Gene Rat Rattus norvegicus

Col11a1

collagen type XI alpha 1 chain

protein coding

HumanMouseRat Col11a1

Reading the ortholog votes for human and mouse.

HGNC and MANE Select: not available for rat. HGNC names human genes; RGD is the authority here, and MANE Select is defined for human transcripts only.

Location: Cytogenetic band 2q42NCBI: 2:204,509,136-204,702,264 on the plus strand, GRCr8 (GCF_036323735.1), sequence NC_086020.1, annotation GCF_036323735.1-RS_2026_08 of 2026-08-17Ensembl: no location was read.Coordinates are one-based with both ends included, as each source reports them.

Gene identity, from NCBI Datasets · NCBI Datasets 18.37.0 · read 2026-09-24 ET · RGD:2372Data from NCBI, provided as is; NCBI's policies and disclaimers apply.

Notes from the sources

Ensembl did not answer (upstream error).
Ensembl did not answer (upstream error); the Ensembl location and release are missing

Silence this gene

The order page opens with Col11a1 and rat filled in. The sequences are designed against the transcripts below; the price is on that page.

Order for Col11a1

sdASO, toASO or siRNA, chosen on the next page

Bring your own sequence Transcripts

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

Summary
Transcripts
Expression
Protein
Interactions
Pathways
Disease
Variants
Constraint
Orthologs
MicroRNAs
Long non-coding RNAs
Literature
Silencing this gene

A line below that says it is reading needs JavaScript to be replaced: with scripts off, it stays at that line however long you wait. Opening a card also needs JavaScript.

Ready in a moment

01 Summary and function

What Col11a1 does

Enables heparan sulfate binding activity and heparin binding activity.

NCBI Gene summary

Ready in a moment

02 Transcripts and isoforms

The RNA a design targets

3 RefSeq transcripts on GRCr8; RefSeq Select NM_013117.1. Ensembl is not answering, so the Ensembl transcripts could not be shown. Try again later. Reference e39db104-d23.

NCBI Datasets

Ready in a moment

03 Expression by tissue

Where Col11a1 is expressed

Expression by tissue: not available for rat. GTEx holds human tissues only, and the Human Protein Atlas is keyed on human genes.

Ready in a moment

04 Protein

The protein Col11a1 encodes

1,804 residues, reviewed P20909; 13 entries from the member databases this page shows along the chain; mean pLDDT 51.5; no experimental structure at PDBe.

UniProt · InterPro · AlphaFold DB · PDBe

Ready in a moment

05 Interactions

Proteins STRING associates with Col11a1

Reading STRING.Still reading. A first read of a gene can take a while; this page waits up to 50 seconds for it, and its scripts then bring in this line, or a line saying what did not arrive.

Ready in a moment

06 Pathways

Where Col11a1 acts, as Reactome curates it

0 curated, 6 inferred Reactome pathways for P20909 in rat, v97.

Reactome

Ready in a moment

07 Disease associations

Diseases linked to Col11a1

Disease associations: not available for rat. Open Targets and ClinGen curate human genes only. The human ortholog's page carries the associations.

Ready in a moment

08 Variants

Classified variants of Col11a1

Clinical variants: not available for rat. ClinVar holds human variants only.

Ready in a moment

09 Constraint

How much variation Col11a1 tolerates

Constraint: not available for rat. gnomAD and Open Targets carry constraint for human genes only.

Ready in a moment

10 Orthologs

The same gene in mouse, rat and human

Human COL11A1 by 2 of 2 votes; mouse Col11a1 by 2 of 2 votes. RGD is not answering, so the ortholog list could not be shown. Try again later. Reference 540e1673-f7f.

Alliance · NCBI

Ready in a moment

11 MicroRNAs

MicroRNAs hosted within Col11a1

Ensembl is not answering, so the non-coding annotation could not be shown. Try again later. Reference 03e40116-f8c.

Ready in a moment

12 Long non-coding RNAs

Long non-coding RNAs at the Col11a1 locus

Ensembl is not answering, so the non-coding annotation could not be shown. Try again later. Reference 03e40116-f8c.

Ready in a moment

13 Literature

Papers that mention Col11a1

Reading Europe PMC.Still reading. A first read of a gene can take a while; this page waits up to 55 seconds for it, and its scripts then bring in this line, or a line saying what did not arrive.

Ready in a moment

14 Silencing this gene

From Col11a1 to a sequence that silences it

The AUMsilence platform designs the sequences against the rat transcripts on this page. Six decisions are yours before it does. What is written under each is AUM's guidance; the timings and the concentrations are in the usage guide below.

