P14713

PR
Gene name
PHYB
Protein name
Phytochrome B
Names
Protein LONG HYPOCOTYL 3, Protein OUT OF PHASE 1
Species
Arabidopsis thaliana (Mouse-ear cress)
KEGG Pathway
ath:AT2G18790
EC number
Protein Class

Descriptions

The autoinhibited protein was predicted that may have potential autoinhibitory elements via cis-regPred.

Autoinhibitory domains (AIDs)

1-73 (Predicted disordered autoinhibitory region) PR

Target domain

Relief mechanism

Assay

cis-regPred

Accessory elements

No accessory elements

References

Autoinhibited structure

Activated structure

3 structures for P14713

Entry ID Method Resolution Chain Position Source
4OUR X-ray 340 A A/B 90-624 PDB
7RZW EM 330 A A/B 1-1172 PDB
AF-P14713-F1 Predicted AlphaFoldDB

55 variants for P14713

Variant ID(s) Position Change Description Diseaes Association Provenance
tmp_2_8140086_C_A 3 S>Y No 1000Genomes
9 G>del strain: cv. Kas-1 [UniProt] No
ENSVATH01839675 19 E>K strain: cv. Kas-1 [UniProt] No 1000Genomes
tmp_2_8140145_T_C 23 S>P No 1000Genomes
ENSVATH01839676 40 S>L No 1000Genomes
ENSVATH13268388 69 A>V No 1000Genomes
tmp_2_8140301_G_A 75 G>S No 1000Genomes
tmp_2_8140344_C_A 89 T>K No 1000Genomes
ENSVATH01839678 93 G>D No 1000Genomes
ENSVATH14517390 129 R>Q No 1000Genomes
tmp_2_8140476_A_T 133 Y>F No 1000Genomes
ENSVATH00237392 143 I>L strain: cv. Kas-1 [UniProt] No 1000Genomes
ENSVATH01839688 247 A>S No 1000Genomes
ENSVATH05527854 264 V>M No 1000Genomes
ENSVATH14517392 295 L>F No 1000Genomes
ENSVATH05527856 461 A>V No 1000Genomes
ENSVATH01839699 501 D>E No 1000Genomes
tmp_2_8141582_G_C 502 V>L No 1000Genomes
ENSVATH05527857 509 N>Y No 1000Genomes
ENSVATH05527858 543 Y>F No 1000Genomes
tmp_2_8141895_C_T 606 A>V No 1000Genomes
ENSVATH00237406 624 A>D No 1000Genomes
ENSVATH13268394 637 C>S No 1000Genomes
ENSVATH05527861 706 K>Q No 1000Genomes
ENSVATH01839705 709 E>K No 1000Genomes
tmp_2_8142241_A_T 721 R>S No 1000Genomes
ENSVATH01839707 736 S>T No 1000Genomes
tmp_2_8142391_A_C 742 K>T No 1000Genomes
tmp_2_8142453_G_A 763 V>I No 1000Genomes
tmp_2_8142550_A_T 795 N>I No 1000Genomes
ENSVATH00237414 826 S>G No 1000Genomes
tmp_2_8142648_G_A 828 V>M No 1000Genomes
ENSVATH13268417 830 G>E No 1000Genomes
ENSVATH05527865 837 V>M No 1000Genomes
tmp_2_8142791_C_G 875 D>E No 1000Genomes
tmp_2_8142795_A_G 877 N>D No 1000Genomes
tmp_2_8142807_G_C 881 V>L No 1000Genomes
tmp_2_8142913_C_G 916 A>G No 1000Genomes
ENSVATH05527868 924 E>V No 1000Genomes
tmp_2_8142967_A_T 934 Y>F No 1000Genomes
ENSVATH13268419 946 M>L No 1000Genomes
ENSVATH00237418 948 F>L No 1000Genomes
ENSVATH01839714 949 A>T No 1000Genomes
tmp_2_8143051_A_T 962 Q>L No 1000Genomes
ENSVATH05527869 967 E>G No 1000Genomes
ENSVATH00237420 980 V>I strain: cv. Kas-1 [UniProt] No 1000Genomes
ENSVATH01839715 989 E>D No 1000Genomes
tmp_2_8143294_C_T 1013 A>V No 1000Genomes
ENSVATH05527873 1017 L>F No 1000Genomes
tmp_2_8143364_G_C 1036 E>D No 1000Genomes
tmp_2_8143401_G_T 1049 A>S No 1000Genomes
ENSVATH05527874 1068 H>R No 1000Genomes
ENSVATH00237425 1072 L>V strain: cv. Kas-1 [UniProt] No 1000Genomes
tmp_2_8144016_G_A 1128 M>I No 1000Genomes
ENSVATH05527885 1166 M>T No 1000Genomes

