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5  structures 1452  species 0  interactions 2997  sequences 70  architectures

Family: Cir_N (PF10197)

Summary: N-terminal domain of CBF1 interacting co-repressor CIR

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N-terminal domain of CBF1 interacting co-repressor CIR Provide feedback

This is a 45 residue conserved region at the N-terminal end of a family of proteins referred to as CIRs (CBF1-interacting co-repressors). CBF1 (centromere-binding factor 1) acts as a transcription factor that causes repression by binding specifically to GTGGGAA motifs in responsive promoters, and it requires CIR as a co-repressor. CIR binds to histone deacetylase and to SAP30 and serves as a linker between CBF1 and the histone deacetylase complex [1].

Literature references

  1. Hsieh JJ, Zhou S, Chen L, Young DB, Hayward SD; , Proc Natl Acad Sci U S A. 1999;96:23-28.: CIR, a corepressor linking the DNA binding factor CBF1 to the histone deacetylase complex. PUBMED:9874765 EPMC:9874765


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR019339

This entry represents a 45 residue conserved domain found at the N-terminal end CIR protein (CBF1-interacting co-repressor, also known as corepressor interacting with RBPJ 1). This domain can be found in the fungal CWC25 family members and mammlian LENG1 (leukocyte receptor cluster member 1) protein.

CBF1 (centromere-binding factor 1) acts as a transcription factor that causes repression by binding specifically to GTGGGAA motifs in responsive promoters, and it requires CIR as a co-repressor. CIR binds to histone deacetylase and to SAP30 and serves as a linker between CBF1 and the histone deacetylase complex [ PUBMED:9874765 ]. CIR also plays a role in alternative splicing [ PUBMED:15652350 ].

Budding yeast Cwc25 is a pre-mRNA-splicing factor involved in pre-mRNA splicing [ PUBMED:14690591 ].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(121)
Full
(2997)
Representative proteomes UniProt
(4777)
RP15
(589)
RP35
(1365)
RP55
(2268)
RP75
(3063)
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PP/heatmap 1 View           

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(121)
Full
(2997)
Representative proteomes UniProt
(4777)
RP15
(589)
RP35
(1365)
RP55
(2268)
RP75
(3063)
Alignment:
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Sequence:
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Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(121)
Full
(2997)
Representative proteomes UniProt
(4777)
RP15
(589)
RP35
(1365)
RP55
(2268)
RP75
(3063)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: KOGs (KOG3869)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: KOGs, Finn RD , Coggill P
Number in seed: 121
Number in full: 2997
Average length of the domain: 37.00 aa
Average identity of full alignment: 37 %
Average coverage of the sequence by the domain: 9.46 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.6 22.6
Trusted cut-off 22.6 22.6
Noise cut-off 22.5 22.5
Model length: 37
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Cir_N domain has been found. There are 5 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0P0XW29 View 3D Structure Click here
A0A0R0G8I6 View 3D Structure Click here
A0A1D6FH18 View 3D Structure Click here
A0A1D6GVY0 View 3D Structure Click here
A0A1D6PBH8 View 3D Structure Click here
A0A2R8PXM2 View 3D Structure Click here
A0A3P6MY32 View 3D Structure Click here
C0PH10 View 3D Structure Click here
D3ZER8 View 3D Structure Click here
G3V6I3 View 3D Structure Click here
G5EBE3 View 3D Structure Click here
I1J883 View 3D Structure Click here
I1L084 View 3D Structure Click here
I1LIF8 View 3D Structure Click here
O64855 View 3D Structure Click here
P53854 View 3D Structure Click here
Q0D9M1 View 3D Structure Click here
Q1PEU6 View 3D Structure Click here
Q54QA7 View 3D Structure Click here
Q54QF2 View 3D Structure Click here
Q59LQ5 View 3D Structure Click here
Q5U2T8 View 3D Structure Click here
Q66HZ8 View 3D Structure Click here
Q6ZKL9 View 3D Structure Click here
Q7ZVW8 View 3D Structure Click here
Q86X95 View 3D Structure Click here
Q8IDL7 View 3D Structure Click here
Q8VZ67 View 3D Structure Click here
Q96BZ8 View 3D Structure Click here
Q9DA19 View 3D Structure Click here
Q9DB98 View 3D Structure Click here
Q9DBF7 View 3D Structure Click here
Q9NXE8 View 3D Structure Click here
Q9VH00 View 3D Structure Click here
Q9VQF5 View 3D Structure Click here
Q9VVU4 View 3D Structure Click here
Q9Y805 View 3D Structure Click here