Human Gene TULP1 (uc003okv.4) Description and Page Index
  Description: Homo sapiens tubby like protein 1 (TULP1), mRNA.
RefSeq Summary (NM_003322): This gene encodes a member of the tubby-like gene family (TULPs). Members of this family have been identified in plants, vertebrates, and invertebrates. TULP proteins share a conserved C-terminal region of approximately 200 amino acid residues. The protein encoded by this gene is thought to play a role in the physiology of photoreceptors. Mutations in this gene are associated with recessive juvenile retinitis pigmentosa and Leber congenital amaurosis-15. [provided by RefSeq, Nov 2016].
Transcript (Including UTRs)
   Position: hg19 chr6:35,465,651-35,480,647 Size: 14,997 Total Exon Count: 15 Strand: -
Coding Region
   Position: hg19 chr6:35,466,104-35,480,635 Size: 14,532 Coding Exon Count: 15 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesGeneReviewsModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:35,465,651-35,480,647)mRNA (may differ from genome)Protein (542 aa)
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Wikipedia

-  Comments and Description Text from UniProtKB
  ID: TULP1_HUMAN
DESCRIPTION: RecName: Full=Tubby-related protein 1; AltName: Full=Tubby-like protein 1;
FUNCTION: Required for normal development of photoreceptor synapses. Required for normal photoreceptor function and for long- term survival of photoreceptor cells. Interacts with cytoskeleton proteins and may play a role in protein transport in photoreceptor cells (By similarity). Binds lipids, especially phosphatidylinositol 3-phosphate, phosphatidylinositol 4- phosphate, phosphatidylinositol 5-phosphate, phosphatidylinositol 3,4-bisphosphate, phosphatidylinositol 4,5-bisphosphate, phosphatidylinositol 3,4,5-bisphosphate, phosphatidylserine and phosphatidic acid (in vitro). Contribute to stimulation of phagocytosis of apoptotic retinal pigment epithelium (RPE) cells and macrophages.
SUBUNIT: Homodimer (Probable). May interact with ABCF1, PSIP1, ZEB1 and HMGB2 (Potential). Interacts with DNM1 (By similarity). Interacts with F-actin. Interacts with TUB (By similarity).
INTERACTION: P16333:NCK1; NbExp=2; IntAct=EBI-1756778, EBI-389883;
SUBCELLULAR LOCATION: Cytoplasm. Cell membrane; Peripheral membrane protein; Cytoplasmic side. Secreted (By similarity). Cell junction, synapse (By similarity). Note=Detected at synapses between photoreceptor cells and second-order neurons. Does not have a cleavable signal peptide and is secreted by an alternative pathway (By similarity).
TISSUE SPECIFICITY: Retina-specific.
DISEASE: Defects in TULP1 are the cause of retinitis pigmentosa type 14 (RP14) [MIM:600132]. RP leads to degeneration of retinal photoreceptor cells. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. RP14 inheritance is autosomal recessive.
DISEASE: Defects in TULP1 are the cause of Leber congenital amaurosis type 15 (LCA15) [MIM:613843]. LCA15 is a severe dystrophy of the retina, typically becoming evident in the first years of life. Visual function is usually poor and often accompanied by nystagmus, sluggish or near-absent pupillary responses, photophobia, high hyperopia and keratoconus.
SIMILARITY: Belongs to the TUB family.
SEQUENCE CAUTION: Sequence=CAI20251.1; Type=Erroneous gene model prediction;
WEB RESOURCE: Name=Mutations of the TULP1 gene; Note=Retina International's Scientific Newsletter; URL="http://www.retina-international.org/files/sci-news/tulpmut.htm";
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/TULP1";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TULP1
CDC HuGE Published Literature: TULP1
Positive Disease Associations: Waist Circumference
Related Studies:
  1. Waist Circumference
    , , . [PubMed 0]
  2. Waist Circumference
    , , . [PubMed 0]

-  MalaCards Disease Associations
  MalaCards Gene Search: TULP1
Diseases sorted by gene-association score: leber congenital amaurosis 15* (1241), retinitis pigmentosa 14* (1237), tulp1-related retinitis pigmentosa* (500), leber congenital amaurosis* (260), retinitis pigmentosa* (247), rhyns syndrome* (133), tulp1-related leber congenital amaurosis* (100), leber congenital amaurosis 9 (10), retinal degeneration (9), achromatopsia 3 (7), myasthenic syndrome, congenital, 6, presynaptic (6), cancer-associated retinopathy (6), retinal disease (3), fundus dystrophy (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 0.66 RPKM in Prostate
Total median expression: 7.51 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
3' UTR -207.07453-0.457 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000007 - Tubby_C
IPR025659 - Tubby_C-like
IPR018066 - Tubby_C_CS

Pfam Domains:
PF01167 - Tub family

SCOP Domains:
54518 - Transcriptional factor tubby, C-terminal domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help

