HIF1A-AS3 (HIF1A antisense RNA 3) - Rat Genome Database

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Gene: HIF1A-AS3 (HIF1A antisense RNA 3) Homo sapiens
Analyze
Symbol: HIF1A-AS3
Name: HIF1A antisense RNA 3
RGD ID: 14400143
HGNC Page HGNC:54284
Description: ASSOCIATED WITH Cholangiocarcinoma; cholangiocarcinoma; Maffucci syndrome; INTERACTS WITH 3,3',5,5'-tetrabromobisphenol A; benzalkonium chloride; bisphenol A
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: HIFAL
RGD Orthologs
Mouse
Alliance Orthologs
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381461,715,558 - 61,751,097 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1461,680,723 - 61,751,163 (-)EnsemblGRCh38hg38GRCh38
GRCh371462,182,276 - 62,217,815 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map14q23.2NCBI
CHM1_11462,121,472 - 62,157,253 (-)NCBICHM1_1
T2T-CHM13v2.01455,922,126 - 55,957,665 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References
Additional References at PubMed
PMID:16344560   PMID:33637716  


Genomics

Comparative Map Data
HIF1A-AS3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381461,715,558 - 61,751,097 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1461,680,723 - 61,751,163 (-)EnsemblGRCh38hg38GRCh38
GRCh371462,182,276 - 62,217,815 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map14q23.2NCBI
CHM1_11462,121,472 - 62,157,253 (-)NCBICHM1_1
T2T-CHM13v2.01455,922,126 - 55,957,665 (-)NCBIT2T-CHM13v2.0
Gm15283
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391273,981,498 - 73,999,213 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1273,889,813 - 73,996,588 (-)EnsemblGRCm39 Ensembl
GRCm381273,934,724 - 73,952,439 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1273,843,039 - 73,949,814 (-)EnsemblGRCm38mm10GRCm38
Celera1275,048,460 - 75,063,862 (-)NCBICelera
Cytogenetic Map12C3NCBI
cM Map1232.0NCBI

Variants

.
Variants in HIF1A-AS3
45 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_001530.4(HIF1A):c.1994G>A (p.Arg665Gln) single nucleotide variant not specified [RCV004320903] Chr14:61741089 [GRCh38]
Chr14:62207807 [GRCh37]
Chr14:14q23.2		 uncertain significance
GRCh38/hg38 14q23.1-23.3(chr14:59917051-66750803)x1 copy number loss See cases [RCV000050892] Chr14:59917051..66750803 [GRCh38]
Chr14:60383769..67217521 [GRCh37]
Chr14:59453522..66287274 [NCBI36]
Chr14:14q23.1-23.3		 pathogenic
NM_001530.4(HIF1A):c.2035C>G (p.Gln679Glu) single nucleotide variant not specified [RCV000202793] Chr14:61741130 [GRCh38]
Chr14:62207848 [GRCh37]
Chr14:14q23.2		 uncertain significance
NM_001530.4(HIF1A):c.780C>T (p.Thr260=) single nucleotide variant not provided [RCV000906019] Chr14:61732424 [GRCh38]
Chr14:62199142 [GRCh37]
Chr14:14q23.2		 benign
NM_001530.4(HIF1A):c.768T>C (p.Asp256=) single nucleotide variant not provided [RCV000901718] Chr14:61727650 [GRCh38]
Chr14:62194368 [GRCh37]
Chr14:14q23.2		 benign
GRCh38/hg38 14q23.1-23.2(chr14:57653413-64093528)x1 copy number loss See cases [RCV000138348] Chr14:57653413..64093528 [GRCh38]
Chr14:58120131..64560246 [GRCh37]
Chr14:57189884..63629999 [NCBI36]
Chr14:14q23.1-23.2		 pathogenic
GRCh38/hg38 14q11.2-32.33(chr14:20043514-106877229)x3 copy number gain See cases [RCV000143373] Chr14:20043514..106877229 [GRCh38]
