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Protein

Cold shock protein 2

Gene

CSP2

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Chaperone that binds to RNA, single- (ssDNA) and double-stranded (dsDNA) DNA, and unwinds nucleic acid duplex. Accelerates seed germination and seedling growth under cold stress, and contributes to enhancement of cold and freezing tolerance. Regulates flowering transition, and flower and seed development. Promotes seed germination under salt stress. May regulate respiratory oxygen uptake.6 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri129 – 14618CCHC-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri183 – 20018CCHC-type 2PROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  • double-stranded DNA binding Source: UniProtKB
  • mRNA binding Source: UniProtKB
  • nucleic acid binding Source: TAIR
  • single-stranded DNA binding Source: TAIR
  • zinc ion binding Source: InterPro

GO - Biological processi

  • cold acclimation Source: UniProtKB
  • DNA duplex unwinding Source: TAIR
  • regulation of cellular respiration Source: UniProtKB
  • regulation of transcription, DNA-templated Source: InterPro
  • response to abscisic acid Source: UniProtKB
  • response to cold Source: UniProtKB
  • response to desiccation Source: UniProtKB
  • response to water deprivation Source: UniProtKB
  • seed development Source: TAIR
  • stamen development Source: TAIR
  • vegetative to reproductive phase transition of meristem Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Chaperone

Keywords - Ligandi

DNA-binding, Metal-binding, RNA-binding, Zinc

Enzyme and pathway databases

ReactomeiR-ATH-72163. mRNA Splicing - Major Pathway.
R-ATH-72165. mRNA Splicing - Minor Pathway.

Names & Taxonomyi

Protein namesi
Recommended name:
Cold shock protein 2
Short name:
AtCSP2
Alternative name(s):
Cold shock domain-containing protein 2
Glycine-rich protein 2
Short name:
AtGRP2
Gene namesi
Name:CSP2
Synonyms:CSDP2, GRP2
Ordered Locus Names:At4g38680
ORF Names:F20M13.240
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 4

Organism-specific databases

TAIRiAT4G38680.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB
  • cytosol Source: TAIR
  • nucleolus Source: TAIR
  • nucleus Source: TAIR
  • plasma membrane Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Disruption phenotypei

Early flowering, altered stamen number and impaired seed development.2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedBy similarity
Chaini2 – 203202Cold shock protein 2PRO_0000418159Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylserineBy similarity

Keywords - PTMi

Acetylation

Proteomic databases

PaxDbiQ41188.
PRIDEiQ41188.

PTM databases

iPTMnetiQ41188.

Expressioni

Tissue specificityi

Mostly expressed in shoot apices, seeds and siliques, and, to a lower extent, in roots, cotyledons, stems, shoots, leaves, floral buds and flowers. Present in shoot apical meristems and siliques (at protein level).4 Publications

Developmental stagei

Active in meristematic tissues. During vegetative growth, expressed in root and shoot apical regions, leaves and roots primordia, root vascular cylinder and procambium. In reproductive organs, present in developing floral meristem, meristematic tissues of young flower buds, and placentae, pollen, ovules and seeds, mostly in embryos. High expression in the earliest stage of silique development, with a decrease during the middle stages of silique development and subsequently an increase during the later stages. In mature seeds, mostly localized in hypocotyl and radicule. During seed germination, first observed in the tip of the radicule and, upon opening of the cotyledons, expressed in the radicule and hypocotyl/radicule transition zone.3 Publications

Inductioni

Induced by abscisic acid (ABA), transiently by ethylene, salicylic acid and water fload, but down-regulated by dehydration stress. Accumulates during cold acclimation. Accumulation during silique development is AGL15-dependent.5 Publications

Gene expression databases

GenevisibleiQ41188. AT.

Interactioni

Protein-protein interaction databases

BioGridi15304. 1 interaction.
STRINGi3702.AT4G38680.1.

Structurei

3D structure databases

ProteinModelPortaliQ41188.
SMRiQ41188. Positions 10-75, 95-201.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini12 – 7665CSDAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi76 – 202127Gly-richAdd
BLAST

