RetrogeneDB ID:

retro_hsap_2320

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:132200216..132202438(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000217950
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:NOC2L
Ensembl ID:ENSG00000188976
Aliases:NOC2L, NET15, NET7, NIR
Description:nucleolar complex associated 2 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:24517]


Retrocopy-Parental alignment summary:






>retro_hsap_2320
ATGGCAGGAGCGCGGCGCCGCAGGAGGCGCCTGGCGGAGCTGACGGTGGACGAGTTCCTAGCTTCGGGCTTTGACTCTAA
GTCCGAATACTCTCCAGAAGCGGAGACGCGGGAGGCACGCGAGGCTGCCCGGAGTCCGGATGAGCCGGGCGGGAGCTCCT
TGGCCAGCCGGCGTAAAGGCTGTGCCTCTGAGCACAAAGATCAGCTCTCTCGGCTGAAGGACAGAGACCCCGAGTTCTAC
AAGTTCCTGCAGGAGAATGACCAGAGCCAGCTAAACTTCAGTGACTCAGCTCTGAGGAGGAAGAGGAGCCGTTCAACTCC
CTGCCAGATGTGCTGGAGGAAGCCAGTGAGGATGAGGATGGAGCGGAGGAGGGGGAAGATGGGGACAGAGTCCCCAGAGG
GCTGAAGGGGAAGAATTGTGTTCCTGTGACCCTCGCCATGGTTGAGAGATGGAAGCAGGCAGCAAAGCAACACCTCACTC
CAAAGCTGTTCCATGAAGTGGTACAGGCATTCGGAGCAGCTGTGGCCACCACCCAAGGGGACCAGGAAAGTGCTGAGGCC
AACAAATTCCAGGTCAGGGACAGTGCTGTGTTCAATGCTCTGGTCACCTTCTGCATCAGAGACCTTATTGGCTGTCTCCA
GAAGCTGCTGTTTGGAAAGGCGGCAAAGGACAGCAGCAGGATGCTGCAGCCGTCCAGCAGCCGGCTCTGGGGGAAGCTCC
ATGTGGACATCAAGGCGTACCTGGGCTCGGTCATACAGCTAGTGTCCTGTGTGGCAGAGACGATGGTGTTGGCGGCCGTG
CTGTGGCACATCAGCGTGCTAGTGCCCTGCTTCCTGACCTTCCCCAAGCAGTGCCGTATGCTGCTTAAGAGAATGGTGGT
CGTATGGAGCACAGGGGAGGAGTCCCTGCGGGTGCTGGCTTTCCTGGTCCTCAGCAGAGTCTGCCGGCACAAGAAGGACA
CTTTCCTTGGCCCCGTCCTCAAGCAAATGTACATCATGTATGTGAGGAACTGCAAGTTCACCTCGCCTGGTGCCCTCCCC
TTCATCAGTTTCATGCAGCGGACCCTGAGGGAGCTGCTGGCCTTGGAGCCGGGTGTGGCCTACCAGCACGCCTTCCTCTA
CATCCGCCAGCTCGCCATACACCTGCACAATGCCATGACCACCCGCAAGAAGGAAACGTCTGTGTACAACTGGCAGTACG
TGCACTGCCTCTTCCTGTGGTGCCGGGTCCTGAGCACTGTGGGCCCCAGCGAAGCCCTCCAACCCTTGTTCTACTCCCTT
GCCCATGTCATCATTGGCTGTATCAAGCTTATCCCCACTGCCCGCTTCTACCCACTGCGAATGCACTGCATCCGTGCCCT
GACGCTGCTCTCGGGGAGCTCGGGGGCCTTCATCCCAGTGCTGCCTTTCATCCTGGAGATGTTCCAGCAGGTCGACTTCA
GCAGGAAGCCGGGGCGCATGAGCTCCAAGCCCATCAACTTCTCCGTGATCCTGAAGCTGTCCAGTGTCAACCTGCAGGAG
AAGGCGTACCAGGACGGCCTGGTGGAGCAGCTGTACGACCTCACCCTGGAGTACCTGCACAGCCAGGCACACTGCATCGG
CTTCCCGGAGCTGGCGCTGCCTGTGGTCCTGCGGCTGAAGTCGTTCCTCCGGGAGTGCAAGGTGGCCAACTACTGCCGGC
AGGTGCAGCAGCTGCTTGGGAAGGTTCAGGAGAACTCGGAACACATCTGCAGCCGCCGCCAGAGGGTTTCCTTCGGCGTC
TCTGACCAGCAGGCAGTGGAAGCCTGGCAGAAGCTGACCCTGGAAGAGGGGACCCCCCTGACCTTGTACTACAGCCACTG
GTGCAAGCTGCGTGACTGGGAGATCCAGCTGGAGATCAGTGGCAAAGAGCGGCTGGAAGACCTGAACTTTCCTGAGATCA
AACGAAGGAAGGTGGCTGACAGGAAGGATGAGGACAGGAAGCAATTTAAAGACCTCTTTGACCTGAACAGCTGTGAAGAG
GACGACACCGAGGGATTCTTGGAAAGAGGGATACTGGGGCCCCTGAGCACTCGGCGTGGGGTGGAAGAGGATAAAGAGGA
CGAGGAGGAGGGCGAGGAGGACAGCAGCAACTCGGAGGATGGAGACCCAGACGCAGAGGCGGGGCTGGCCCCTGGGGAGC
TGCAGCGGCTGGCCCAGGGGCCAGAGGATGAGCTGGAGGATCTACAGCTCTCAGAGGAGGAC

