LINC01446 (long intergenic non-protein coding RNA 1446) - Rat Genome Database

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Gene: LINC01446 (long intergenic non-protein coding RNA 1446) Homo sapiens
Analyze
Symbol: LINC01446
Name: long intergenic non-protein coding RNA 1446
RGD ID: 1602028
HGNC Page HGNC:50773
Description: ASSOCIATED WITH Autism; autistic disorder; INTERACTS WITH 4,4'-sulfonyldiphenol; arsenite(3-)
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: GS1-179L18.1
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38753,655,509 - 53,811,931 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl753,655,508 - 53,811,952 (-)EnsemblGRCh38hg38GRCh38
GRCh37753,723,202 - 53,879,624 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36753,801,332 - 53,847,112 (-)NCBINCBI36Build 36hg18NCBI36
Celera753,783,722 - 53,940,133 (-)NCBICelera
Cytogenetic Map7p12.1NCBI
HuRef753,572,306 - 53,729,239 (-)NCBIHuRef
CHM1_1753,725,882 - 53,882,311 (-)NCBICHM1_1
T2T-CHM13v2.0753,817,107 - 53,973,533 (-)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v2753,728,628 - 53,885,030 (-)NCBI
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
Autism  (IAGP)
References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations

Genomics

Variants

.
Variants in LINC01446
3 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NR_038371.1(LINC01446):n.425-9792C>G single nucleotide variant Lung cancer [RCV000106138] Chr7:53789830 [GRCh38]
Chr7:53857523 [GRCh37]
Chr7:7p12.1		 uncertain significance
NR_038371.1(LINC01446):n.425-15297G>T single nucleotide variant Lung cancer [RCV000106139] Chr7:53795335 [GRCh38]
Chr7:53863028 [GRCh37]
Chr7:7p12.1		 uncertain significance
GRCh38/hg38 7p22.3-q36.3(chr7:54185-159282390)x1 copy number loss See cases [RCV000135401] Chr7:54185..159282390 [GRCh38]
Chr7:54185..159075079 [GRCh37]
Chr7:149268..158767840 [NCBI36]
Chr7:7p22.3-q36.3		 pathogenic
GRCh38/hg38 7p13-12.1(chr7:44571949-53699760)x1 copy number loss See cases [RCV000134973] Chr7:44571949..53699760 [GRCh38]
Chr7:44611548..53767453 [GRCh37]
Chr7:44578073..53734947 [NCBI36]
Chr7:7p13-12.1		 pathogenic
GRCh38/hg38 7p14.1-11.2(chr7:40534157-56107122)x1 copy number loss See cases [RCV000136092] Chr7:40534157..56107122 [GRCh38]
Chr7:40573756..56174815 [GRCh37]
Chr7:40540281..56142309 [NCBI36]
Chr7:7p14.1-11.2		 pathogenic
GRCh38/hg38 7p22.3-q36.3(chr7:53985-159282531)x1 copy number loss See cases [RCV000052250] Chr7:53985..159282531 [GRCh38]
Chr7:53985..159075220 [GRCh37]
Chr7:149068..158767981 [NCBI36]
Chr7:7p22.3-q36.3		 pathogenic
GRCh38/hg38 7p12.1-11.2(chr7:52114454-57434735)x1 copy number loss See cases [RCV000052656] Chr7:52114454..57434735 [GRCh38]
Chr7:52182150..57493216 [GRCh37]
Chr7:52149644..57498383 [NCBI36]
Chr7:7p12.1-11.2		 uncertain significance
GRCh38/hg38 7p12.1-11.2(chr7:52192528-57823293)x3 copy number gain See cases [RCV000053439] Chr7:52192528..57823293 [GRCh38]
Chr7:52260224..57882999 [GRCh37]
Chr7:52227718..57886941 [NCBI36]
Chr7:7p12.1-11.2		 uncertain significance
GRCh38/hg38 7p12.1-11.2(chr7:53450330-56107195)x3 copy number gain See cases [RCV000053440] Chr7:53450330..56107195 [GRCh38]
Chr7:53518023..56174888 [GRCh37]
Chr7:53485517..56142382 [NCBI36]
Chr7:7p12.1-11.2		 uncertain significance
GRCh38/hg38 7p14.3-q11.21(chr7:33328312-62377476)x3 copy number gain See cases [RCV000053532] Chr7:33328312..62377476 [GRCh38]
Chr7:33367924..61831899 [GRCh37]
Chr7:33334449..61469334 [NCBI36]
Chr7:7p14.3-q11.21		 pathogenic
GRCh38/hg38 7p12.1-q11.22(chr7:53274059-68576213)x3 copy number gain See cases [RCV000053534] Chr7:53274059..68576213 [GRCh38]
Chr7:53341752..68041200 [GRCh37]
Chr7:53309246..67679136 [NCBI36]
Chr7:7p12.1-q11.22		 pathogenic
Single allele duplication Autism [RCV000754332] Chr7:52551984..56315037 [GRCh38]
Chr7:7p12.1-11.2		 likely pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:48
Count of miRNA genes:48
Interacting mature miRNAs:48
Transcripts:ENST00000380970
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 adipose tissue appendage entire extraembryonic component
High
Medium 4 4 2 2 2 11 2 3 17
Low 24 6 62 49 43 51 61 18 30 17 300 78 2 2 4 2
Below cutoff 742 642 594 155 236 120 874 474 721 63 418 498 36 338 582 3