Chr14:20511673..107285437 [GRCh37]
Chr14:19581513..106356482 [NCBI36]
Chr14:14q11.2-32.33		 pathogenic
NM_001530.4(HIF1A):c.700G>A (p.Glu234Lys) single nucleotide variant Malignant tumor of prostate [RCV000149379] Chr14:61727582 [GRCh38]
Chr14:62194300 [GRCh37]
Chr14:14q23.2		 uncertain significance
GRCh38/hg38 14q22.3-23.3(chr14:57041036-67208231)x1 copy number loss See cases [RCV000051521] Chr14:57041036..67208231 [GRCh38]
Chr14:57507754..67674948 [GRCh37]
Chr14:56577507..66744701 [NCBI36]
Chr14:14q22.3-23.3		 pathogenic
GRCh38/hg38 14q11.2-32.33(chr14:20151149-106855263)x3 copy number gain See cases [RCV000135543] Chr14:20151149..106855263 [GRCh38]
Chr14:20619308..107263478 [GRCh37]
Chr14:19689148..106334523 [NCBI36]
Chr14:14q11.2-32.33		 pathogenic
NM_001530.4(HIF1A):c.1242C>G (p.Gly414=) single nucleotide variant not provided [RCV000896931] Chr14:61737102 [GRCh38]
Chr14:62203820 [GRCh37]
Chr14:14q23.2		 benign
NM_001530.4(HIF1A):c.1264G>T (p.Asp422Tyr) single nucleotide variant Enchondromatosis [RCV002468100]|not provided [RCV000964219] Chr14:61738101 [GRCh38]
Chr14:62204819 [GRCh37]
Chr14:14q23.2		 likely pathogenic|benign
NM_001530.4(HIF1A):c.633G>A (p.Gly211=) single nucleotide variant not provided [RCV000906018] Chr14:61727515 [GRCh38]
Chr14:62194233 [GRCh37]
Chr14:14q23.2		 benign
NM_001530.4(HIF1A):c.2352G>A (p.Gly784=) single nucleotide variant not provided [RCV000880884] Chr14:61746956 [GRCh38]
Chr14:62213674 [GRCh37]
Chr14:14q23.2		 benign
NM_001530.4(HIF1A):c.1744C>T (p.Pro582Ser) single nucleotide variant Cholangiocarcinoma [RCV003312797]|not provided [RCV003481485] Chr14:61740839 [GRCh38]
Chr14:62207557 [GRCh37]
Chr14:14q23.2		 conflicting interpretations of pathogenicity|uncertain significance|other
NM_001530.4(HIF1A):c.1506C>T (p.Ser502=) single nucleotide variant not provided [RCV000896604] Chr14:61738343 [GRCh38]
Chr14:62205061 [GRCh37]
Chr14:14q23.2		 likely benign
NM_001530.4(HIF1A):c.1289T>C (p.Leu430Ser) single nucleotide variant not specified [RCV004291639] Chr14:61738126 [GRCh38]
Chr14:62204844 [GRCh37]
Chr14:14q23.2		 uncertain significance
NM_001530.4(HIF1A):c.1800A>T (p.Thr600=) single nucleotide variant not provided [RCV000954476] Chr14:61740895 [GRCh38]
Chr14:62207613 [GRCh37]
Chr14:14q23.2		 benign
NM_001530.4(HIF1A):c.881-4dup duplication not provided [RCV000901719] Chr14:61734128..61734129 [GRCh38]
Chr14:62200846..62200847 [GRCh37]
Chr14:14q23.2		 benign
NM_001530.4(HIF1A):c.1045G>A (p.Asp349Asn) single nucleotide variant not provided [RCV000889262] Chr14:61736905 [GRCh38]
Chr14:62203623 [GRCh37]
Chr14:14q23.2		 benign|likely benign
NM_001530.4(HIF1A):c.1740G>A (p.Leu580=) single nucleotide variant not provided [RCV000889476] Chr14:61740835 [GRCh38]
Chr14:62207553 [GRCh37]
Chr14:14q23.2		 benign
NM_001530.4(HIF1A):c.1253C>T (p.Thr418Ile) single nucleotide variant not provided [RCV000957907] Chr14:61738090 [GRCh38]
Chr14:62204808 [GRCh37]
Chr14:14q23.2		 benign|likely benign
NM_001530.4(HIF1A):c.1892G>A (p.Arg631His) single nucleotide variant Enchondromatosis [RCV002468427] Chr14:61740987 [GRCh38]
Chr14:62207705 [GRCh37]
Chr14:14q23.2		 likely pathogenic
NM_001530.4(HIF1A):c.644C>T (p.Pro215Leu) single nucleotide variant Enchondromatosis [RCV002468425] Chr14:61727526 [GRCh38]
