Long non-coding RNA Human Homo sapiens

MALAT1

metastasis associated lung adenocarcinoma transcript 1

Long non-coding RNA (HGNC: RNA, long non-coding)

Human MALAT1MouseRat

Reading the ortholog votes for mouse and rat.

Long non-coding RNA Human Homo sapiens

MALAT1

Reading the record for MALAT1 from HGNC, NCBI Gene and Ensembl.Still reading. A first read of a long non-coding RNA can take a while; this page waits up to 130 seconds for it, and its scripts then bring in the page, or a line saying what did not arrive.

The full name, the identifiers, the location and the notes from the sources arrive with the record. Nothing is filled in ahead of it.

Order door

The door to order for MALAT1 opens with the record, which decides which product it carries. The order page itself is open now.

Bring your own sequence

For research use only. Not for use in diagnostic or therapeutic procedures.

This page is still reading the record. Its scripts replace this shell with the record when it arrives; with scripts off, it stays at this shell however long you wait.

01 What this RNA is

What MALAT1 is, by each authority

Waiting for the record before reading NCBI Gene, the Alliance and RGD.

02 Transcripts and the map

The transcripts of MALAT1, drawn

Waiting for the record before reading NCBI Datasets and Ensembl.

03 The locus

The MALAT1 locus: partners, antisense genes and small RNAs

Waiting for the record before reading Ensembl and miRBase.

04 In other species

The same gene in mouse, rat and human

Waiting for the record before reading the Alliance, NCBI, Ensembl Compara and RGD.

05 Cross-references

MALAT1 at RNAcentral and in HGNC's cross-references

Waiting for the record before reading RNAcentral.

06 Expression

Where MALAT1 is expressed

Waiting for the record before reading GTEx and the Human Protein Atlas.

07 Literature

Papers that mention MALAT1

Waiting for the record before reading Europe PMC.

08 AUM BioTech's studies on this RNA

AUM BioTech's published work on MALAT1

Waiting for the record before reading the publication records.

Knocking down MALAT1

The order page opens with MALAT1 and human filled in, on AUMlnc sdASO, with AUMlnc toASO beside it, and the price on that page. Six steps come first, each with the sources it rests on.

Choose the transcript

The map above shows the isoforms Ensembl and RefSeq annotate and which exons they share; the MANE Select, where one exists, identifies a representative transcript [R09], and MANE Select lncRNAs began in MANE v1.4 available in Ensembl release 113 [R10]. An oligonucleotide acts on every transcript that carries its target sequence, so a region every isoform shares reaches all of them and a region unique to one isoform reaches that one. (reasoning from the cited findings, not a finding) [R45] [R09] [R10] [R11] [R45]

Know what the transcript holds

A snoRNA or a microRNA hosted inside it is encoded within the host gene [R36] [R54]; an RNase H design pairs with its target strand by hybridization of an ASO to the RNA target [R47]. Whether the small RNA changes when the host is knocked down is not claimed. [R36] [R54] [R47] [R02] [R39]

Check where it is expressed

GTEx's medians (card 6) say which human tissues carry it [R29]; a cell line's own level is measured before the knockdown, by RT-qPCR against a matched control [R47], because lncRNA expression is strongly tissue- and cell-type-specific and a tissue median does not give a line's level. [R44] [R08] [R01] [R29] [R28] [R47] [R44] [R08] [R01] [R50] [R51]

Read the second species from its own transcript

Card 4 names the ortholog where a curated assertion or a method names one [R23]; lncRNA conservation lies in short patches of specific sequences [R42], so the mouse or rat design is made against that species' own sequence, and where no gene is named the sequence door is the route. [R23] [R42] [R45] [R43]

Run the controls

The published practice is the appropriate chemically modified negative control oligonucleotide at the same dose [R47] and a positive control against a gene known to respond, which shows that delivery worked [R47]; the order page offers a scramble control at the same size, and a positive control for the same species at the same size. [R47]

Measure the knockdown at the RNA

LncRNA knockdown was measured by reverse transcription quantitative PCR (RT-qPCR) [R47], with assays at more than one position along the transcript; RNase H ASOs act upon nascent transcripts and, consequently, induce premature transcription termination downstream of the cleavage site [R48] and reduce the level of spliced RNA associated with chromatin [R49], so where the primer pair sits on the transcript decides what it measures. The gene is annotated as non-coding, so there is no annotated protein to blot. [R44] [R07] [R51] The studies in card 8 show what AUM BioTech's customers measured. [R47] [R48] [R49] [R51] [R44] [R07]

What the sources say

A knockdown antisense oligonucleotide is a short single strand that binds its target RNA by base pairing. The RNA strand of the resulting RNA:DNA duplex is cut by RNase H1, and the fragments are cleared by the cell's normal RNA decay. [R45] [R47] [R46]

One study of lncRNA knockdown reagents in cultured cells reports: We found that nuclear lncRNAs were more effectively suppressed using ASOs, cytoplasmic lncRNAs were more effectively suppressed using RNAi and dual-localized lncRNAs were suppressed using both methods. [R47] The same paper records evidence against a simple rule: Contrary to this evidence, the degradative RNAi protein AGO2 has been detected in the nucleus (45,58–61) and reports show that the nuclear 7SK RNA can successfully be silenced by siRNAs (62,63). [R47] This is one study's finding, about reagents transfected into HeLa cells in culture.