01
Choose the region
A knockdown oligonucleotide can sit in the 5' untranslated region, the coding sequence or the 3' untranslated region, and all three are used. The coding sequence and the 3' untranslated region are the usual first choices for an RNase H design; the 5' end near the start codon suits a steric block. The map above shows where each region sits on the isoforms it draws.
02
Cover the isoforms you mean
An exon every isoform carries silences the whole gene; an exon only some isoforms carry silences those and spares the rest. Decide which you want before a sequence is chosen, and check the reference transcript (MANE Select in human; RefSeq Select and Ensembl canonical in mouse and rat) is the one your cells express.
03
Think across species early
The orthologs panel says whether mouse and rat carry the same gene. Whether one oligonucleotide can serve two species is a sequence question, settled at design by matching the candidate against each transcript, not by the protein identity shown there.
04
Check expression in your model
A transcript that is not expressed in your cells cannot show knockdown. Confirm the gene is expressed in the cell type and condition you will use, from your own data or a reference atlas, before the order. The expression panel above gives GTEx's median per tissue for a human gene; for mouse and rat it says that no atlas is on this page yet.
05
Run the controls
A scramble control of the same chemistry, a positive control against a gene known to knock down in your cells, untreated cells, and a mock condition where a transfection reagent is used. Read knockdown at the RNA level first, then at the protein; the usage guide gives the timing and the concentrations to start from.
06
Pick the product
AUMsilence sdASO needs no transfection reagent and works in the cells that resist one. AUMsilence toASO is the transfection-optimised version of the same design, and AUMsiRNA is the siRNA route. The selection guide compares them.

Order for Col11a1 Bring your own sequence The usage guide Selection guide

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

Gene Rat Rattus norvegicus

Col11a1

Reading the record for Col11a1 from NCBI Gene and Ensembl.Still reading. A first read of a gene can take a while; this page waits up to 115 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 Col11a1 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 Summary and function

What Col11a1 does

Waiting for the record before reading NCBI Gene and UniProt.

02 Transcripts and isoforms

The RNA a design targets

Waiting for the record before reading NCBI Datasets and Ensembl.

03 Expression by tissue

Where Col11a1 is expressed

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

04 Protein

The protein Col11a1 encodes

Waiting for the record before reading UniProt, InterPro, AlphaFold DB and PDBe.

05 Interactions

Proteins STRING associates with Col11a1

Waiting for the record before reading STRING.

06 Pathways

Where Col11a1 acts, as Reactome curates it

Waiting for the record before reading UniProt and Reactome.

07 Disease associations

Diseases linked to Col11a1

Waiting for the record before reading Open Targets and ClinGen.

08 Variants

Classified variants of Col11a1

Waiting for the record before reading ClinVar.

09 Constraint

How much variation Col11a1 tolerates

Waiting for the record before reading gnomAD and Open Targets.

10 Orthologs

The same gene in mouse, rat and human

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

11 MicroRNAs

MicroRNAs hosted within Col11a1

Waiting for the record before reading Ensembl and miRBase.

12 Long non-coding RNAs

Long non-coding RNAs at the Col11a1 locus

Waiting for the record before reading Ensembl.

13 Literature

Papers that mention Col11a1

Waiting for the record before reading Europe PMC.

Col11a1

collagen type XI alpha 1 chain

protein coding

HumanMouseRat Col11a1

Reading the ortholog votes for human and mouse.

HGNC and MANE Select: not available for rat. HGNC names human genes; RGD is the authority here, and MANE Select is defined for human transcripts only.

Location

Cytogenetic band 2q42NCBI: 2:204,509,136-204,702,264 on the plus strand, GRCr8 (GCF_036323735.1), sequence NC_086020.1, annotation GCF_036323735.1-RS_2026_08 of 2026-08-17Ensembl: no location was read.Coordinates are one-based with both ends included, as each source reports them.

Gene identity, from NCBI Datasets · NCBI Datasets 18.37.0 · read 2026-09-24 ET · RGD:2372Data from NCBI, provided as is; NCBI's policies and disclaimers apply.

Notes from the sources

Ensembl did not answer (upstream error).
Ensembl did not answer (upstream error); the Ensembl location and release are missing

RefSeq transcripts of this gene
Accession	Name	Biotype	Labels	Exons	Spliced length	Protein	Sequence
NM_013117.1matches ENSRNOT00000068413.5	none given	protein coding	RefSeq Select	67	7,673 nt	1,804 aaNP_037249.1	Ready in a moment
XM_087607814.1matches ENSRNOT00000164805.1	transcript variant X2	protein coding model	none	68	7,307 nt	1,855 aaXP_087463940.1	Ready in a moment
XM_087607813.1	transcript variant X1	protein coding model	none	66	6,905 nt	1,719 aaXP_087463939.1	Ready in a moment

Accession

Name

Biotype

Labels

Exons

Spliced length

Protein

Sequence

NM_013117.1matches ENSRNOT00000068413.5

none given

protein coding

RefSeq Select

7,673 nt

1,804 aaNP_037249.1

Ready in a moment

XM_087607814.1matches ENSRNOT00000164805.1

transcript variant X2

protein coding model

none

7,307 nt

1,855 aaXP_087463940.1

Ready in a moment

XM_087607813.1

transcript variant X1

protein coding model

none

6,905 nt

1,719 aaXP_087463939.1

Ready in a moment

From Col11a1 to a sequence that silences it

Choose the region

A knockdown oligonucleotide can sit in the 5' untranslated region, the coding sequence or the 3' untranslated region, and all three are used. The coding sequence and the 3' untranslated region are the usual first choices for an RNase H design; the 5' end near the start codon suits a steric block. The map above shows where each region sits on the isoforms it draws.

