RetrogeneDB ID:

retro_hsap_4016

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:8:6331365..6331809(-)
Located in intron of:ENSG00000147316
Retrocopy
information
Ensembl ID:ENSG00000253550
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TAF9
Ensembl ID:ENSG00000085231
Aliases:TAF9, MGC:5067, STAF31/32, TAF2G, TAFII-31, TAFII-32, TAFII31, TAFII32, TAFIID32
Description:TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 32kDa [Source:HGNC Symbol;Acc:11542]


Retrocopy-Parental alignment summary:






>retro_hsap_4016
TCAAAATCAGGATTGAAATACATTAATGTGGGTGATTTAGCTTGAGAAAAGCAATTGTATGACGACTATGATGAAGAGTA
TAATTGTCCCATTTTAGATGAAGACAGAGTAGCTGATGAGTTAGATAACCAAATGAGAGAATGTGGAGTTATTGTTGATT
ACCACGGTTGTGATTTCTTCCCTGAACGCTGGTTTCACATAGTTTTTGTGTTGAGAATAGATGCCAACATATTGTACGAA
ATACTTCAAATGAGGGGTTATAATGAGAAGAAACTAAAAGACAATATTCAGTGTGAGATTTTCCAAGTTCTTTATGAAGA
AGCCACGGCATCCTACAAGGAAGAAGTTGTGCATCGGCTGCCCAGCAATAAACCAGAAGAGCTAGAAAATAATGTAGATC
AGATCTTGAAATGGATTGAGCAGTGGATCAAAGATTATAACTCT

ORF - retro_hsap_4016 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.19 %
Parental protein coverage: 87.57 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalSKSGLKYINVGDLAREEQLYDGYDEEYDCPILDEDRVVDELDNQMREGGVIVDYHGCDFFPERWFHIVFV
SKSGLKYINVGDLA.E.QLYD.YDEEY.CPILDEDRV.DELDNQMRE.GVIVDYHGCDFFPERWFHIVFV
RetrocopySKSGLKYINVGDLA*EKQLYDDYDEEYNCPILDEDRVADELDNQMRECGVIVDYHGCDFFPERWFHIVFV
ParentalLRTDTNVLYERLETRGYNEKKLTDNIQCEIFQVLYEEATASYKEEIVHQLPSNKPEELENNVDQILKWIE
LR.D.N.LYE.L..RGYNEKKL.DNIQCEIFQVLYEEATASYKEE.VH.LPSNKPEELENNVDQILKWIE
RetrocopyLRIDANILYEILQMRGYNEKKLKDNIQCEIFQVLYEEATASYKEEVVHRLPSNKPEELENNVDQILKWIE
ParentalQWIKDHNS
QWIKD.NS
RetrocopyQWIKDYNS

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 48 .30 RPM
bodymap2_adrenal 0 .20 RPM 58 .05 RPM
bodymap2_brain 0 .16 RPM 72 .31 RPM
bodymap2_breast 0 .00 RPM 52 .69 RPM
bodymap2_colon 0 .00 RPM 49 .73 RPM
bodymap2_heart 0 .00 RPM 42 .53 RPM
bodymap2_kidney 0 .00 RPM 55 .96 RPM
bodymap2_liver 0 .00 RPM 39 .14 RPM
bodymap2_lung 0 .00 RPM 48 .29 RPM
bodymap2_lymph_node 0 .00 RPM 54 .62 RPM
bodymap2_ovary 0 .00 RPM 58 .10 RPM
bodymap2_prostate 0 .00 RPM 51 .79 RPM
bodymap2_skeletal_muscle 0 .00 RPM 39 .45 RPM
bodymap2_testis 0 .11 RPM 137 .33 RPM
bodymap2_thyroid 0 .00 RPM 71 .33 RPM
bodymap2_white_blood_cells 0 .00 RPM 51 .64 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4016 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4016 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4016 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4016 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4016 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2726
Pongo abelii retro_pabe_3298
Macaca mulatta retro_mmul_2317
Parental genes homology:
Parental genes homology involve 3 parental genes, and 6 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000085231 4 retrocopies
retro_hsap_134, retro_hsap_4016 , retro_hsap_4925, retro_hsap_987,
Homo sapiens ENSG000001873251 retrocopy
retro_hsap_2619,
Macaca mulatta ENSMMUG000000091401 retrocopy
retro_mmul_2317,

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 = 0.12 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .04 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .07 RPM
CEU_NA12004 0 .08 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .05 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .11 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .12 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .02 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .08 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .10 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .04 RPM
TSI_NA20771 0 .06 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .05 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .05 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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