No associated diseases with P14713

1 regional properties for P14713

Type Name Position InterPro Accession
domain AMMECR1 domain 8 - 202 IPR002733

Functions

Description
EC Number
Subcellular Localization
  • Cytoplasm
  • Nucleus, nucleoplasm
  • Nucleus speckle
  • Nucleus
  • Cytoplasmic in darkness, but translocated to the nucleus upon illumination, when associated with PAPP5 into speckles
PANTHER Family
PANTHER Subfamily
PANTHER Protein Class
PANTHER Pathway Category No pathway information available

4 GO annotations of cellular component

Name Definition
cytosol The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
nuclear body Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins.
nuclear speck A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
nucleus A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

8 GO annotations of molecular function

Name Definition
far-red light photoreceptor activity The function of absorbing and responding to electromagnetic radiation with a wavelength of approximately 730nm. The response may involve a change in conformation.
identical protein binding Binding to an identical protein or proteins.
phosphorelay sensor kinase activity Catalysis of the phosphorylation of a histidine residue in response to detection of an extracellular signal such as a chemical ligand or change in environment, to initiate a change in cell state or activity. The two-component sensor is a histidine kinase that autophosphorylates a histidine residue in its active site. The phosphate is then transferred to an aspartate residue in a downstream response regulator, to trigger a response.
promoter-specific chromatin binding Binding to a section of chromatin that is associated with gene promoter sequences of DNA.
protein homodimerization activity Binding to an identical protein to form a homodimer.
red light photoreceptor activity The function of absorbing and responding to electromagnetic radiation with a wavelength of approximately 660nm. The response may involve a change in conformation.
red or far-red light photoreceptor activity The function of absorbing and responding to electromagnetic radiation with a wavelength of approximately 660-730nm. The response may involve a change in conformation.
sequence-specific DNA binding Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.

23 GO annotations of biological process

Name Definition
abscisic acid metabolic process The chemical reactions and pathways involving abscisic acid, 5-(1-hydroxy-2,6,6,trimethyl-4-oxocyclohex-2-en-1-y1)-3-methylpenta-2,4-dienoic acid.
chromatin organization The assembly or remodeling of chromatin composed of DNA complexed with histones, other associated proteins, and sometimes RNA.
circadian regulation of calcium ion oscillation Any process that modulates the concentration of cytosolic free calcium ion
detection of visible light The series of events in which a visible light stimulus is received by a cell and converted into a molecular signal. A visible light stimulus is electromagnetic radiation that can be perceived visually by an organism; for organisms lacking a visual system, this can be defined as light with a wavelength within the range 380 to 780 nm.
entrainment of circadian clock The synchronization of a circadian rhythm to environmental time cues such as light.
gravitropism The orientation of plant parts under the stimulation of gravity.
jasmonic acid mediated signaling pathway The series of molecular signals mediated by jasmonic acid.
negative regulation of DNA-templated transcription Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
photomorphogenesis The control of plant growth, development, and differentiation by the duration and nature of light, independent of photosynthesis.
photosynthesis The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
phototropism The movement of an organism, or part of an organism, in response to a light stimulus, usually toward or away from it.
protein-phytochromobilin linkage The linkage of the chromophore phytochromobilin to phycocyanin or allophycocyanin.
red light signaling pathway The series of molecular signals initiated upon sensing of red light by a photoreceptor molecule. Red light is electromagnetic radiation of wavelength of 580-700nm. An example of this response is seen at the beginning of many plant species developmental stages. These include germination, and the point when cotyledon expansion is triggered. In certain species these processes take place in response to absorption of red light by the pigment molecule phytochrome, but the signal can be reversed by exposure to far red light. During the initial phase the phytochrome molecule is only present in the red light absorbing form, but on absorption of red light it changes to a far red light absorbing form, triggering progress through development. An immediate short period of exposure to far red light entirely returns the pigment to its initial state and prevents triggering of the developmental process. A thirty minute break between red and subsequent far red light exposure renders the red light effect irreversible, and development then occurs regardless of whether far red light exposure subsequently occurs.
regulation of defense response Any process that modulates the frequency, rate or extent of a defense response.
regulation of photoperiodism, flowering Any process that modulates the frequency, rate or extent of photoperiodism, flowering.
regulation of seed germination Any process that modulates the frequency, rate or extent of seed germination.
response to cold Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cold stimulus, a temperature stimulus below the optimal temperature for that organism.
response to far red light Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of far red light stimulus. Far red light is electromagnetic radiation of wavelength 700-800nm. An example of this response is seen at the beginning of many plant species developmental stages. These include germination, and the point when cotyledon expansion is triggered. In certain species these processes take place in response to absorption of red light by the pigment molecule phytochrome, but the signal can be reversed by exposure to far red light. During the initial phase the phytochrome molecule is only present in the red light absorbing form, but on absorption of red light it changes to a far red light absorbing form, triggering progress through development. An immediate short period of exposure to far red light entirely returns the pigment to its initial state and prevents triggering of the developmental process. A thirty minute break between red and subsequent far red light exposure renders the red light effect irreversible, and development then occurs regardless of whether far red light exposure subsequently occurs.
response to low fluence blue light stimulus by blue low-fluence system Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of the detection of a low fluence blue light stimulus by the blue low-fluence system. Blue light is electromagnetic radiation with a wavelength of between 440 and 500nm. The blue low-fluence system responds to blue light at or below 0.1 micromols/m2. In certain species excitation of the blue low fluence system induces the transcription of a number of nuclear and plastid coded genes.
response to low fluence red light stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a low fluence red light stimulus. Red light is electromagnetic radiation of wavelength of 580-700nm. Low fluence red light is defined in this case as short pulses of red light followed by darkness, providing a light level of 0.001-0.1 mmol/m2/sec.
response to temperature stimulus Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a temperature stimulus.
stomatal complex development The process whose specific outcome is the progression of the stomatal complex over time from its formation to the mature structure. The stomatal complex is the stomatal guard cells and their associated epidermal cells.
transpiration Release of water by the plant into the air as water vapor mainly through leaves.

