RetrogeneDB ID:

retro_hsap_1063

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:12:120720054..120720516(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000123009
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:NME2
Ensembl ID:ENSG00000011052
Aliases:None
Description:NME/NM23 nucleoside diphosphate kinase 2 [Source:HGNC Symbol;Acc:7850]


Retrocopy-Parental alignment summary:






>retro_hsap_1063
CGGACCACGGCCAACCTCGAGCGCACCTTCATCACCATCAGGCCGGACAGCATGCAGTGCGGCCTGGTGGGCAAGATCAT
CAAGCGCTTCGAGCAGAAGGGGTTCCGCCTCGTGGCCATGAAGTTCCTCCCGGCCTCTGAAGAACACCTGAAGCAGCACT
ACATTGACCTGAAGGACCGCCCATTCTTCCCTGGGCTGGTGAAGTACATGAACTCAGGGCCGGTCGTGGCCATGGTCTGG
GAGGGGCTGAACGTCGTGAAGACAGGCCGAGTGATGCTTGGGGAGACCAATCCAGCAGATTCTAAGCCAGGCACCATTCG
TGGGGACTTTTGCATTCAGGTTGGCAGGAACATCATTCATGGCAGTGATTCAGTAAAAAGTGCTGAAAAAGAAATCAGCC
TACGGTTTAAGCCTGAAGAACTGGTTGACTACAAGTCTTGTGCTCATGACTGGGTCTATGAA

ORF - retro_hsap_1063 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.16 %
Parental protein coverage: 52.74 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalRTMANLERTFIAIKPDGVQRGLVGEIIKRFEQKGFRLVAMKFLRASEEHLKQHYIDLKDRPFFPGLVKYM
RT.ANLERTFI.I.PD..Q.GLVG.IIKRFEQKGFRLVAMKFL.ASEEHLKQHYIDLKDRPFFPGLVKYM
RetrocopyRTTANLERTFITIRPDSMQCGLVGKIIKRFEQKGFRLVAMKFLPASEEHLKQHYIDLKDRPFFPGLVKYM
ParentalNSGPVVAMVWEGLNVVKTGRVMLGETNPADSKPGTIRGDFCIQVGRNIIHGSDSVKSAEKEISLWFKPEE
NSGPVVAMVWEGLNVVKTGRVMLGETNPADSKPGTIRGDFCIQVGRNIIHGSDSVKSAEKEISL.FKPEE
RetrocopyNSGPVVAMVWEGLNVVKTGRVMLGETNPADSKPGTIRGDFCIQVGRNIIHGSDSVKSAEKEISLRFKPEE
ParentalLVDYKSCAHDWVYE
LVDYKSCAHDWVYE
RetrocopyLVDYKSCAHDWVYE

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 .06 RPM 0 .60 RPM
bodymap2_adrenal 0 .27 RPM 0 .94 RPM
bodymap2_brain 0 .02 RPM 0 .47 RPM
bodymap2_breast 0 .08 RPM 0 .27 RPM
bodymap2_colon 0 .00 RPM 0 .56 RPM
bodymap2_heart 0 .00 RPM 0 .00 RPM
bodymap2_kidney 0 .10 RPM 0 .04 RPM
bodymap2_liver 0 .02 RPM 0 .08 RPM
bodymap2_lung 0 .23 RPM 0 .04 RPM
bodymap2_lymph_node 0 .26 RPM 0 .00 RPM
bodymap2_ovary 0 .08 RPM 0 .40 RPM
bodymap2_prostate 0 .29 RPM 0 .10 RPM
bodymap2_skeletal_muscle 0 .15 RPM 0 .02 RPM
bodymap2_testis 0 .30 RPM 0 .26 RPM
bodymap2_thyroid 0 .06 RPM 0 .98 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_1063 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1063 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_21893216 libraries230 libraries762 libraries456 libraries165 libraries