Sequence similaritiesi

Belongs to the cold shock protein (CSP) family.Curated
Contains 2 CCHC-type zinc fingers.PROSITE-ProRule annotation
Contains 1 CSD (cold-shock) domain.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri129 – 14618CCHC-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri183 – 20018CCHC-type 2PROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG3070. Eukaryota.
COG1278. LUCA.
HOGENOMiHOG000186262.
InParanoidiQ41188.
OMAiECPSKTY.
PhylomeDBiQ41188.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
4.10.60.10. 2 hits.
InterProiIPR019844. Cold-shock_CS.
IPR011129. Cold_shock_prot.
IPR002059. CSP_DNA-bd.
IPR012340. NA-bd_OB-fold.
IPR001878. Znf_CCHC.
[Graphical view]
PfamiPF00313. CSD. 1 hit.
PF00098. zf-CCHC. 2 hits.
[Graphical view]
PRINTSiPR00050. COLDSHOCK.
SMARTiSM00357. CSP. 1 hit.
SM00343. ZnF_C2HC. 2 hits.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
SSF57756. SSF57756. 2 hits.
PROSITEiPS00352. COLD_SHOCK. 1 hit.
PS50158. ZF_CCHC. 2 hits.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q41188-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MSGDNGGGER RKGSVKWFDT QKGFGFITPD DGGDDLFVHQ SSIRSEGFRS
60 70 80 90 100
LAAEEAVEFE VEIDNNNRPK AIDVSGPDGA PVQGNSGGGS SGGRGGFGGG
110 120 130 140 150
RGGGRGSGGG YGGGGGGYGG RGGGGRGGSD CYKCGEPGHM ARDCSEGGGG
160 170 180 190 200
YGGGGGGYGG GGGYGGGGGG YGGGGRGGGG GGGSCYSCGE SGHFARDCTS

GGR
Length:203
Mass (Da):19,153
Last modified:November 1, 1996 - v1
Checksum:i9310C89C1BC44F55
GO
Isoform 2 (identifier: Q41188-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     177-203: GGGGGGGSCYSCGESGHFARDCTSGGR → LLSLYYPLFAYYDGSLSLLVGFFLMVSD

Note: No experimental confirmation available.
Show »
Length:204
Mass (Da):19,881
Checksum:i0924242CFB0BD144
GO

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei177 – 20327GGGGG…TSGGR → LLSLYYPLFAYYDGSLSLLV GFFLMVSD in isoform 2. 1 PublicationVSP_044000Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
S47408 mRNA. Translation: AAB24074.1.
AL035540 Genomic DNA. Translation: CAB37524.1.
AL161593 Genomic DNA. Translation: CAB80532.1.
CP002687 Genomic DNA. Translation: AEE86964.1.
AF360202 mRNA. Translation: AAK25912.1.
AF385696 mRNA. Translation: AAK60289.1.
AY040049 mRNA. Translation: AAK64107.1.
AY133591 mRNA. Translation: AAM91421.1.
AK318762 mRNA. Translation: BAH56877.1.
PIRiJQ1061.
RefSeqiNP_195580.1. NM_120029.2. [Q41188-1]
UniGeneiAt.24348.
At.75605.

Genome annotation databases

EnsemblPlantsiAT4G38680.1; AT4G38680.1; AT4G38680. [Q41188-1]
GeneIDi830024.
KEGGiath:AT4G38680.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
S47408 mRNA. Translation: AAB24074.1.
AL035540 Genomic DNA. Translation: CAB37524.1.
AL161593 Genomic DNA. Translation: CAB80532.1.
CP002687 Genomic DNA. Translation: AEE86964.1.
AF360202 mRNA. Translation: AAK25912.1.
AF385696 mRNA. Translation: AAK60289.1.
AY040049 mRNA. Translation: AAK64107.1.
AY133591 mRNA. Translation: AAM91421.1.
AK318762 mRNA. Translation: BAH56877.1.
PIRiJQ1061.
RefSeqiNP_195580.1. NM_120029.2. [Q41188-1]
UniGeneiAt.24348.
At.75605.

3D structure databases

ProteinModelPortaliQ41188.
SMRiQ41188. Positions 10-75, 95-201.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi15304. 1 interaction.
STRINGi3702.AT4G38680.1.

PTM databases

iPTMnetiQ41188.

Proteomic databases

PaxDbiQ41188.
PRIDEiQ41188.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT4G38680.1; AT4G38680.1; AT4G38680. [Q41188-1]
GeneIDi830024.
KEGGiath:AT4G38680.

Organism-specific databases

TAIRiAT4G38680.

Phylogenomic databases

eggNOGiKOG3070. Eukaryota.
COG1278. LUCA.
HOGENOMiHOG000186262.
InParanoidiQ41188.
OMAiECPSKTY.
PhylomeDBiQ41188.

Enzyme and pathway databases

ReactomeiR-ATH-72163. mRNA Splicing - Major Pathway.
R-ATH-72165. mRNA Splicing - Minor Pathway.

Miscellaneous databases

PROiQ41188.