ORF - retro_hsap_2320 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.53 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMAAAGSRKRRLAELTVDEFLASGFDSESESESENSPQAETREAREAARSPDKPGGSPSASRRKGRASEHK
MA.A..R.RRLAELTVDEFLASGF.....S.SE.SP.AETREAREAARSPD.PGGS..ASRRKG.ASEHK
RetrocopyMAGARRRRRRLAELTVDEFLASGF----DSKSEYSPEAETREAREAARSPDEPGGSSLASRRKGCASEHK
ParentalDQLSRLKDRDPEFYKFLQENDQSLLNFSDS-DSSEEEEGPFHSLPDVLEEASEEEDGAEEGEDGDRVPRG
DQLSRLKDRDPEFYKFLQENDQS.LNFSDS..S.EEEE.PF.SLPDVLEEASE.EDGAEEGEDGDRVPRG
RetrocopyDQLSRLKDRDPEFYKFLQENDQSQLNFSDS<SSEEEEE-PFNSLPDVLEEASEDEDGAEEGEDGDRVPRG
ParentalLKGKKNSVPVTVAMVERWKQAAKQRLTPKLFHEVVQAFRAAVATTRGDQESAEANKFQVTDSAAFNALVT
LKG.KN.VPVT.AMVERWKQAAKQ.LTPKLFHEVVQAF.AAVATT.GDQESAEANKFQV.DSA.FNALVT
RetrocopyLKG-KNCVPVTLAMVERWKQAAKQHLTPKLFHEVVQAFGAAVATTQGDQESAEANKFQVRDSAVFNALVT
ParentalFCIRDLIGCLQKLLFGKVAKDSSRMLQPSSSPLWGKLRVDIKAYLGSAIQLVSCLSETTVLAAVLRHISV
FCIRDLIGCLQKLLFGK.AKDSSRMLQPSSS.LWGKL.VDIKAYLGS.IQLVSC..ET.VLAAVL.HISV
RetrocopyFCIRDLIGCLQKLLFGKAAKDSSRMLQPSSSRLWGKLHVDIKAYLGSVIQLVSCVAETMVLAAVLWHISV
ParentalLVPCFLTFPKQCRMLLKRMVIVWSTGEESLRVLAFLVLSRVCRHKKDTFLGPVLKQMYITYVRNCKFTSP
LVPCFLTFPKQCRMLLKRMV.VWSTGEESLRVLAFLVLSRVCRHKKDTFLGPVLKQMYI.YVRNCKFTSP
RetrocopyLVPCFLTFPKQCRMLLKRMVVVWSTGEESLRVLAFLVLSRVCRHKKDTFLGPVLKQMYIMYVRNCKFTSP
ParentalGALPFISFMQWTLTELLALEPGVAYQHAFLYIRQLAIHLRNAMTTRKKETYQSVYNWQYVHCLFLWCRVL
GALPFISFMQ.TL.ELLALEPGVAYQHAFLYIRQLAIHL.NAMTTRKKET..SVYNWQYVHCLFLWCRVL
RetrocopyGALPFISFMQRTLRELLALEPGVAYQHAFLYIRQLAIHLHNAMTTRKKET--SVYNWQYVHCLFLWCRVL
ParentalSTAGPSEALQPLVYPLAQVIIGCIKLIPTARFYPLRMHCIRALTLLSGSSGAFIPVLPFILEMFQQVDFN
ST.GPSEALQPL.Y.LA.VIIGCIKLIPTARFYPLRMHCIRALTLLSGSSGAFIPVLPFILEMFQQVDF.
RetrocopySTVGPSEALQPLFYSLAHVIIGCIKLIPTARFYPLRMHCIRALTLLSGSSGAFIPVLPFILEMFQQVDFS
ParentalRKPGRMSSKPINFSVILKLSNVNLQEKAYRDGLVEQLYDLTLEYLHSQAHCIGFPELVLPVVLQLKSFLR
RKPGRMSSKPINFSVILKLS.VNLQEKAY.DGLVEQLYDLTLEYLHSQAHCIGFPEL.LPVVL.LKSFLR
RetrocopyRKPGRMSSKPINFSVILKLSSVNLQEKAYQDGLVEQLYDLTLEYLHSQAHCIGFPELALPVVLRLKSFLR
ParentalECKVANYCRQVQQLLGKVQENSAYICSRRQRVSFGVSEQQAVEAWEKLTREEGTPLTLYYSHWRKLRDRE
ECKVANYCRQVQQLLGKVQENS..ICSRRQRVSFGVS.QQAVEAW.KLT.EEGTPLTLYYSHW.KLRD.E
RetrocopyECKVANYCRQVQQLLGKVQENSEHICSRRQRVSFGVSDQQAVEAWQKLTLEEGTPLTLYYSHWCKLRDWE
ParentalIQLEISGKERLEDLNFPEIKRRKMADRKDEDRKQFKDLFDLNSSEEDDTEGFSERGILRPLSTRHGVEDD
IQLEISGKERLEDLNFPEIKRRK.ADRKDEDRKQFKDLFDLNS.EEDDTEGF.ERGIL.PLSTR.GVE.D
RetrocopyIQLEISGKERLEDLNFPEIKRRKVADRKDEDRKQFKDLFDLNSCEEDDTEGFLERGILGPLSTRRGVEED
ParentalEEDEEEGEEDSSNSEDGDPDAEAGLAPGELQQLAQGPEDELEDLQLSEDD
.EDEEEGEEDSSNSEDGDPDAEAGLAPGELQ.LAQGPEDELEDLQLSE.D
RetrocopyKEDEEEGEEDSSNSEDGDPDAEAGLAPGELQRLAQGPEDELEDLQLSEED