Chr14:62194244 [GRCh37]
Chr14:14q23.2		 likely pathogenic
NM_001530.4(HIF1A):c.293G>A (p.Gly98Asp) single nucleotide variant not provided [RCV001269606] Chr14:61721575 [GRCh38]
Chr14:62188293 [GRCh37]
Chr14:14q23.2		 pathogenic
NM_001530.4(HIF1A):c.148G>C (p.Val50Leu) single nucleotide variant Maffucci syndrome [RCV002468421] Chr14:61720494 [GRCh38]
Chr14:62187212 [GRCh37]
Chr14:14q23.2		 likely pathogenic
NM_001530.4(HIF1A):c.1961C>T (p.Ala654Val) single nucleotide variant Maffucci syndrome [RCV002468428] Chr14:61741056 [GRCh38]
Chr14:62207774 [GRCh37]
Chr14:14q23.2		 likely pathogenic
NM_001530.4(HIF1A):c.2075C>G (p.Ser692Cys) single nucleotide variant Enchondromatosis [RCV002468429] Chr14:61741170 [GRCh38]
Chr14:62207888 [GRCh37]
Chr14:14q23.2		 likely pathogenic
NM_001530.4(HIF1A):c.1369G>A (p.Glu457Lys) single nucleotide variant Maffucci syndrome [RCV002468430] Chr14:61738206 [GRCh38]
Chr14:62204924 [GRCh37]
Chr14:14q23.2		 likely pathogenic
NM_001530.4(HIF1A):c.2411C>G (p.Ala804Gly) single nucleotide variant not specified [RCV004160216] Chr14:61747015 [GRCh38]
Chr14:62213733 [GRCh37]
Chr14:14q23.2		 uncertain significance
NM_001530.4(HIF1A):c.359T>C (p.Met120Thr) single nucleotide variant not specified [RCV004209319] Chr14:61721641 [GRCh38]
Chr14:62188359 [GRCh37]
Chr14:14q23.2		 uncertain significance
NM_001530.4(HIF1A):c.155C>T (p.Ser52Leu) single nucleotide variant not specified [RCV004240480] Chr14:61720501 [GRCh38]
Chr14:62187219 [GRCh37]
Chr14:14q23.2		 uncertain significance
NM_001530.4(HIF1A):c.613A>G (p.Ser205Gly) single nucleotide variant not specified [RCV004234684] Chr14:61727495 [GRCh38]
Chr14:62194213 [GRCh37]
Chr14:14q23.2		 uncertain significance
NM_001530.4(HIF1A):c.1091T>C (p.Val364Ala) single nucleotide variant not specified [RCV004071490] Chr14:61736951 [GRCh38]
Chr14:62203669 [GRCh37]
Chr14:14q23.2		 uncertain significance
NM_001530.4(HIF1A):c.1993C>T (p.Arg665Trp) single nucleotide variant not specified [RCV004238093] Chr14:61741088 [GRCh38]
Chr14:62207806 [GRCh37]
Chr14:14q23.2		 uncertain significance
NM_001530.4(HIF1A):c.1573A>G (p.Ser525Gly) single nucleotide variant not specified [RCV004096537] Chr14:61740541 [GRCh38]
Chr14:62207259 [GRCh37]
Chr14:14q23.2		 uncertain significance
NM_001530.4(HIF1A):c.180G>A (p.Met60Ile) single nucleotide variant not specified [RCV004161557] Chr14:61720526 [GRCh38]
Chr14:62187244 [GRCh37]
Chr14:14q23.2		 uncertain significance
NM_001530.4(HIF1A):c.1572T>G (p.Asp524Glu) single nucleotide variant not specified [RCV004099545] Chr14:61740540 [GRCh38]
Chr14:62207258 [GRCh37]
Chr14:14q23.2		 uncertain significance
NM_001530.4(HIF1A):c.121G>T (p.Ala41Ser) single nucleotide variant not specified [RCV004148661] Chr14:61720467 [GRCh38]
Chr14:62187185 [GRCh37]
Chr14:14q23.2		 uncertain significance
NM_001530.4(HIF1A):c.1065A>T (p.Gln355His) single nucleotide variant not specified [RCV004229710] Chr14:61736925 [GRCh38]
Chr14:62203643 [GRCh37]
Chr14:14q23.2		 uncertain significance
NM_001530.4(HIF1A):c.722C>A (p.Thr241Asn) single nucleotide variant not provided [RCV003393456] Chr14:61727604 [GRCh38]
Chr14:62194322 [GRCh37]
Chr14:14q23.2		 uncertain significance