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000380970
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl753,655,509 - 53,811,931 (-)Ensembl
RefSeq Acc Id: ENST00000650830
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl753,710,389 - 53,811,942 (-)Ensembl
RefSeq Acc Id: ENST00000651244
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl753,656,791 - 53,694,059 (-)Ensembl
RefSeq Acc Id: ENST00000651506
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl753,770,673 - 53,811,942 (-)Ensembl
RefSeq Acc Id: ENST00000651858
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl753,770,399 - 53,811,942 (-)Ensembl
RefSeq Acc Id: ENST00000651951
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl753,771,113 - 53,811,942 (-)Ensembl
RefSeq Acc Id: ENST00000652029
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl753,766,019 - 53,780,038 (-)Ensembl
RefSeq Acc Id: ENST00000652104
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl753,765,495 - 53,811,942 (-)Ensembl
RefSeq Acc Id: ENST00000652440
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl753,691,177 - 53,811,942 (-)Ensembl
RefSeq Acc Id: ENST00000654050
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl753,770,080 - 53,811,769 (-)Ensembl
RefSeq Acc Id: ENST00000656718
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl753,765,495 - 53,811,935 (-)Ensembl
RefSeq Acc Id: ENST00000656885
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl753,770,080 - 53,811,942 (-)Ensembl
RefSeq Acc Id: ENST00000658338
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl753,770,701 - 53,811,942 (-)Ensembl
RefSeq Acc Id: ENST00000659250
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl753,691,182 - 53,811,931 (-)Ensembl
RefSeq Acc Id: ENST00000659481
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl753,691,182 - 53,811,937 (-)Ensembl
RefSeq Acc Id: ENST00000659794
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl753,691,181 - 53,811,942 (-)Ensembl
RefSeq Acc Id: ENST00000660413
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl753,691,170 - 53,811,942 (-)Ensembl
RefSeq Acc Id: ENST00000660945
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl753,656,152 - 53,811,942 (-)Ensembl
RefSeq Acc Id: ENST00000660958
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl753,770,080 - 53,811,952 (-)Ensembl
RefSeq Acc Id: ENST00000661502
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl753,656,792 - 53,811,931 (-)Ensembl
RefSeq Acc Id: ENST00000662259
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl753,691,182 - 53,811,931 (-)Ensembl
RefSeq Acc Id: ENST00000662931
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl753,656,478 - 53,811,931 (-)Ensembl
RefSeq Acc Id: ENST00000663138
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl753,655,863 - 53,811,951 (-)Ensembl
RefSeq Acc Id: ENST00000663312
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl753,691,169 - 53,811,951 (-)Ensembl
RefSeq Acc Id: ENST00000663872
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl753,770,079 - 53,811,935 (-)Ensembl
RefSeq Acc Id: ENST00000665927
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl753,691,177 - 53,811,942 (-)Ensembl
RefSeq Acc Id: ENST00000666213
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl753,691,167 - 53,811,935 (-)Ensembl
RefSeq Acc Id: ENST00000668489
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl753,764,481 - 53,811,928 (-)Ensembl
RefSeq Acc Id: ENST00000669638
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl753,691,186 - 53,811,931 (-)Ensembl
RefSeq Acc Id: ENST00000670507
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl753,691,182 - 53,811,942 (-)Ensembl
RefSeq Acc Id: ENST00000670902
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl753,655,508 - 53,780,235 (-)Ensembl
RefSeq Acc Id: ENST00000670945
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl753,656,794 - 53,811,931 (-)Ensembl
RefSeq Acc Id: NR_038371
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38753,655,509 - 53,811,931 (-)NCBI
GRCh37753,723,202 - 53,879,624 (-)NCBI
HuRef753,572,306 - 53,729,239 (-)RGD
CHM1_1753,725,882 - 53,882,311 (-)NCBI
T2T-CHM13v2.0753,817,107 - 53,973,533 (-)NCBI
CRA_TCAGchr7v2753,728,628 - 53,885,030 (-)ENTREZGENE
Sequence:
Protein Sequences
GenBank Protein BAC87170 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences

Promoters
RGD ID:15096140
Promoter ID:EPDNEWNC_H970
Type:initiation region
Name:LINC01446_1
Description:long intergenic non-protein coding RNA 1446 [Source:HGNCSymbol;Acc:HGNC:50773]
SO ACC ID:SO:0000170
Source:EPDNEWNC (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38753,811,940 - 53,812,000EPDNEWNC
RGD ID:6805601
Promoter ID:HG_KWN:57449
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:K562
Transcripts:ENST00000380970
Position:
Human AssemblyChrPosition (strand)Source
Build 36753,846,856 - 53,847,356 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
COSMIC LINC01446 COSMIC
Ensembl Genes ENSG00000205628 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000380970 ENTREZGENE
GTEx ENSG00000205628 GTEx
HGNC ID HGNC:50773 ENTREZGENE
Human Proteome Map LINC01446 Human Proteome Map
NCBI Gene 401337 ENTREZGENE
RNAcentral URS00003AA7A2 RNACentral


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-06-24 LINC01446  long intergenic non-protein coding RNA 1446  FLJ45974  uncharacterized LOC401337  Symbol and/or name change 5135510 APPROVED
2011-11-01 FLJ45974  uncharacterized LOC401337  FLJ45974  hypothetical LOC401337  Symbol and/or name change 5135510 APPROVED
2011-07-27 FLJ45974  hypothetical LOC401337  FLJ45974  FLJ45974 protein  Symbol and/or name change 5135510 APPROVED