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 .08 RPM 38 .40 RPM
bodymap2_adrenal 0 .00 RPM 52 .48 RPM
bodymap2_brain 0 .00 RPM 28 .90 RPM
bodymap2_breast 0 .02 RPM 33 .85 RPM
bodymap2_colon 0 .02 RPM 36 .06 RPM
bodymap2_heart 0 .00 RPM 16 .84 RPM
bodymap2_kidney 0 .00 RPM 31 .33 RPM
bodymap2_liver 0 .00 RPM 21 .15 RPM
bodymap2_lung 0 .00 RPM 19 .11 RPM
bodymap2_lymph_node 0 .00 RPM 30 .32 RPM
bodymap2_ovary 0 .00 RPM 45 .09 RPM
bodymap2_prostate 0 .00 RPM 35 .56 RPM
bodymap2_skeletal_muscle 0 .00 RPM 79 .72 RPM
bodymap2_testis 1 .98 RPM 59 .42 RPM
bodymap2_thyroid 0 .15 RPM 45 .44 RPM
bodymap2_white_blood_cells 0 .00 RPM 29 .06 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2320 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2320 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2320 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2320 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2320 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000188976 1 retrocopy
retro_hsap_2320 ,
Pongo abelii ENSPPYG000000296452 retrocopies
retro_pabe_2173, retro_pabe_3535,

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 = 0.14 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .07 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .05 RPM
CEU_NA12760 0 .13 RPM
CEU_NA12827 0 .14 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 .05 RPM
FIN_HG00338 0 .06 RPM
FIN_HG00349 0 .06 RPM
FIN_HG00375 0 .12 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .06 RPM
GBR_HG00111 0 .04 RPM
GBR_HG00114 0 .11 RPM
GBR_HG00119 0 .12 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .04 RPM
GBR_HG00137 0 .08 RPM
GBR_HG00142 0 .06 RPM
GBR_HG00143 0 .10 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .11 RPM
TSI_NA20532 0 .10 RPM
TSI_NA20538 0 .09 RPM
TSI_NA20756 0 .06 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .06 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .06 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .10 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .08 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .12 RPM
YRI_NA19213 0 .02 RPM
YRI_NA19214 0 .05 RPM
YRI_NA19223 0 .04 RPM

Indel association:

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





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