Gene expression databases

GenevisibleiQ41188. AT.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
4.10.60.10. 2 hits.
InterProiIPR019844. Cold-shock_CS.
IPR011129. Cold_shock_prot.
IPR002059. CSP_DNA-bd.
IPR012340. NA-bd_OB-fold.
IPR001878. Znf_CCHC.
[Graphical view]
PfamiPF00313. CSD. 1 hit.
PF00098. zf-CCHC. 2 hits.
[Graphical view]
PRINTSiPR00050. COLDSHOCK.
SMARTiSM00357. CSP. 1 hit.
SM00343. ZnF_C2HC. 2 hits.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
SSF57756. SSF57756. 2 hits.
PROSITEiPS00352. COLD_SHOCK. 1 hit.
PS50158. ZF_CCHC. 2 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Differential expression of five Arabidopsis genes encoding glycine-rich proteins."
    de Oliveira D.E., Seurinck J., Inze D., Van Montagu M., Botterman J.
    Plant Cell 2:427-436(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), TISSUE SPECIFICITY, INDUCTION BY ABSCISIC ACID AND DROUGHT.
    Strain: cv. C24.
  2. "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana."
    Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T., Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B., Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M., de Simone V., Obermaier B.
    , Mache R., Mueller M., Kreis M., Delseny M., Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D., Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J., Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B., Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J., Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R., Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M., Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S., Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C., Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J., Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S., Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A., Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M., Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D., Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E., Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S., Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R., Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M., Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E., Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P., Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K., Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K., de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K., Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M., Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G., Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K., Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K., Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W., Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H., Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B., Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J., Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K., O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N., Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A., Martienssen R., McCombie W.R.
    Nature 402:769-777(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  4. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
    , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Strain: cv. Columbia.
  5. "Analysis of multiple occurrences of alternative splicing events in Arabidopsis thaliana using novel sequenced full-length cDNAs."
    Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M., Shinozaki K.
    DNA Res. 16:155-164(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    Strain: cv. Columbia.
    Tissue: Flower and Silique.
  6. "Conservation of the cold shock domain protein family in plants."
    Karlson D., Imai R.
    Plant Physiol. 131:12-15(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION BY COLD, GENE FAMILY.
  7. "Arabidopsis COLD SHOCK DOMAIN PROTEIN2 is a RNA chaperone that is regulated by cold and developmental signals."
    Sasaki K., Kim M.-H., Imai R.
    Biochem. Biophys. Res. Commun. 364:633-638(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INDUCTION BY COLD, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, SUBCELLULAR LOCATION.
    Strain: cv. Columbia.
  8. "Cold shock domain proteins and glycine-rich RNA-binding proteins from Arabidopsis thaliana can promote the cold adaptation process in Escherichia coli."
    Kim J.S., Park S.J., Kwak K.J., Kim Y.O., Kim J.Y., Song J., Jang B., Jung C.-H., Kang H.
    Nucleic Acids Res. 35:506-516(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INDUCTION BY COLD.
    Strain: cv. Columbia.
  9. "AtGRP2, a cold-induced nucleo-cytoplasmic RNA-binding protein, has a role in flower and seed development."
    Fusaro A.F., Bocca S.N., Ramos R.L., Barroco R.M., Magioli C., Jorge V.C., Coutinho T.C., Rangel-Lima C.M., De Rycke R., Inze D., Engler G., Sachetto-Martins G.
    Planta 225:1339-1351(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, SUBCELLULAR LOCATION, INDUCTION BY COLD.
    Strain: cv. C24.
  10. "Functional characterization of a glycine-rich RNA-binding protein 2 in Arabidopsis thaliana under abiotic stress conditions."
    Kim J.Y., Park S.J., Jang B., Jung C.-H., Ahn S.J., Goh C.-H., Cho K., Han O., Kang H.
    Plant J. 50:439-451(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, DISRUPTION PHENOTYPE.
    Strain: cv. Columbia.
  11. "Arabidopsis cold shock domain proteins: relationships to floral and silique development."
    Nakaminami K., Hill K., Perry S.E., Sentoku N., Long J.A., Karlson D.T.
    J. Exp. Bot. 60:1047-1062(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, GENE FAMILY, NOMENCLATURE.
    Strain: cv. Columbia and cv. Landsberg erecta.
  12. "Cold shock domain proteins affect seed germination and growth of Arabidopsis thaliana under abiotic stress conditions."
    Park S.J., Kwak K.J., Oh T.R., Kim Y.O., Kang H.
    Plant Cell Physiol. 50:869-878(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.

Entry informationi

Entry nameiCSP2_ARATH
AccessioniPrimary (citable) accession number: Q41188
Secondary accession number(s): C0Z2E8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 11, 2012
Last sequence update: November 1, 1996
Last modified: July 6, 2016
This is version 145 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.