PANDIT+

KeywordFamilyClanGene   

Entry: 5HT_transporter (PF03491)

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Very fast search for clan entries. The
search can be done either by clan ID
(e.g. CL0192) or by clan name (e.g. GPCR_A).

Pfam summary

Description

Serotonin (5-HT) neurotransmitter transporter, N-terminus

 
Literature
 
 
InterPro entry IPR002437
 

Alignment

New Hampshire tree

The seed alignment for this family in the PANDIT database contains 3 aligned sequences:

  SC6A4_CAVPO/23-64   SC6A4_HUMAN/23-64   SC6A4_MOUSE/23-64  

The full alignment for this family in the Pfam database contains 23 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.

  Homo sapiens (1);   Mus musculus (1);   Cavia porcellus (1);  

The full alignment covers 16 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  

-348.54-347.924455-347.924455-347.966918-347.9168

Tree Length  

2.302.302842.302842.302842.30284

κ  

5.365.4350695.4350695.3988785.430314

ω-ratio  

ω=0.22126p0=0.893625 ~ ω0=0.175251
p1=0.106375 ~ ω1=1
p0=0.893625 ~ ω0=0.175251
p1=0.062878 ~ ω1=1
p2=0.043497 ~ ω2=1
ω~Β(1.102054,3.255311)p0=0.9203 ~ ω~Β(3.689438,15.352687)
p1=0.0797 ~ ω=1.041424

P-value for testing  
positive selection  

M1 vs M2: P-value=1
family classification: conserved
M7 vs M8: P-value=0.951117
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  

-347.91559-347.91893

Mean ω-ratio  

ω = 0.26018ω = 0.26057

Coeff. of variation  
of ω-ratio  

CVω = 0.93168CVω = 0.9081
 

Annotations

InteractionsThis family has 0 known interactions:

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

Gene Ontologies
Cellular component
 integral to plasma membrane[GO:0005887]
Biological Process
 neurotransmitter transport[GO:0006836]
Molecular Function
 serotonin:sodium symporter activity[GO:0005335]

KEGG Pathways - for genes coding for sequences from full alignment
Metabolism
Carbohydrate Metabolism
Citrate cycle (TCA cycle) [KEGG]
Amino Acid Metabolism
Lysine degradation [KEGG]
Environmental Information Processing
Signal Transduction
Calcium signaling pathway [KEGG]
Wnt signaling pathway [KEGG]
VEGF signaling pathway [KEGG]
Cellular Processes
Cell Growth and Death
Apoptosis [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
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
 
182138 (1)