTGACGAATTGAATGAAATTATTATGAGGATGTTAAAGGATTACCATCGACCTTCTGTTGAAGAAATTCTCGAGAACCC
TTTAATAGCAGATTTGGTTGCAGAAGAACGAAGAAGAAATCTTGAGAGAAGAGGGCGACAATTAGGAGAGCCAGAAAAAT
TGCAGGATTCCAGCCCTGTATTGAGTGAGCTGAAACTAAAGGAAATTCAGTTAGAGGAGCGAGAGCGAGCTCTCAAAGCA
AGAGAAGAAAGATTGGAGCAGAAAGAACAGGAGTTTTGTGTCCGTGAGAGACTAGCAGAGGACAGACTGGCTAGAGCAGA
AAATCTGTTGAAGAATTACAGCTTGCTAAAGAAGTTCCTGTCTCTGGCAAGTAGTCCAGAACTTCTTAGTCTTCCATCCT
CAGTAATTAAGAAGAAAGGTCATTTCAGTGGGGAAAGTAAAGAGAATGTCATGAGGAGTGAGAATTCTGAGAGTCAGCTC
ACATCTAAGTCCAAGTGCAAGGACCTGAAGGTCCTTGCTTCATGCTTCATGCTGCCCAGCTGCGGGCTCAAGCCCTGTCA
GATATTGAGAAAAATTATCAACTAAAAAG

ORF - retro_hsap_2317 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.62 %
Parental protein coverage: 98.88 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMPSRAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAEKQMLVSEVNLLRELKHPNIVRY
MPSRAE.YEVLYTIGTGS.GRCQKI.RKSDGKILVWKEL.YGSMTEAEKQMLVSEVNLL.ELK.PNIV.Y
RetrocopyMPSRAENYEVLYTIGTGSCGRCQKIQRKSDGKILVWKELHYGSMTEAEKQMLVSEVNLLCELKNPNIVHY
ParentalYDRIIDRTNTTLYIVMEYCEGGDLASVITKGTKERQYLDEEFVLRVMTQLTLALKECHRRSDGGHTVLHR
YDRIIDRTNTTLYIVMEYCE.GDLASVITKGTKERQYLDEEFVLRV.TQLTLALK.CHRRSDG.HTV..R
RetrocopyYDRIIDRTNTTLYIVMEYCEEGDLASVITKGTKERQYLDEEFVLRVTTQLTLALK*CHRRSDGDHTVVRR
ParentalDLKPANVFLDGKQNVKLGDFGLARILNHDTSFAKTFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELC
DLKPA.VFLDGKQNVKLGD.GLARILNHDTSFAKTFVGTPYYMSPEQ.N.MSYNEK.DIWSLG.LLYEL.
RetrocopyDLKPASVFLDGKQNVKLGDLGLARILNHDTSFAKTFVGTPYYMSPEQTNHMSYNEKPDIWSLGRLLYELG
ParentalALMPPFTAFSQKELAGKIREGKFRRIPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLIADLVADEQR
ALMPPFTAFSQKELAGKIREGKFR.I.YR.SDELNEII.RM..LKDYHRPSVEEILENPLIADLVA.E.R
RetrocopyALMPPFTAFSQKELAGKIREGKFRQILYRDSDELNEIIMRM--LKDYHRPSVEEILENPLIADLVAEERR
ParentalRNLERRGRQLGEPEKSQDSSPVLSELKLKEIQLQERERALKAREERLEQKEQELCVRERLAEDKLARAEN
RNLERRGRQLGEPEK.QDSSPVLSELKLKEIQL.ERERALKAREERLEQKEQE.CVRERLAED.LARAEN
RetrocopyRNLERRGRQLGEPEKLQDSSPVLSELKLKEIQLEERERALKAREERLEQKEQEFCVRERLAEDRLARAEN
ParentalLLKNYSLLKERKFLSLASNPELLNLPSSVIKKKVHFSGESKENIMRSENSESQLTSKSKCKDLK-KRLHA
LLKNYSLLK..KFLSLAS.PELL.LPSSVIKKK.HFSGESKEN.MRSENSESQLTSKSKCKDLK...LHA
RetrocopyLLKNYSLLK--KFLSLASSPELLSLPSSVIKKKGHFSGESKENVMRSENSESQLTSKSKCKDLK>SLLHA
ParentalAQLRAQALSDIEKNYQLKSRQ
....A...S.......L....
RetrocopySCCPAAGSSPVRY*EKLSTKK

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 .62 RPM
bodymap2_adrenal 0 .00 RPM 0 .59 RPM
bodymap2_brain 0 .00 RPM 0 .49 RPM
bodymap2_breast 0 .00 RPM 0 .70 RPM
bodymap2_colon 0 .00 RPM 1 .74 RPM
bodymap2_heart 0 .00 RPM 0 .04 RPM
bodymap2_kidney 0 .00 RPM 0 .29 RPM
bodymap2_liver 0 .00 RPM 0 .11 RPM
bodymap2_lung 0 .00 RPM 2 .04 RPM
bodymap2_lymph_node 0 .00 RPM 1 .55 RPM
bodymap2_ovary 0 .00 RPM 0 .79 RPM
bodymap2_prostate 0 .00 RPM 0 .16 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .00 RPM
bodymap2_testis 1 .43 RPM 116 .15 RPM
bodymap2_thyroid 0 .00 RPM 0 .75 RPM
bodymap2_white_blood_cells 0 .00 RPM 0 .49 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2317 was not detected

EST - click to see more details

1 EST(s) were mapped to retro_hsap_2317 retrocopy
EST ID Start End Identity Match Mis-match Score
BF174235 131936096 131936318 97.8 220 2 217

TSS - click to see more details

No TSS is located nearby retro_hsap_2317 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2317 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2317 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1691
Parental genes homology:
Parental genes homology involve 5 parental genes, and 9 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000117650 4 retrocopies
retro_hsap_1301, retro_hsap_1385, retro_hsap_2317 , retro_hsap_2538,
Gorilla gorilla ENSGGOG000000054391 retrocopy
retro_ggor_1018,
Myotis lucifugus ENSMLUG000000112811 retrocopy
retro_mluc_22,
Pan troglodytes ENSPTRG000000019532 retrocopies
retro_ptro_1691, retro_ptro_890,
Rattus norvegicus ENSRNOG000000044871 retrocopy
retro_rnor_2552,

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 = 0.06 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 .00 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 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .06 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 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 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .03 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 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 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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