[R45] Crooke ST, Liang XH, Baker BF, Crooke RM (2021). Antisense technology: A review. Journal of Biological Chemistry 296:100416. PMID 33600796, doi 10.1016/j.jbc.2021.100416.
[R46] Liang XH, Sun H, Nichols JG, Crooke ST (2017). RNase H1-Dependent Antisense Oligonucleotides Are Robustly Active in Directing RNA Cleavage in Both the Cytoplasm and the Nucleus. Molecular Therapy 25:2075-2092. PMID 28663102, doi 10.1016/j.ymthe.2017.06.002.
[R47] Lennox KA, Behlke MA (2016). Cellular localization of long non-coding RNAs affects silencing by RNAi more than by antisense oligonucleotides. Nucleic Acids Research 44:863-877. PMID 26578588, doi 10.1093/nar/gkv1206.

AUMlnc sdASO or toASO, chosen on the next page

[R01] Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen LL, et al. (2023). Long non-coding RNAs: definitions, functions, challenges and recommendations. Nature Reviews Molecular Cell Biology 24:430-447. PMID 36596869, doi 10.1038/s41580-022-00566-8.
[R02] Seal RL, Chen LL, Griffiths-Jones S, Lowe TM, Mathews MB, O'Reilly D, et al. (2020). A guide to naming human non‐coding RNA genes. The EMBO Journal 39:e103777. PMID 32090359, doi 10.15252/embj.2019103777.
[R07] Frankish A, Carbonell-Sala S, Diekhans M, Jungreis I, Loveland JE, Mudge JM, et al. (2023). GENCODE: reference annotation for the human and mouse genomes in 2023. Nucleic Acids Research 51:D942-D949. PMID 36420896, doi 10.1093/nar/gkac1071.
[R08] Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, et al. (2012). The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Genome Research 22:1775-1789. PMID 22955988, doi 10.1101/gr.132159.111.
[R09] Morales J, Pujar S, Loveland JE, Astashyn A, Bennett R, Berry A, et al. (2022). A joint NCBI and EMBL-EBI transcript set for clinical genomics and research. Nature 604:310-315. PMID 35388217, doi 10.1038/s41586-022-04558-8.
[R10] Dyer SC, Austine-Orimoloye O, Azov AG, Barba M, Barnes I, Barrera-Enriquez VP, et al. (2025). Ensembl 2025. Nucleic Acids Research 53:D948-D957. PMID 39656687, doi 10.1093/nar/gkae1071.
[R11] Yates AD, Austine-Orimoloye O, Azov AG, Barba M, Barnes I, Barrera-Enriquez VP, et al. (2026). Ensembl 2026. Nucleic Acids Research 54:D1053-D1060. PMID 41296548, doi 10.1093/nar/gkaf1239.
[R23] Alliance of Genome Resources Consortium (2020). Alliance of Genome Resources Portal: unified model organism research platform. Nucleic Acids Research 48:D650-D658. PMID 31552413, doi 10.1093/nar/gkz813.
[R28] GTEx Consortium (2013). The Genotype-Tissue Expression (GTEx) project. Nature Genetics 45:580-585. PMID 23715323, doi 10.1038/ng.2653.
[R29] GTEx Consortium (2020). The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science 369:1318-1330. PMID 32913098, doi 10.1126/science.aaz1776.
[R36] Smith CM, Steitz JA (1998). Classification of gas5 as a Multi-Small-Nucleolar-RNA (snoRNA) Host Gene and a Member of the 5′-Terminal Oligopyrimidine Gene Family Reveals Common Features of snoRNA Host Genes. Molecular and Cellular Biology 18:6897-6909. PMID 9819378, doi 10.1128/mcb.18.12.6897.
[R39] Rodriguez A, Griffiths-Jones S, Ashurst JL, Bradley A (2004). Identification of Mammalian microRNA Host Genes and Transcription Units. Genome Research 14:1902-1910. PMID 15364901, doi 10.1101/gr.2722704.
[R42] Hezroni H, Koppstein D, Schwartz MG, Avrutin A, Bartel DP, Ulitsky I (2015). Principles of Long Noncoding RNA Evolution Derived from Direct Comparison of Transcriptomes in 17 Species. Cell Reports 11:1110-1122. PMID 25959816, doi 10.1016/j.celrep.2015.04.023.
[R43] Ulitsky I (2016). Evolution to the rescue: using comparative genomics to understand long non-coding RNAs. Nature Reviews Genetics 17:601-614. PMID 27573374, doi 10.1038/nrg.2016.85.
[R44] Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, et al. (2011). Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes & Development 25:1915-1927. PMID 21890647, doi 10.1101/gad.17446611.
[R45] Crooke ST, Liang XH, Baker BF, Crooke RM (2021). Antisense technology: A review. Journal of Biological Chemistry 296:100416. PMID 33600796, doi 10.1016/j.jbc.2021.100416.
[R46] Liang XH, Sun H, Nichols JG, Crooke ST (2017). RNase H1-Dependent Antisense Oligonucleotides Are Robustly Active in Directing RNA Cleavage in Both the Cytoplasm and the Nucleus. Molecular Therapy 25:2075-2092. PMID 28663102, doi 10.1016/j.ymthe.2017.06.002.
[R47] Lennox KA, Behlke MA (2016). Cellular localization of long non-coding RNAs affects silencing by RNAi more than by antisense oligonucleotides. Nucleic Acids Research 44:863-877. PMID 26578588, doi 10.1093/nar/gkv1206.
[R48] Lee JS, Mendell JT (2020). Antisense-Mediated Transcript Knockdown Triggers Premature Transcription Termination. Molecular Cell 77:1044-1054.e3. PMID 31924448, doi 10.1016/j.molcel.2019.12.011.
[R49] Lai F, Damle SS, Ling KK, Rigo F (2020). Directed RNase H Cleavage of Nascent Transcripts Causes Transcription Termination. Molecular Cell 77:1032-1043.e4. PMID 31924447, doi 10.1016/j.molcel.2019.12.029.
[R50] Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, et al. (2009). The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments. Clinical Chemistry 55:611-622. PMID 19246619, doi 10.1373/clinchem.2008.112797.
[R51] Bustin SA, Ruijter JM, van den Hoff MJB, Kubista M, Pfaffl MW, Shipley GL, et al. (2025). MIQE 2.0: Revision of the Minimum Information for Publication of Quantitative Real-Time PCR Experiments Guidelines. Clinical Chemistry 71:634-651. PMID 40272429, doi 10.1093/clinchem/hvaf043.
[R54] Cai X, Cullen BR (2007). The imprinted H19 noncoding RNA is a primary microRNA precursor. RNA 13:313-316. PMID 17237358, doi 10.1261/rna.351707.

