AC099342.1 (novel transcript) - Rat Genome Database

Name: AC099342.1
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: AC099342.1 (novel transcript) Homo sapiens

Analyze

Symbol:

AC099342.1

Name:

novel transcript

RGD ID:

16553385

Description:

Type:

ncrna (Ensembl: lncRNA)

RefSeq Status:

VALIDATED

Previously known as:

LOC101927769; uncharacterized LOC101927769

Allele / Splice:

See ClinVar data

Latest Assembly:

GRCh38.p14 Ensembl - Human Genome Assembly GRCh38 Ensembl

Position:

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	7	20,296,708 - 20,311,712 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	7	20,296,637 - 20,314,512 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	7	20,336,331 - 20,351,335 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Cytogenetic Map	7	p21.1	NCBI
HuRef	7	20,228,316 - 20,239,010 (+)	NCBI		HuRef
CHM1_1	7	20,340,895 - 20,351,576 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	7	20,431,666 - 20,446,657 (+)	NCBI		T2T-CHM13v2.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

References

Additional References at PubMed

PMID:9847074

Genomics

Variants

Variants in AC099342.1
2 total Variants

Clinical Variants

Name	Type	Condition(s)	Position(s)	Clinical significance
GRCh38/hg38 7p21.1(chr7:19178547-20733512)x3	copy number gain	See cases [RCV000136582]	Chr7:19178547..20733512 [GRCh38] Chr7:19218170..20773135 [GRCh37] Chr7:19184695..20739660 [NCBI36] Chr7:7p21.1	uncertain significance
GRCh38/hg38 7p21.1-15.3(chr7:19145712-22193713)x1	copy number loss	See cases [RCV000136842]	Chr7:19145712..22193713 [GRCh38] Chr7:19185335..22233331 [GRCh37] Chr7:19151860..22199856 [NCBI36] Chr7:7p21.1-15.3	pathogenic
GRCh38/hg38 7p22.3-15.3(chr7:45130-25221165)x3	copy number gain	See cases [RCV000137824]	Chr7:45130..25221165 [GRCh38] Chr7:45130..25260784 [GRCh37] Chr7:140213..25227309 [NCBI36] Chr7:7p22.3-15.3	pathogenic
GRCh38/hg38 7p22.3-14.2(chr7:54185-37089712)x3	copy number gain	See cases [RCV000053530]	Chr7:54185..37089712 [GRCh38] Chr7:54185..37129317 [GRCh37] Chr7:149268..37095842 [NCBI36] Chr7:7p22.3-14.2	pathogenic
GRCh38/hg38 7p22.3-15.2(chr7:54185-26827634)x3	copy number gain	See cases [RCV000136557]	Chr7:54185..26827634 [GRCh38] Chr7:54185..26867253 [GRCh37] Chr7:149268..26833778 [NCBI36] Chr7:7p22.3-15.2	pathogenic
GRCh38/hg38 7p21.1-15.2(chr7:20210912-27849400)x1	copy number loss	See cases [RCV000134333]	Chr7:20210912..27849400 [GRCh38] Chr7:20250535..27889019 [GRCh37] Chr7:20217060..27855544 [NCBI36] Chr7:7p21.1-15.2	pathogenic
GRCh38/hg38 7p22.3-15.2(chr7:43360-27196404)x3	copy number gain	See cases [RCV000143586]	Chr7:43360..27196404 [GRCh38] Chr7:43360..27236023 [GRCh37] Chr7:138443..27202548 [NCBI36] Chr7:7p22.3-15.2	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 7p21.3-15.2(chr7:10610069-25760560)x1	copy number loss	See cases [RCV000142708]	Chr7:10610069..25760560 [GRCh38] Chr7:10649696..25800180 [GRCh37] Chr7:10616221..25766705 [NCBI36] Chr7:7p21.3-15.2	pathogenic
GRCh38/hg38 7p22.3-15.3(chr7:53985-24361531)x3	copy number gain	See cases [RCV000053528]	Chr7:53985..24361531 [GRCh38] Chr7:53985..24401150 [GRCh37] Chr7:149068..24367675 [NCBI36] Chr7:7p22.3-15.3	pathogenic
