RetrogeneDB ID:

retro_hsap_65

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:14:102027833..102028748(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000197406
Aliases:DIO3, 5DIII, D3, DIOIII, TXDI3
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:DIO1
Ensembl ID:ENSG00000211452
Aliases:DIO1, 5DI, TXDI1
Description:deiodinase, iodothyronine, type I [Source:HGNC Symbol;Acc:2883]


Retrocopy-Parental alignment summary:






>retro_hsap_65
ATGCCTCGCCAGGCCACGTCGCGGTTGGTGGTCGGAGAGGGCGAGGGGTCCCAGGGGGCTTCGGGGCCTGCAGCCACCAT
GCTCCGCTCCCTGCTGCTTCACTCCTTGAGGCTCTGCGCCCAGACCGCCTCGTGCCTCGTGCTCTTCCCGCGCTTCCTCG
GCACGGCCTTCATGCTCTGGCTTCTCGATTTCTTGTGTATCCGCAAGCATTTCCTGGGCCGCCGCCGCCGGGGGCAGCCC
GAGCCCGAAGTGGAGCTCAACAGTGAAGGCGAGGAGGTGCCTCCCGATGACCCGCCCATCTGCGTGTCCGACGACAACCG
CCTGTGCACCCTGGCGTCGCTCAAGGCGGTGTGGCATGGCCAGAAGTTGGATTTCTTCAAGCAGGCGCACGAGGGCGGTC
CGGCGCCCAACTCCGAGGTGGTTCTGCCCGACGGCTTCCAGAGCCAGCACATCCTCGACTACGCGCAAGGGAACCGCCCG
CTGGTTCTCAATTTCGGCAGCTGCACCTGACCACCGTTCATGGCGCGCATGAGCGCCTTCCAGCGCCTGGTCACTAAGTA
CCAGCGCGACGTCGACTTCCTCATCATCTACATCGAGGAAGCGCACCCCTCCGACGGCTGGGTCACCACGGACTCTCCCT
ACATCATCCCACAGCACCGGAGCCTGGAGGACCGGGTCAGCGCAGCGAGGGTACTGCAGCAAGGTGCACCCGGCTGCGCT
CTGGTCCTCGACACCATGGCCAACTCCAGCAGCTCGGCCTATGGCGCCTACTTCGAGCGTCTCTATGTCATCCAGAGTGG
CACTATTATGTACCAGGGCGGCCGTGGCCCCGACGGCTACCAGGTCTCTGAGCTGCGCACTTGGTTGGAACGCTATGATG
AGCAACTGCACGGCGCTCGGCCCCGGAGGGTGTAA

ORF - retro_hsap_65 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 50.62 %
Parental protein coverage: 63.45 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalGGLAPNCPVVRLSG-QRCNIWEFMQGNRPLVLNFGSCTUPSFMFKFDQFKRLIEDFSSIADFLVIYIEEA
GG.APN..VV...G.Q...I....QGNRPLVLNFGSCTUP.FM.....F.RL........DFL.IYIEEA
RetrocopyGGPAPNSEVVLPDGFQSQHILDYAQGNRPLVLNFGSCTUPPFMARMSAFQRLVTKYQRDVDFLIIYIEEA
ParentalHASDGWAFKNN-MDIRNHQNLQDRLQAAHLLLARSPQCPVVVDTMQNQSSQLYAALPERLYIIQEGRILY
H.SDGW........I..H..L.DR..AA..L....P.C..V.DTM.N.SS..Y.A..ERLY.IQ.G.I.Y
RetrocopyHPSDGWVTTDSPYIIPQHRSLEDRVSAARVLQQGAPGCALVLDTMANSSSSAYGAYFERLYVIQSGTIMY
ParentalKGKSGPWNYNPEEVRAVLEK
.G..GP..Y...E.R..LE.
RetrocopyQGGRGPDGYQVSELRTWLER

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 1 .25 RPM 0 .18 RPM
bodymap2_adrenal 0 .68 RPM 0 .39 RPM
bodymap2_brain 0 .02 RPM 0 .14 RPM
bodymap2_breast 0 .06 RPM 0 .29 RPM
bodymap2_colon 1 .28 RPM 0 .29 RPM
bodymap2_heart 0 .11 RPM 0 .06 RPM
bodymap2_kidney 0 .27 RPM 29 .43 RPM
bodymap2_liver 0 .06 RPM 48 .97 RPM
bodymap2_lung 0 .60 RPM 1 .14 RPM
bodymap2_lymph_node 1 .39 RPM 0 .71 RPM
bodymap2_ovary 5 .78 RPM 0 .33 RPM
bodymap2_prostate 1 .13 RPM 0 .05 RPM
bodymap2_skeletal_muscle 0 .11 RPM 0 .25 RPM
bodymap2_testis 1 .62 RPM 0 .32 RPM
bodymap2_thyroid 1 .00 RPM 62 .48 RPM
bodymap2_white_blood_cells 0 .00 RPM 0 .08 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_65 in 4 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CRK POLR2A 14:102027599..102028123
ENCFF002DBO POLR2A 14:102027768..102027996
ENCFF002DBP POLR2A 14:102027785..102027996
ENCFF002DBQ POLR2A 14:102027652..102028022

EST - click to see more details

5 EST(s) were mapped to retro_hsap_65 retrocopy
EST ID Start End Identity Match Mis-match Score
BJ991894 102027831 102028303 100 472 0 472
DA008598 102027830 102028289 100 459 0 459
DA420866 102027830 102028321 100 490 0 489
DA845233 102027831 102028285 100 454 0 454
DB249205 102027830 102028270 99.8 438 1 437

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_353311303 libraries187 libraries209 libraries57 libraries73 libraries

The graphical summary, for retro_hsap_65 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_65 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_65 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_1072
Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000211452 1 retrocopy
retro_hsap_65 ,
Gorilla gorilla ENSGGOG000000154061 retrocopy
retro_ggor_1072,
Microcebus murinus ENSMICG000000142901 retrocopy
retro_mmur_1532,
Tursiops truncatus ENSTTRG000000091051 retrocopy
retro_ttru_1421,

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 = 0.05 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .04 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .02 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 .02 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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