3 homologous proteins in AiPD

UniProt AC Gene Name Protein Name Species Evidence Code
Q10MG9 PHYB Phytochrome B Oryza sativa subsp japonica (Rice) PR
P42497 PHYD Phytochrome D Arabidopsis thaliana (Mouse-ear cress) PR
P14714 PHYC Phytochrome C Arabidopsis thaliana (Mouse-ear cress) PR
10 20 30 40 50 60
MVSGVGGSGG GRGGGRGGEE EPSSSHTPNN RRGGEQAQSS GTKSLRPRSN TESMSKAIQQ
70 80 90 100 110 120
YTVDARLHAV FEQSGESGKS FDYSQSLKTT TYGSSVPEQQ ITAYLSRIQR GGYIQPFGCM
130 140 150 160 170 180
IAVDESSFRI IGYSENAREM LGIMPQSVPT LEKPEILAMG TDVRSLFTSS SSILLERAFV
190 200 210 220 230 240
AREITLLNPV WIHSKNTGKP FYAILHRIDV GVVIDLEPAR TEDPALSIAG AVQSQKLAVR
250 260 270 280 290 300
AISQLQALPG GDIKLLCDTV VESVRDLTGY DRVMVYKFHE DEHGEVVAES KRDDLEPYIG
310 320 330 340 350 360
LHYPATDIPQ ASRFLFKQNR VRMIVDCNAT PVLVVQDDRL TQSMCLVGST LRAPHGCHSQ
370 380 390 400 410 420
YMANMGSIAS LAMAVIINGN EDDGSNVASG RSSMRLWGLV VCHHTSSRCI PFPLRYACEF
430 440 450 460 470 480
LMQAFGLQLN MELQLALQMS EKRVLRTQTL LCDMLLRDSP AGIVTQSPSI MDLVKCDGAA
490 500 510 520 530 540
FLYHGKYYPL GVAPSEVQIK DVVEWLLANH ADSTGLSTDS LGDAGYPGAA ALGDAVCGMA
550 560 570 580 590 600
VAYITKRDFL FWFRSHTAKE IKWGGAKHHP EDKDDGQRMH PRSSFQAFLE VVKSRSQPWE
610 620 630 640 650 660
TAEMDAIHSL QLILRDSFKE SEAAMNSKVV DGVVQPCRDM AGEQGIDELG AVAREMVRLI
670 680 690 700 710 720
ETATVPIFAV DAGGCINGWN AKIAELTGLS VEEAMGKSLV SDLIYKENEA TVNKLLSRAL
730 740 750 760 770 780
RGDEEKNVEV KLKTFSPELQ GKAVFVVVNA CSSKDYLNNI VGVCFVGQDV TSQKIVMDKF
790 800 810 820 830 840
INIQGDYKAI VHSPNPLIPP IFAADENTCC LEWNMAMEKL TGWSRSEVIG KMIVGEVFGS
850 860 870 880 890 900
CCMLKGPDAL TKFMIVLHNA IGGQDTDKFP FPFFDRNGKF VQALLTANKR VSLEGKVIGA
910 920 930 940 950 960
FCFLQIPSPE LQQALAVQRR QDTECFTKAK ELAYICQVIK NPLSGMRFAN SLLEATDLNE
970 980 990 1000 1010 1020
DQKQLLETSV SCEKQISRIV GDMDLESIED GSFVLKREEF FLGSVINAIV SQAMFLLRDR
1030 1040 1050 1060 1070 1080
GLQLIRDIPE EIKSIEVFGD QIRIQQLLAE FLLSIIRYAP SQEWVEIHLS QLSKQMADGF
1090 1100 1110 1120 1130 1140
AAIRTEFRMA CPGEGLPPEL VRDMFHSSRW TSPEGLGLSV CRKILKLMNG EVQYIRESER
1150 1160 1170
SYFLIILELP VPRKRPLSTA SGSGDMMLMM PY