Cover the isoforms you mean

An exon every isoform carries silences the whole gene; an exon only some isoforms carry silences those and spares the rest. Decide which you want before a sequence is chosen, and check the reference transcript (MANE Select in human; RefSeq Select and Ensembl canonical in mouse and rat) is the one your cells express.

Think across species early

The orthologs panel says whether mouse and rat carry the same gene. Whether one oligonucleotide can serve two species is a sequence question, settled at design by matching the candidate against each transcript, not by the protein identity shown there.

Check expression in your model

A transcript that is not expressed in your cells cannot show knockdown. Confirm the gene is expressed in the cell type and condition you will use, from your own data or a reference atlas, before the order. The expression panel above gives GTEx's median per tissue for a human gene; for mouse and rat it says that no atlas is on this page yet.

Run the controls

A scramble control of the same chemistry, a positive control against a gene known to knock down in your cells, untreated cells, and a mock condition where a transfection reagent is used. Read knockdown at the RNA level first, then at the protein; the usage guide gives the timing and the concentrations to start from.

Pick the product

AUMsilence sdASO needs no transfection reagent and works in the cells that resist one. AUMsilence toASO is the transfection-optimised version of the same design, and AUMsiRNA is the siRNA route. The selection guide compares them.

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
NM_013117.1matches ENSRNOT00000068413.5	none given	protein coding	RefSeq Select	67	7,673 nt	1,804 aaNP_037249.1	Ready in a moment
XM_087607814.1matches ENSRNOT00000164805.1	transcript variant X2	protein coding model	none	68	7,307 nt	1,855 aaXP_087463940.1	Ready in a moment
XM_087607813.1	transcript variant X1	protein coding model	none	66	6,905 nt	1,719 aaXP_087463939.1	Ready in a moment

Accession

Name

Biotype

Labels

Exons

Spliced length

Protein

Sequence

NM_013117.1matches ENSRNOT00000068413.5

none given

protein coding

RefSeq Select

7,673 nt

1,804 aaNP_037249.1

Ready in a moment

XM_087607814.1matches ENSRNOT00000164805.1

transcript variant X2

protein coding model

none

7,307 nt

1,855 aaXP_087463940.1

Ready in a moment

XM_087607813.1

transcript variant X1

protein coding model

none

6,905 nt

1,719 aaXP_087463939.1

Ready in a moment

Col11a1

What Col11a1 does

The RNA a design targets

Where Col11a1 is expressed

The protein Col11a1 encodes

Proteins STRING associates with Col11a1

Where Col11a1 acts, as Reactome curates it

Diseases linked to Col11a1

Classified variants of Col11a1

How much variation Col11a1 tolerates

The same gene in mouse, rat and human

MicroRNAs hosted within Col11a1

Long non-coding RNAs at the Col11a1 locus

Papers that mention Col11a1

From Col11a1 to a sequence that silences it

Choose the region

Cover the isoforms you mean

Think across species early

Check expression in your model

Run the controls

Pick the product

Col11a1

What Col11a1 does

The RNA a design targets

Where Col11a1 is expressed

The protein Col11a1 encodes

Proteins STRING associates with Col11a1

Where Col11a1 acts, as Reactome curates it

Diseases linked to Col11a1

Classified variants of Col11a1

How much variation Col11a1 tolerates

The same gene in mouse, rat and human

MicroRNAs hosted within Col11a1

Long non-coding RNAs at the Col11a1 locus

Papers that mention Col11a1

Col11a1

What Col11a1 does

Gene summary

Protein function

The RNA a design targets

RefSeq 3 transcripts

A window on one transcript

Ensembl 0 transcripts

Where Col11a1 is expressed

The protein Col11a1 encodes

Proteins STRING associates with Col11a1

Where Col11a1 acts, as Reactome curates it

Diseases linked to Col11a1

Classified variants of Col11a1

How much variation Col11a1 tolerates

The same gene in mouse, rat and human

MicroRNAs hosted within Col11a1

Long non-coding RNAs at the Col11a1 locus

Papers that mention Col11a1

From Col11a1 to a sequence that silences it

Choose the region

Cover the isoforms you mean

Think across species early

Check expression in your model

Run the controls

Pick the product

Gene summary

Protein function

RefSeq 3 transcripts

A window on one transcript

Ensembl 0 transcripts