The graphical summary, for retro_hsap_1063 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_1063 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1063 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_91
Gorilla gorilla retro_ggor_71
Pongo abelii retro_pabe_102
Parental genes homology:
Parental genes homology involve 21 parental genes, and 59 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000080223 retrocopies
retro_amel_1573, retro_amel_390, retro_amel_538,
Bos taurus ENSBTAG000000471861 retrocopy
retro_btau_1329,
Callithrix jacchus ENSCJAG000000183955 retrocopies
retro_cjac_1765, retro_cjac_2517, retro_cjac_2642, retro_cjac_3940, retro_cjac_471,
Equus caballus ENSECAG000000216581 retrocopy
retro_ecab_404,
Erinaceus europaeus ENSEEUG000000037832 retrocopies
retro_eeur_156, retro_eeur_5,
Felis catus ENSFCAG000000067425 retrocopies
retro_fcat_1083, retro_fcat_1117, retro_fcat_1475, retro_fcat_216, retro_fcat_663,
Homo sapiens ENSG00000011052 1 retrocopy
retro_hsap_1063 ,
Homo sapiens ENSG000001032021 retrocopy
retro_hsap_1740,
Loxodonta africana ENSLAFG000000077841 retrocopy
retro_lafr_636,
Myotis lucifugus ENSMLUG000000169293 retrocopies
retro_mluc_1422, retro_mluc_1882, retro_mluc_637,
Macaca mulatta ENSMMUG000000019401 retrocopy
retro_mmul_1827,
Monodelphis domestica ENSMODG000000125801 retrocopy
retro_mdom_1811,
Mustela putorius furoENSMPUG000000155734 retrocopies
retro_mputfur_1236, retro_mputfur_1590, retro_mputfur_327, retro_mputfur_912,
Mus musculus ENSMUSG000000208571 retrocopy
retro_mmus_221,
Oryctolagus cuniculus ENSOCUG000000249461 retrocopy
retro_ocun_418,
Otolemur garnettii ENSOGAG000000253319 retrocopies
retro_ogar_1326, retro_ogar_1875, retro_ogar_1997, retro_ogar_2373, retro_ogar_2393, retro_ogar_2779, retro_ogar_3299, retro_ogar_483, retro_ogar_95,
Rattus norvegicus ENSRNOG000000026718 retrocopies
retro_rnor_1129, retro_rnor_1610, retro_rnor_1708, retro_rnor_1784, retro_rnor_1966, retro_rnor_2646, retro_rnor_2951, retro_rnor_628,
Sarcophilus harrisii ENSSHAG000000144703 retrocopies
retro_shar_130, retro_shar_554, retro_shar_781,
Sus scrofa ENSSSCG000000175911 retrocopy
retro_sscr_854,
Tupaia belangeri ENSTBEG000000130536 retrocopies
retro_tbel_1271, retro_tbel_1386, retro_tbel_2497, retro_tbel_294, retro_tbel_4620, retro_tbel_820,
Tursiops truncatus ENSTTRG000000074331 retrocopy
retro_ttru_1821,

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 = 0.78 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .56 RPM
CEU_NA11843 0 .37 RPM
CEU_NA11930 0 .52 RPM
CEU_NA12004 0 .42 RPM
CEU_NA12400 0 .46 RPM
CEU_NA12751 0 .32 RPM
CEU_NA12760 0 .45 RPM
CEU_NA12827 0 .75 RPM
CEU_NA12872 0 .22 RPM
CEU_NA12873 0 .64 RPM
FIN_HG00183 0 .47 RPM
FIN_HG00277 0 .44 RPM
FIN_HG00315 0 .30 RPM
FIN_HG00321 0 .24 RPM
FIN_HG00328 0 .26 RPM
FIN_HG00338 0 .47 RPM
FIN_HG00349 0 .26 RPM
FIN_HG00375 0 .29 RPM
FIN_HG00377 0 .38 RPM
FIN_HG00378 0 .59 RPM
GBR_HG00099 0 .46 RPM
GBR_HG00111 0 .37 RPM
GBR_HG00114 0 .37 RPM
GBR_HG00119 0 .31 RPM
GBR_HG00131 0 .23 RPM
GBR_HG00133 0 .22 RPM
GBR_HG00134 0 .22 RPM
GBR_HG00137 0 .41 RPM
GBR_HG00142 0 .31 RPM
GBR_HG00143 0 .48 RPM
TSI_NA20512 0 .62 RPM
TSI_NA20513 0 .15 RPM
TSI_NA20518 0 .42 RPM
TSI_NA20532 0 .78 RPM
TSI_NA20538 0 .41 RPM
TSI_NA20756 0 .73 RPM
TSI_NA20765 0 .27 RPM
TSI_NA20771 0 .14 RPM
TSI_NA20786 0 .29 RPM
TSI_NA20798 0 .34 RPM
YRI_NA18870 0 .27 RPM
YRI_NA18907 0 .21 RPM
YRI_NA18916 0 .29 RPM
YRI_NA19093 0 .36 RPM
YRI_NA19099 0 .21 RPM
YRI_NA19114 0 .10 RPM
YRI_NA19118 0 .41 RPM
YRI_NA19213 0 .29 RPM
YRI_NA19214 0 .10 RPM
YRI_NA19223 0 .46 RPM

Indel association:

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



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