RetrogeneDB ID:

retro_hsap_3143

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:17525337..17525937(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000250055
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TAF11
Ensembl ID:ENSG00000064995
Aliases:TAF11, MGC:15243, TAF2I, TAFII28
Description:TAF11 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 28kDa [Source:HGNC Symbol;Acc:11544]


Retrocopy-Parental alignment summary:






>retro_hsap_3143
TCACCCATGGAGACCGGCAGGCAAACAGGTGTGTCTGCTGAGATGCTCGCCATGCCCCGAGGTCTGAAGGGCAGCAAGAA
GGATGGAATCCCTGAGGACCTAGACGGGAACTTGGAAGCACCCAGGGATCAGGAAGGTGAGCTCAGGAGTGAGGATGTCA
TGGACCTCACAGAAGGTGACAGTGAGGCCTCAGCCTCAGCTCCTCCTGCAGCCAAAAGACGGAAAACACATACGAAAGGC
AAGAAGGAGAGCAAGCCCACCGTGGATGCGGAGGAGGCTCAGAGGATGACAACCCTGCTGTCTGCCATGTCTGAGGAGCA
GCTGTCCCGCTACGAAGTGTGTCGCCGGTCAGCGTTCCCGAGAGCACGCGTTGCGGGTCTGATGCGGGCTATCACTGGCA
GTTCGGTGTCGGAGAACGCGGCCATTGCCATGGCTGGAATAGCCAAGCTCTTTGTTGGAGAGGTGGTGGAAGAGGCCCTG
GACGTGTGTGAGATGTGGGGAGAGACGCCCCCGCTGCAGCCCAAGCATTTAAGGGAGGCCGTTCGCAGGTTAAAGCCCAA
GGGCCTCTTCCCCAACAGCAACTGCAAAAGAATCATGTTC

ORF - retro_hsap_3143 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 56.86 %
Parental protein coverage: 96.68 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalSPSDKGGETGESDETAAVPGDPGATDTDGIPEETDGDADVDLKEAAAEEGELESQDVSDLTTVEREDSSL
SP...G..TG.S.E..A.P........DGIPE..DG.....L......EGEL.S.DV.DLT....E.S..
RetrocopySPMETGRQTGVSAEMLAMPRGLKGSKKDGIPEDLDGN----LEAPRDQEGELRSEDVMDLTEGDSEASAS
ParentalLNPAAKKLKIDTKEKKEKKQKVDEDEIQKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKRLIQSITGTSV
..PAAK..K..TK.KKE.K..VD..E.Q.M..L.S..SEEQL.RYE..RRSAFP.A....L...ITG.SV
RetrocopyAPPAAKRRKTHTKGKKESKPTVDAEEAQRMTTLLSAMSEEQLSRYEVCRRSAFPRARVAGLMRAITGSSV
ParentalSQNVVIAMSGISKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAVRRLKSKGQIPNSKHKKIIF
S.N..IAM.GI.K.FVGEVVEEALDVCE.WGE.PPLQPKH.REAVRRLK.KG..PNS..K.I.F
RetrocopySENAAIAMAGIAKLFVGEVVEEALDVCEMWGETPPLQPKHLREAVRRLKPKGLFPNSNCKRIMF

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 13 .80 RPM
bodymap2_adrenal 0 .00 RPM 31 .36 RPM
bodymap2_brain 0 .00 RPM 17 .91 RPM
bodymap2_breast 0 .00 RPM 18 .74 RPM
bodymap2_colon 0 .00 RPM 20 .01 RPM
bodymap2_heart 0 .00 RPM 13 .05 RPM
bodymap2_kidney 0 .00 RPM 16 .67 RPM
bodymap2_liver 0 .00 RPM 11 .09 RPM
bodymap2_lung 0 .00 RPM 16 .77 RPM
bodymap2_lymph_node 0 .00 RPM 22 .70 RPM
bodymap2_ovary 0 .00 RPM 19 .62 RPM
bodymap2_prostate 0 .00 RPM 23 .57 RPM
bodymap2_skeletal_muscle 0 .00 RPM 10 .53 RPM
bodymap2_testis 0 .00 RPM 28 .36 RPM
bodymap2_thyroid 0 .00 RPM 24 .61 RPM
bodymap2_white_blood_cells 0 .00 RPM 21 .07 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3143 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3143 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3143 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3143 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3143 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2125
Parental genes homology:
Parental genes homology involve 15 parental genes, and 70 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000168871 retrocopy
retro_btau_218,
Callithrix jacchus ENSCJAG000000153885 retrocopies
retro_cjac_1342, retro_cjac_1980, retro_cjac_2310, retro_cjac_2402, retro_cjac_2657,
Cavia porcellus ENSCPOG000000154281 retrocopy
retro_cpor_629,
Dipodomys ordii ENSDORG000000093521 retrocopy
retro_dord_4,
Equus caballus ENSECAG000000167251 retrocopy
retro_ecab_83,
Felis catus ENSFCAG000000229311 retrocopy
retro_fcat_1628,
Homo sapiens ENSG00000064995 15 retrocopies
retro_hsap_3139, retro_hsap_3140, retro_hsap_3141, retro_hsap_3142, retro_hsap_3143 , retro_hsap_3144, retro_hsap_3145, retro_hsap_3146, retro_hsap_3147, retro_hsap_3148, retro_hsap_3149, retro_hsap_3295, retro_hsap_3296, retro_hsap_3297, retro_hsap_3298,
Loxodonta africana ENSLAFG000000114821 retrocopy
retro_lafr_1108,
Microcebus murinus ENSMICG000000140631 retrocopy
retro_mmur_1196,
Myotis lucifugus ENSMLUG000000017661 retrocopy
retro_mluc_87,
Nomascus leucogenys ENSNLEG0000000845729 retrocopies
retro_nleu_149, retro_nleu_151, retro_nleu_152, retro_nleu_1742, retro_nleu_1743, retro_nleu_2976, retro_nleu_2977, retro_nleu_2998, retro_nleu_3041, retro_nleu_3042, retro_nleu_3043, retro_nleu_3044, retro_nleu_3049, retro_nleu_3050, retro_nleu_3051, retro_nleu_3053, retro_nleu_3054, retro_nleu_3055, retro_nleu_3081, retro_nleu_3082, retro_nleu_3083, retro_nleu_3084, retro_nleu_3093, retro_nleu_3094, retro_nleu_3109, retro_nleu_3113, retro_nleu_3120, retro_nleu_3125, retro_nleu_3127,
Otolemur garnettii ENSOGAG000000085222 retrocopies
retro_ogar_3055, retro_ogar_922,
Pongo abelii ENSPPYG000000165211 retrocopy
retro_pabe_200,
Pan troglodytes ENSPTRG000000180759 retrocopies
retro_ptro_2123, retro_ptro_2124, retro_ptro_2125, retro_ptro_2126, retro_ptro_2127, retro_ptro_2128, retro_ptro_2129, retro_ptro_2130, retro_ptro_2977,
Tursiops truncatus ENSTTRG000000078551 retrocopy
retro_ttru_1063,

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 ) 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 .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 .00 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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