GRCh38/hg38 7p22.3-14.1(chr7:54185-41875885)x3	copy number gain	See cases [RCV000051159]	Chr7:54185..41875885 [GRCh38] Chr7:54185..41915483 [GRCh37] Chr7:149268..41882008 [NCBI36] Chr7:7p22.3-14.1	pathogenic
GRCh38/hg38 7p21.2-15.3(chr7:15533812-24851432)x1	copy number loss	See cases [RCV000137924]	Chr7:15533812..24851432 [GRCh38] Chr7:15573437..24891051 [GRCh37] Chr7:15539962..24857576 [NCBI36] Chr7:7p21.2-15.3	pathogenic
GRCh38/hg38 7p21.2-15.2(chr7:16234212-26167278)x3	copy number gain	See cases [RCV000053531]	Chr7:16234212..26167278 [GRCh38] Chr7:16273837..26206898 [GRCh37] Chr7:16240362..26173423 [NCBI36] Chr7:7p21.2-15.2	pathogenic
GRCh38/hg38 7p22.3-15.2(chr7:1698124-27207295)x3	copy number gain	See cases [RCV000143060]	Chr7:1698124..27207295 [GRCh38] Chr7:1737760..27246914 [GRCh37] Chr7:1704286..27213439 [NCBI36] Chr7:7p22.3-15.2	pathogenic
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 7p21.2-21.1(chr7:16121516-20607899)x1	copy number loss	See cases [RCV000137236]	Chr7:16121516..20607899 [GRCh38] Chr7:16161141..20647522 [GRCh37] Chr7:16127666..20614047 [NCBI36] Chr7:7p21.2-21.1	pathogenic
GRCh38/hg38 7p22.1-15.2(chr7:5682209-27230311)x3	copy number gain	See cases [RCV000136649]	Chr7:5682209..27230311 [GRCh38] Chr7:5721840..27269930 [GRCh37] Chr7:5688366..27236455 [NCBI36] Chr7:7p22.1-15.2	pathogenic
GRCh38/hg38 7p21.1(chr7:18660228-20666885)x3	copy number gain	See cases [RCV000138724]	Chr7:18660228..20666885 [GRCh38] Chr7:18699851..20706508 [GRCh37] Chr7:18666376..20673033 [NCBI36] Chr7:7p21.1	uncertain significance
GRCh38/hg38 7p21.1-15.3(chr7:18505390-21417733)x1	copy number loss	See cases [RCV000052304]	Chr7:18505390..21417733 [GRCh38] Chr7:18545013..21457351 [GRCh37] Chr7:18511538..21423876 [NCBI36] Chr7:7p21.1-15.3	pathogenic

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	168
Count of miRNA genes:	127
Interacting mature miRNAs:	129
Transcripts:	ENST00000446399, ENST00000453564, ENST00000455373
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
High
Medium					6						2
Low	13		1	1	95	2	3	1		5	373	15	2
Below cutoff	174	53	75	47	252	19	363	37	212	138	158	176	34	39	215

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NR_110117	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC099342	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AK026386	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BX091547	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CP068271	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENST00000446399

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	7	20,296,638 - 20,311,717 (+)	Ensembl

RefSeq Acc Id:

ENST00000453564

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	7	20,298,294 - 20,300,625 (+)	Ensembl

RefSeq Acc Id:

ENST00000455373

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	7	20,305,711 - 20,311,712 (+)	Ensembl

RefSeq Acc Id:

ENST00000664310

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	7	20,296,637 - 20,314,512 (+)	Ensembl

RefSeq Acc Id:

ENST00000668568

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	7	20,296,656 - 20,311,464 (+)	Ensembl

RefSeq Acc Id:

ENST00000668992

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	7	20,305,468 - 20,311,714 (+)	Ensembl

RefSeq Acc Id:

ENST00000669469

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	7	20,296,687 - 20,314,483 (+)	Ensembl

RefSeq Acc Id:

ENST00000669632

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	7	20,296,644 - 20,300,652 (+)	Ensembl

RefSeq Acc Id:

NR_110117

RefSeq Status:

VALIDATED

Type:

NON-CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	7	20,296,708 - 20,311,712 (+)	NCBI
T2T-CHM13v2.0	7	20,431,666 - 20,446,657 (+)	NCBI

Sequence:

show sequence

GACAGTGAAAGATTTCGCCAACATATTCAGAATAGCATGCAATTTAAAACTTATTTTGAAGTTG
GAAGAAGTGGCAAAATGTGAAAAGCAAGAAGCAAGTATTACCAGAGACACCTATGAAAAAGAAA
TCTTTCTGAAGAACATTTTTAAAGTGCCATAATCTGTTCGGTGAATCCAAAGGCTGAAAGAGAC
TGAGTAACAGCTATTAAGTAAGGTGAAAATGTTATTTTACATGGAAACCTATTTTGTTCCATAA
AACTAAATAAACCATAACCCAGAAGTGCAATGAGACACACACAGCATGACCACATTATTTCTGA
AAGCTGAAGAGTTGCCAGTCTGTTGATCTCAAACTTCATGAACCACACAGTTCAGTTCAAATTG
TTTCCCTGAAATTGCTTTGAGCCTCTGCCAAACAGCCACTGAAGGACTCCGAAAAATACAAGAA
CTGAAAGGGGCACATGGCAGATACAATCATAAACTTTCATTTCGGAGAGCAGTAAAAAAGGAGA
AGAAGAACACACTGGTACTCCAACAAGTCATAGTTTCTGCCAGATGTTGCAAAAGTGAGTTAGA
TAACTGACCTTTCTTCTGGGGCCTGTGTCAACTTTGAATGGAGCTTTCAATTGTACAATAAGCA
TCTGGACAGTTTTGACATCTTTATAACACTCTTTGAGTTCTTAAAAAGCTACCATTTTGTTTAA
AGATGATTTATGTGAAGATTAAAACAATTACTTAAGTGCTAAGAATAATTAATCCTGTAACTCC
ATATCAATACCATTATCTTCCCAGAACTGGGTCTCTAACTACTAATCATAATCAAGACACCAAC
TGTCAAATCAAATCAAAATTAAAATTTGATTAATTATTTGATGATATTAACATTCAAATCTAGT
TCCTTCTTAGGCCTAATTTTGTCCTTATGTTTGCTTTGCACTGAATTATTGTGGTTTAAATAGC
CCATTTTACATGACAACTTTCAAACAAGAGCATAAATTCTCATAAAAACAGGCTAAGGAATTCA
TAATGATAGCTCTTGGCCGCCACCTAAAGGTTTATTTCTTGTTTTATTTTACATGAGACCTACT
ATGCATTCCTTTTATAATAAAATTGTTGTCTTGTCAAAAAAAAAAAAAAAAAAAA

hide sequence

Additional Information

External Database Links

Database	Acc Id	Source(s)
COSMIC	AC099342.1	COSMIC
Ensembl Genes	ENSG00000226097	Ensembl, ENTREZGENE
Ensembl Transcript	ENST00000446399	ENTREZGENE
GTEx	ENSG00000226097	GTEx
Human Proteome Map	AC099342.1	Human Proteome Map
NCBI Gene	LOC101927769	ENTREZGENE
RNAcentral	URS000075C617	RNACentral

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2020-06-25	AC099342.1	novel transcript	LOC101927769	uncharacterized LOC101927769	Symbol and/or name change	19259462	PROVISIONAL
2020-06-18	LOC101927769	uncharacterized LOC101927769	AC099342.1	novel transcript	Symbol and/or name change	5135510	APPROVED

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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