NM_001530.4(HIF1A):c.2194G>A (p.Val732Ile) single nucleotide variant not specified [RCV004280991] Chr14:61744805 [GRCh38]
Chr14:62211523 [GRCh37]
Chr14:14q23.2		 uncertain significance
NM_001530.4(HIF1A):c.868A>T (p.Thr290Ser) single nucleotide variant not specified [RCV004262238] Chr14:61732512 [GRCh38]
Chr14:62199230 [GRCh37]
Chr14:14q23.2		 uncertain significance
NM_001530.4(HIF1A):c.1282G>A (p.Val428Ile) single nucleotide variant not specified [RCV004251457] Chr14:61738119 [GRCh38]
Chr14:62204837 [GRCh37]
Chr14:14q23.2		 uncertain significance
NM_001530.4(HIF1A):c.232T>A (p.Leu78Met) single nucleotide variant not specified [RCV004323454] Chr14:61721514 [GRCh38]
Chr14:62188232 [GRCh37]
Chr14:14q23.2		 uncertain significance
NM_001530.4(HIF1A):c.1964C>T (p.Thr655Ile) single nucleotide variant not specified [RCV004352888] Chr14:61741059 [GRCh38]
Chr14:62207777 [GRCh37]
Chr14:14q23.2		 uncertain significance
NM_001530.4(HIF1A):c.1762G>A (p.Ala588Thr) single nucleotide variant not provided [RCV003482120] Chr14:61740857 [GRCh38]
Chr14:62207575 [GRCh37]
Chr14:14q23.2		 conflicting interpretations of pathogenicity|uncertain significance
NM_001530.4(HIF1A):c.639G>A (p.Lys213=) single nucleotide variant not provided [RCV003736353] Chr14:61727521 [GRCh38]
Chr14:62194239 [GRCh37]
Chr14:14q23.2		 benign
NM_001530.4(HIF1A):c.774-3C>T single nucleotide variant not provided [RCV003736355] Chr14:61732415 [GRCh38]
Chr14:62199133 [GRCh37]
Chr14:14q23.2		 likely benign
NM_001530.4(HIF1A):c.880+16G>T single nucleotide variant not provided [RCV003736371] Chr14:61732540 [GRCh38]
Chr14:62199258 [GRCh37]
Chr14:14q23.2		 likely benign
NM_001530.4(HIF1A):c.1496C>T (p.Pro499Leu) single nucleotide variant not specified [RCV004397131] Chr14:61738333 [GRCh38]
Chr14:62205051 [GRCh37]
Chr14:14q23.2		 uncertain significance
NM_001530.4(HIF1A):c.1631C>A (p.Thr544Lys) single nucleotide variant not specified [RCV004397132] Chr14:61740599 [GRCh38]
Chr14:62207317 [GRCh37]
Chr14:14q23.2		 uncertain significance
NM_001530.4(HIF1A):c.2438T>C (p.Leu813Pro) single nucleotide variant not specified [RCV004397140] Chr14:61747042 [GRCh38]
Chr14:62213760 [GRCh37]
Chr14:14q23.2		 uncertain significance
NM_001530.4(HIF1A):c.1471A>G (p.Met491Val) single nucleotide variant not specified [RCV004397130] Chr14:61738308 [GRCh38]
Chr14:62205026 [GRCh37]
Chr14:14q23.2		 uncertain significance
NM_001530.4(HIF1A):c.1766G>C (p.Ser589Thr) single nucleotide variant not specified [RCV004397134] Chr14:61740861 [GRCh38]
Chr14:62207579 [GRCh37]
Chr14:14q23.2		 uncertain significance
NM_001530.4(HIF1A):c.1788A>C (p.Gln596His) single nucleotide variant not specified [RCV004397135] Chr14:61740883 [GRCh38]
Chr14:62207601 [GRCh37]
Chr14:14q23.2		 uncertain significance
NM_001530.4(HIF1A):c.1732G>A (p.Asp578Asn) single nucleotide variant not specified [RCV004397133] Chr14:61740827 [GRCh38]
Chr14:62207545 [GRCh37]
Chr14:14q23.2		 uncertain significance
NM_001530.4(HIF1A):c.1792A>C (p.Thr598Pro) single nucleotide variant not specified [RCV004397136] Chr14:61740887 [GRCh38]
Chr14:62207605 [GRCh37]
Chr14:14q23.2		 uncertain significance
NM_001530.4(HIF1A):c.2011A>G (p.Arg671Gly) single nucleotide variant not specified [RCV004397137] Chr14:61741106 [GRCh38]
Chr14:62207824 [GRCh37]
