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KeywordFamilyClanGene   

Entry: GCFC (PF07842)

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Pfam summary

Description

GC-rich sequence DNA-binding factor-like protein

Sequences found in this family are similar to a region of a human GC-rich sequence DNA-binding factor homolog (Swiss:Q9Y5B6). This is thought to be a protein involved in transcriptional regulation due to partial homologies to a transcription repressor and histone-interacting protein [1]. This family also contains tuftelin interacting protein 11 which has been identified as both a nuclear and cytoplasmic protein, and has been implicated in the secretory pathway. Sip1, a septin interacting protein [2] is also a member of this family.
 
Literature1. Reymond A, Friedli M, Henrichsen CN, Chapot F, Deutsch S, Ucla C, Rossier C, Lyle R, Guipponi M, Antonarakis SE; Genomics 2001;78:46-54.From PREDs and open reading frames to cDNA isolation: revisiting the human chromosome 21 transcription map. PUBMED:11707072
2. Shih HP, Hales KG, Pringle JR, Peifer M; J Cell Sci. 2002;115:1259-1271.Identification of septin-interacting proteins and characterization of the Smt3/SUMO-conjugation system in Drosophila. PUBMED:11884525
 
 
InterPro entry
 

Alignment

New Hampshire tree

The seed alignment for this family in the PANDIT database contains 7 aligned sequences:

  GCFC_MOUSE/327-830   GCF_HUMAN/272-759   O01989_CAEEL/338-817   Q84T85_ORYSA/411-936   Q8BKT3_MOUSE/68-554   Q8MRQ8_DROME/96-578   Q9FNN3_ARATH/357-889  

The full alignment for this family in the Pfam database contains 217 aligned sequences

Species in the seed alignment

List of species covered in the seed alignment. The number in brackets denotes the number of sequences taken from each organism.

  Mus musculus (2);   Oryza sativa Japonica Group (1);   Homo sapiens (1);   Drosophila melanogaster (1);   Caenorhabditis elegans (1);   Arabidopsis thaliana (1);  

The full alignment covers 104 species.

Pre-computed estimates from Markov codon substitution models (explanation)

Following are maximum-likelihood estimates and log-likelihood scores from codon models M0, M1, M2, M7 and M8, implemented in PAML v.4.1

Model name  

Model M0

Model M1

Model M2

Model M7

Model M8

Log-likelihood score  

-10255.60-10203.794638-10203.794638-10154.648075-10154.648076

Tree Length  

18.7518.7472918.7472918.7472918.74729

κ  

1.641.7039431.7039431.6979531.698614

ω-ratio  

ω=0.14161p0=0.798309 ~ ω0=0.149444
p1=0.201691 ~ ω1=1
p0=0.798309 ~ ω0=0.149444
p1=0.153155 ~ ω1=1
p2=0.048536 ~ ω2=1
ω~Β(1.503335,5.924523)p0=0.999999 ~ ω~Β(1.503471,5.923778)
p1=1e-06 ~ ω=1.064807

P-value for testing  
positive selection  

M1 vs M2: P-value=1
family classification: conserved
M7 vs M8: P-value=1
family classification: conserved

Maximum-likelihood estimates and log-likelihood scores from codon models Nonsynonymous and Dual implemented in HYPHY

Model name  

Model Nonsynonymous

Model Dual

Log-likelihood score  

-11506.05211-11506.05191

Mean ω-ratio  

ω = 0.20076ω = 0.20074

Coeff. of variation  
of ω-ratio  

CVω = 0.56006CVω = 0.55977
 

Annotations

InteractionsThis family has 0 known interactions:

StructuresThis family has 0 structures:
Notation: PDB_ID (PDB chain, PDB residues)

Gene Ontologies
Cellular component
 nucleus[GO:0005634]
Biological Process
 regulation of transcription[GO:0045449]
Molecular Function
 DNA binding[GO:0003677]
 transcription factor activity[GO:0003700]

KEGG Pathways - for genes coding for sequences from full alignment
Metabolism
Metabolism of Cofactors and Vitamins
Folate biosynthesis [KEGG]
Genetic Information Processing
Folding, Sorting and Degradation
Protein export [KEGG]
Ubiquitin mediated proteolysis [KEGG]
Cellular Processes
Cell Motility
Bacterial chemotaxis [KEGG]
 

Expression data (explanation)

 
Bgee expression data - for genes coding for sequences from seed alignment     Click here for overview of Bgee data

The numbers in brackets correspond to the number of genes that are associated with the selected family and are expressed in the corresponding tissue. Click on the tissue to see all the families that possibly have function in that tissue and click on the genes to see the corresponding genes.

Homo sapiens
Drosophila melanogaster
Mus musculus

HumanProteinpedia expression data - for human genes coding for sequences from full alignment     Click here for overview of Human Proteinpedia data

The numbers in brackets correspond to the number of human genes that are associated with the selected family and are expressed in the corresponding tissue. Click on the tissue to see all the families that possibly have function in that tissue and click on the genes to see the corresponding genes.

Healthy tissues
Disease tissues

Human disease association

 
Genetic Association Database - data for human genes coding for sequences from full alignment

The numbers in brackets correspond to the number of genes that are associated with the selected family and are associated with the corresponding disease. Click on the disease name to see all the families possibly associated with that disease and click on the genes to see the corresponding genes.

Associated diseases and disorders

Links to OMIM - for human genes coding for sequences from full alignment
 
189901 (1)