For research use only. Not for use in diagnostic or therapeutic procedures.

RefSeq transcripts of this gene
Accession	Name	Biotype	Labels	Exons	Spliced length	Protein	Sequence
NR_002819.5matches ENST00000850956.1	transcript variant 1	non coding	MANE Select	1	7,472 nt	none	Ready in a moment
NR_144567.1	transcript variant 2	non coding	none	2	8,545 nt	none	Ready in a moment
NR_144568.1	transcript variant 3	non coding	none	3	8,302 nt	none	Ready in a moment

Accession

Name

Biotype

Labels

Exons

Spliced length

Protein

Sequence

NR_002819.5matches ENST00000850956.1

transcript variant 1

non coding

MANE Select

7,472 nt

none

Ready in a moment

NR_144567.1

transcript variant 2

non coding

none

8,545 nt

none

Ready in a moment

NR_144568.1

transcript variant 3

non coding

none

8,302 nt

none

Ready in a moment

Ensembl transcripts of this gene
Accession	Name	Biotype	Labels	Exons	Spliced length	Protein	Sequence
ENST00000850956.1matches NR_002819.5	MALAT1-273	lncrna	MANE SelectEnsembl canonical	1	7,472 nt	none	Ready in a moment

Accession

Name

Biotype

Labels

Exons

Spliced length

Protein

Sequence

ENST00000850956.1matches NR_002819.5

MALAT1-273

lncrna

MANE SelectEnsembl canonical

7,472 nt

none

Ready in a moment

MALAT1

MALAT1

What MALAT1 is, by each authority

The transcripts of MALAT1, drawn

The MALAT1 locus: partners, antisense genes and small RNAs

The same gene in mouse, rat and human

MALAT1 at RNAcentral and in HGNC's cross-references

Where MALAT1 is expressed

Papers that mention MALAT1

AUM BioTech's published work on MALAT1

MALAT1

What MALAT1 is, by each authority

Each authority's word, as its record carries it

HGNC's recordHGNC:29665

NCBI Gene's record378938

Ensembl's recordENSG00000251562.13

The Alliance's recordHGNC:29665

RGD's record

The transcripts of MALAT1, drawn

The MALAT1 locus: partners, antisense genes and small RNAs

The same gene in mouse, rat and human

MALAT1 at RNAcentral and in HGNC's cross-references

Where MALAT1 is expressed

Papers that mention MALAT1

AUM BioTech's published work on MALAT1

Knocking down MALAT1

Choose the transcript

Know what the transcript holds

Check where it is expressed

Read the second species from its own transcript

Run the controls

Measure the knockdown at the RNA

RefSeq 3 transcripts

A window on one transcript

Ensembl 73 transcripts

A window on one transcript

RefSeq 3 transcripts

A window on one transcript

Ensembl 73 transcripts

A window on one transcript

Each authority's word, as its record carries it

HGNC's recordHGNC:29665

NCBI Gene's record378938

Ensembl's recordENSG00000251562.13

The Alliance's recordHGNC:29665

RGD's record