Chr14:14q23.2		 uncertain significance
NM_001530.4(HIF1A):c.2077G>A (p.Val693Ile) single nucleotide variant not specified [RCV004397138] Chr14:61741172 [GRCh38]
Chr14:62207890 [GRCh37]
Chr14:14q23.2		 uncertain significance
NM_001530.4(HIF1A):c.2416A>G (p.Ile806Val) single nucleotide variant not specified [RCV004397139] Chr14:61747020 [GRCh38]
Chr14:62213738 [GRCh37]
Chr14:14q23.2		 likely benign
NM_001530.4(HIF1A):c.62A>G (p.Lys21Arg) single nucleotide variant not specified [RCV004397141] Chr14:61720408 [GRCh38]
Chr14:62187126 [GRCh37]
Chr14:14q23.2		 uncertain significance
NM_001530.4(HIF1A):c.781G>A (p.Glu261Lys) single nucleotide variant not specified [RCV004397142] Chr14:61732425 [GRCh38]
Chr14:62199143 [GRCh37]
Chr14:14q23.2		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:45
Count of miRNA genes:45
Interacting mature miRNAs:45
Transcripts:ENST00000554254
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 5 271 3 2 245 4 114 17 4 65 37 28 2 1 5 104
Low 1057 2134 759 188 868 109 2571 1195 1092 192 824 1169 90 758 1615 4
Below cutoff 1183 484 765 281 690 203 1491 910 2152 132 506 365 80 412 976 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000554254
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1461,715,558 - 61,751,163 (-)Ensembl
RefSeq Acc Id: ENST00000557544
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1461,680,723 - 61,695,892 (-)Ensembl
RefSeq Acc Id: ENST00000660325
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1461,707,313 - 61,751,099 (-)Ensembl
RefSeq Acc Id: ENST00000698324
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1461,707,746 - 61,750,920 (-)Ensembl
RefSeq Acc Id: ENST00000698325
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1461,709,200 - 61,751,098 (-)Ensembl
RefSeq Acc Id: ENST00000698326
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1461,745,662 - 61,751,115 (-)Ensembl
RefSeq Acc Id: ENST00000698327
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1461,718,521 - 61,751,100 (-)Ensembl
RefSeq Acc Id: ENST00000698331
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1461,707,298 - 61,751,041 (-)Ensembl
RefSeq Acc Id: ENST00000698332
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1461,707,305 - 61,750,979 (-)Ensembl
RefSeq Acc Id: ENST00000698333
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1461,709,249 - 61,751,042 (-)Ensembl
RefSeq Acc Id: ENST00000698334
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1461,715,537 - 61,751,056 (-)Ensembl
RefSeq Acc Id: ENST00000698335
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1461,742,964 - 61,750,948 (-)Ensembl
RefSeq Acc Id: ENST00000715697
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1461,680,899 - 61,751,037 (-)Ensembl
RefSeq Acc Id: NR_144368
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381461,715,558 - 61,751,097 (-)NCBI
T2T-CHM13v2.01455,922,126 - 55,957,665 (-)NCBI
Sequence:

Additional Information

Database Acc Id Source(s)
COSMIC HIF1A-AS3 COSMIC
Ensembl Genes ENSG00000258667 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000554254 ENTREZGENE
GTEx ENSG00000258667 GTEx
HGNC ID HGNC:54284 ENTREZGENE
Human Proteome Map HIF1A-AS3 Human Proteome Map
NCBI Gene HIF1A-AS3 ENTREZGENE
RNAcentral URS0000600EEF RNACentral