RetrogeneDB ID:

retro_hsap_13

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:80246341..80247031(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000156269
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:NAA10
Ensembl ID:ENSG00000102030
Aliases:None
Description:N(alpha)-acetyltransferase 10, NatA catalytic subunit [Source:HGNC Symbol;Acc:18704]


Retrocopy-Parental alignment summary:






>retro_hsap_13
ATGAACATCCGCAACGCTCAGCCAGACGACCTGATGAATATGCAACACTGCAACCTCCTTTGCCTTCCTGAGAACTACCA
GATGAAATACTATTTATATCATGGCCTTTCCTGGCCCCAGCTTTCTTACATCGCTGAGGATGAGGACGGGAAGATTGTGG
GCTATGTTCTGGCCAAAATGGAGGAGGAACCAGATGATGTCCCGCATGGCCATATCACCTCACTGGCCGTGAAGCGTTCA
CACCGGCGCCTCGGCCTGGCCCAGAAGCTGATGGACCAGGCCTCCAGGGCCATGATAGAGAACTTTAACGCCAAATACGT
GTCTCTGCACGTCAGGAAGAGTAACCGGCCAGCCTTGCACCTTTATTCTAACACCCTCAACTTTCAGATTAGTGAGGTGG
AACCTAAATACTATGCAGATGGGGAAGATGCTTATGCTATGAAGCGGGATCTCTCGCAGATGGCAGATGAGCTGAGACGA
CAAATGGACCTGAAGAAGGGCGGGTATGTGGTCCTGGGCTCCAGGGAGAACCAGGAGACCCAGGGCAGCACACTTTCTGA
TTCTGAAGAGGCCTGTCAGCAAAAGAACCCGGCTACCGAAGAAAGTGGCAGTGACAGCAAAGAACCTAAGGAGTCTGTGG
AGAGCACCAACGTCCAGGACAGCTCAGAAAGCTCGGATTCCACCTCCTAG

ORF - retro_hsap_13 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.28 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMNIRNARPEDLMNMQHCNLLCLPENYQMKYYFYHGLSWPQLSYIAEDENGKIVGYVLAKMEEDPDDVPHG
MNIRNA.P.DLMNMQHCNLLCLPENYQMKYY.YHGLSWPQLSYIAEDE.GKIVGYVLAKMEE.PDDVPHG
RetrocopyMNIRNAQPDDLMNMQHCNLLCLPENYQMKYYLYHGLSWPQLSYIAEDEDGKIVGYVLAKMEEEPDDVPHG
ParentalHITSLAVKRSHRRLGLAQKLMDQASRAMIENFNAKYVSLHVRKSNRAALHLYSNTLNFQISEVEPKYYAD
HITSLAVKRSHRRLGLAQKLMDQASRAMIENFNAKYVSLHVRKSNR.ALHLYSNTLNFQISEVEPKYYAD
RetrocopyHITSLAVKRSHRRLGLAQKLMDQASRAMIENFNAKYVSLHVRKSNRPALHLYSNTLNFQISEVEPKYYAD
ParentalGEDAYAMKRDLTQMADELRRHLELKEKGRHVVLGAIENKVESKGNSPPSSGEACREEKGLAAEDSGGDSK
GEDAYAMKRDL.QMADELRR...LK.KG..VVLG..EN..E..G.....S.EAC...K..A.E.SG.DSK
RetrocopyGEDAYAMKRDLSQMADELRRQMDLK-KGGYVVLGSRENQ-ETQGSTLSDSEEAC-QQKNPATEESGSDSK
ParentalDLSEVSETTESTDVKDSSEASDSAS
...E..E..EST.V.DSSE.SDS.S
Retrocopy---EPKESVESTNVQDSSESSDSTS

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 11 .21 RPM
bodymap2_adrenal 0 .00 RPM 21 .04 RPM
bodymap2_brain 0 .00 RPM 8 .49 RPM
bodymap2_breast 0 .00 RPM 13 .02 RPM
bodymap2_colon 0 .04 RPM 13 .90 RPM
bodymap2_heart 0 .00 RPM 6 .04 RPM
bodymap2_kidney 0 .00 RPM 17 .50 RPM
bodymap2_liver 0 .00 RPM 7 .29 RPM
bodymap2_lung 0 .00 RPM 11 .59 RPM
bodymap2_lymph_node 0 .00 RPM 26 .02 RPM
bodymap2_ovary 0 .00 RPM 13 .94 RPM
bodymap2_prostate 0 .00 RPM 14 .27 RPM
bodymap2_skeletal_muscle 0 .00 RPM 15 .62 RPM
bodymap2_testis 4 .86 RPM 10 .05 RPM
bodymap2_thyroid 0 .00 RPM 10 .77 RPM
bodymap2_white_blood_cells 0 .00 RPM 6 .40 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_13 in 6 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CMI POLR2A 4:80246958..80247343
ENCFF002CXN POLR2A 4:80246923..80247419
ENCFF002CXO POLR2A 4:80246960..80247384
ENCFF002CXP POLR2A 4:80246902..80247382
ENCFF002CXR POLR2A 4:80246928..80247364
ENCFF002DBE POLR2A 4:80246934..80247430

EST - click to see more details

No EST(s) were mapped for retro_hsap_13 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_1460431725 libraries19 libraries7 libraries4 libraries74 libraries

The graphical summary, for retro_hsap_13 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_13 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_13 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_23
Gorilla gorilla retro_ggor_196
Pongo abelii retro_pabe_2530
Canis familiaris retro_cfam_167
Parental genes homology:
Parental genes homology involve 22 parental genes, and 23 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000184571 retrocopy
retro_amel_162,
Bos taurus ENSBTAG000000477021 retrocopy
retro_btau_177,
Canis familiaris ENSCAFG000000194151 retrocopy
retro_cfam_167,
Callithrix jacchus ENSCJAG000000145061 retrocopy
retro_cjac_132,
Equus caballus ENSECAG000000152031 retrocopy
retro_ecab_717,
Felis catus ENSFCAG000000287051 retrocopy
retro_fcat_51,
Homo sapiens ENSG00000102030 1 retrocopy
retro_hsap_13 ,
Gorilla gorilla ENSGGOG000000097881 retrocopy
retro_ggor_196,
Macropus eugenii ENSMEUG000000060542 retrocopies
retro_meug_1787, retro_meug_554,
Myotis lucifugus ENSMLUG000000142671 retrocopy
retro_mluc_152,
Macaca mulatta ENSMMUG000000003221 retrocopy
retro_mmul_21,
Mustela putorius furoENSMPUG000000089891 retrocopy
retro_mputfur_1424,
Mus musculus ENSMUSG000000313881 retrocopy
retro_mmus_1416,
Nomascus leucogenys ENSNLEG000000137241 retrocopy
retro_nleu_57,
Otolemur garnettii ENSOGAG000000132631 retrocopy
retro_ogar_260,
Pongo abelii ENSPPYG000000208611 retrocopy
retro_pabe_2530,
Pan troglodytes ENSPTRG000000224191 retrocopy
retro_ptro_23,
Pteropus vampyrus ENSPVAG000000004631 retrocopy
retro_pvam_1225,
Sarcophilus harrisii ENSSHAG000000059521 retrocopy
retro_shar_362,
Sus scrofa ENSSSCG000000127911 retrocopy
retro_sscr_987,
Ictidomys tridecemlineatus ENSSTOG000000102371 retrocopy
retro_itri_1435,
Tursiops truncatus ENSTTRG000000074551 retrocopy
retro_ttru_198,

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 = 0.04 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 .04 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 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 .00 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 .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 .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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