2FIM
- X-ray MuPIT

3C5N
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O00294
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0005546 phosphatidylinositol-4,5-bisphosphate binding
GO:0051015 actin filament binding

Biological Process:
GO:0001895 retina homeostasis
GO:0006909 phagocytosis
GO:0006910 phagocytosis, recognition
GO:0007601 visual perception
GO:0016192 vesicle-mediated transport
GO:0016358 dendrite development
GO:0042462 eye photoreceptor cell development
GO:0045494 photoreceptor cell maintenance
GO:0050766 positive regulation of phagocytosis
GO:0050896 response to stimulus
GO:0050908 detection of light stimulus involved in visual perception
GO:0060041 retina development in camera-type eye
GO:0097500 receptor localization to non-motile cilium
GO:1903546 protein localization to photoreceptor outer segment

Cellular Component:
GO:0001750 photoreceptor outer segment
GO:0001917 photoreceptor inner segment
GO:0005576 extracellular region
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005929 cilium
GO:0016020 membrane
GO:0030054 cell junction
GO:0042995 cell projection
GO:0043679 axon terminus
GO:0045202 synapse


-  Descriptions from all associated GenBank mRNAs
  BC065261 - Homo sapiens tubby like protein 1, mRNA (cDNA clone MGC:70753 IMAGE:6144003), complete cds.
U82468 - Homo sapiens tubby related protein 1 TULP1 (TULP1) mRNA, complete cds.
BC032714 - Homo sapiens tubby like protein 1, mRNA (cDNA clone MGC:45167 IMAGE:5495136), complete cds.
JD445693 - Sequence 426717 from Patent EP1572962.
JD138738 - Sequence 119762 from Patent EP1572962.
JD461960 - Sequence 442984 from Patent EP1572962.
JD284434 - Sequence 265458 from Patent EP1572962.
JD562433 - Sequence 543457 from Patent EP1572962.
JD435941 - Sequence 416965 from Patent EP1572962.
JD173525 - Sequence 154549 from Patent EP1572962.
JD415821 - Sequence 396845 from Patent EP1572962.
JD495469 - Sequence 476493 from Patent EP1572962.
JD409553 - Sequence 390577 from Patent EP1572962.
JD524544 - Sequence 505568 from Patent EP1572962.
JD172955 - Sequence 153979 from Patent EP1572962.
JD077867 - Sequence 58891 from Patent EP1572962.
KJ901814 - Synthetic construct Homo sapiens clone ccsbBroadEn_11208 TULP1 gene, encodes complete protein.
KR710897 - Synthetic construct Homo sapiens clone CCSBHm_00018055 TULP1 (TULP1) mRNA, encodes complete protein.
KR710898 - Synthetic construct Homo sapiens clone CCSBHm_00018058 TULP1 (TULP1) mRNA, encodes complete protein.
KR710899 - Synthetic construct Homo sapiens clone CCSBHm_00018061 TULP1 (TULP1) mRNA, encodes complete protein.
KR710900 - Synthetic construct Homo sapiens clone CCSBHm_00018064 TULP1 (TULP1) mRNA, encodes complete protein.
EU446712 - Synthetic construct Homo sapiens clone IMAGE:100070099; IMAGE:100011921; FLH257500.01L tubby like protein 1 (TULP1) gene, encodes complete protein.
AB593124 - Homo sapiens TULP1 mRNA for tubby-related protein 1, complete cds, clone: HP07915-RBdS054P11.
AB593123 - Homo sapiens TULP1 mRNA for tubby-related protein 1, complete cds, clone: HP07915-RBd95E12.
CU689498 - Synthetic construct Homo sapiens gateway clone IMAGE:100019636 5' read TULP1 mRNA.
BC001761 - Homo sapiens tubby like protein 1, mRNA (cDNA clone IMAGE:3355379), **** WARNING: chimeric clone ****.
BC021268 - Homo sapiens tubby like protein 1, mRNA (cDNA clone IMAGE:4634277), **** WARNING: chimeric clone ****.
DQ426893 - Homo sapiens tubby like protein 1 (TULP1) mRNA, partial cds.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_003322, NP_003313, O00294, O43536, Q5TGM5, Q8N571, TUBL1, TULP1_HUMAN
UCSC ID: uc003okv.4
RefSeq Accession: NM_003322
Protein: O00294 (aka TULP1_HUMAN or TUL1_HUMAN)
CCDS: CCDS4807.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene TULP1:
lca-ov (Leber Congenital Amaurosis / Early-Onset Severe Retinal Dystrophy Overview)
rp-overview (Nonsyndromic Retinitis Pigmentosa Overview)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_003322.3
exon count: 15CDS single in 3' UTR: no RNA size: 2107
ORF size: 1629CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3258.00frame shift in genome: no % Coverage: 99.38
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.