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Protein

CTD small phosphatase-like protein

Gene

NFI1

Organism
Gallus gallus (Chicken)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript leveli

Functioni

Preferentially catalyzes the dephosphorylation of 'Ser-5' within the tandem 7 residue repeats in the C-terminal domain (CTD) of the largest RNA polymerase II subunit POLR2A. Negatively regulates RNA polymerase II transcription, possibly by controlling the transition from initiation/capping to processive transcript elongation. Recruited by REST to neuronal genes that contain RE-1 elements, leading to neuronal gene silencing in non-neuronal cells (By similarity).By similarity

Catalytic activityi

[a protein]-serine/threonine phosphate + H2O = [a protein]-serine/threonine + phosphate.

Cofactori

Mg2+By similarityNote: Binds 1 Mg2+ ion per monomer.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei111 – 11114-aspartylphosphate intermediateBy similarity
Metal bindingi111 – 1111MagnesiumBy similarity
Active sitei113 – 1131Proton donorBy similarity
Metal bindingi113 – 1131Magnesium; via carbonyl oxygenBy similarity
Sitei167 – 1671Transition state stabilizerBy similarity
Sitei205 – 2051Transition state stabilizerBy similarity
Metal bindingi222 – 2221MagnesiumBy similarity

GO - Molecular functioni

  1. metal ion binding Source: UniProtKB-KW
  2. phosphoprotein phosphatase activity Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protein phosphatase

Keywords - Ligandi

Magnesium, Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
CTD small phosphatase-like protein (EC:3.1.3.16)
Short name:
CTDSP-like
Alternative name(s):
Nuclear LIM interactor-interacting factor 1
Short name:
NLI-interacting factor 1
Small C-terminal domain phosphatase 3
Gene namesi
Name:NFI1
Synonyms:NIF
OrganismiGallus gallus (Chicken)
Taxonomic identifieri9031 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiArchelosauriaArchosauriaDinosauriaSaurischiaTheropodaCoelurosauriaAvesNeognathaeGalloanseraeGalliformesPhasianidaePhasianinaeGallus
ProteomesiUP000000539 Componenti: Chromosome 2

Subcellular locationi

Nucleus By similarity

GO - Cellular componenti

  1. nucleus Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 275275CTD small phosphatase-like proteinPRO_0000212571Add
BLAST

Expressioni

Gene expression databases

ExpressionAtlasiQ9PTJ6. baseline and differential.

Interactioni

Subunit structurei

Monomer (By similarity). Interacts with LDB1.By similarity

Structurei

3D structure databases

ProteinModelPortaliQ9PTJ6.
SMRiQ9PTJ6. Positions 82-263.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini101 – 259159FCP1 homologyPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 FCP1 homology domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG5190.
GeneTreeiENSGT00390000017194.
HOGENOMiHOG000236379.
HOVERGENiHBG053298.
InParanoidiQ9PTJ6.
KOiK15731.
OrthoDBiEOG71P2C3.
PhylomeDBiQ9PTJ6.
TreeFamiTF313556.

Family and domain databases

Gene3Di3.40.50.1000. 1 hit.
InterProiIPR011948. Dullard_phosphatase.
IPR023214. HAD-like_dom.
IPR004274. NIF.
[Graphical view]
PfamiPF03031. NIF. 1 hit.
[Graphical view]
SMARTiSM00577. CPDc. 1 hit.
[Graphical view]
SUPFAMiSSF56784. SSF56784. 1 hit.
TIGRFAMsiTIGR02251. HIF-SF_euk. 1 hit.
PROSITEiPS50969. FCP1. 1 hit.
[Graphical view]

Sequences (4)i

Sequence statusi: Complete.

This entry describes 4 isoformsi produced by alternative splicing. AlignAdd to basket

Note: Additional isoforms seem to exist. A not yet characterized isoform having a longer N-terminus as seen in human and mouse might exist.

Isoform 1 (identifier: Q9PTJ6-1) [UniParc]FASTAAdd to basket

Also known as: T1

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
MDNPSIITQV TNPKEEEILS CTQDKVSQCN ISLKKQRSRS IFSTLFCCFR
60 70 80 90 100
DYNVEPPSTN STSALPPLVE ENGGLQKGDQ MQVMPIPSPP AKYLLPELTA
110 120 130 140 150
SDYGKKCVVI DLDETLVHSS FKPISNADFI VPVEIDGTIH QVYVLKRPHV
160 170 180 190 200
DEFLQRMGEL FECVLFTASL AKYADPVADL LDRWGVFRAR LFRESCVFHR
210 220 230 240 250
GNYVKDLSRL GRELSKVIIV DNSPASYIFH PENAVPVQSW FDDMTDTELL
260 270
DLIPFFEGLS KEEEVYSMLH KLCNR
Length:275
Mass (Da):31,244
Last modified:December 12, 2001 - v2
Checksum:iF68C357769809347
GO
Isoform 2 (identifier: Q9PTJ6-2) [UniParc]FASTAAdd to basket

Also known as: T2

The sequence of this isoform differs from the canonical sequence as follows:
     78-88: Missing.
     275-275: R → SSFKCKLWGGHSCQKCYSRSSCYIGHKGQS

Show »
Length:293
Mass (Da):33,239
Checksum:iF698C221C1F19949
GO
Isoform 3 (identifier: Q9PTJ6-3) [UniParc]FASTAAdd to basket

Also known as: T3

The sequence of this isoform differs from the canonical sequence as follows:
     173-275: YADPVADLLD...YSMLHKLCNR → CVLCLLVCGMQTQ

Show »
Length:185
Mass (Da):20,615
Checksum:iB9A7126AD2AD2EA0
GO
Isoform 4 (identifier: Q9PTJ6-4) [UniParc]FASTAAdd to basket

Also known as: R5

The sequence of this isoform differs from the canonical sequence as follows:
     78-88: Missing.

Show »
Length:264
Mass (Da):30,059
Checksum:i0405951D4CA8ADFC
GO

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei78 – 8811Missing in isoform 2 and isoform 4. 1 PublicationVSP_003564Add
BLAST
Alternative sequencei173 – 275103YADPV…KLCNR → CVLCLLVCGMQTQ in isoform 3. 1 PublicationVSP_003565Add
BLAST
Alternative sequencei275 – 2751R → SSFKCKLWGGHSCQKCYSRS SCYIGHKGQS in isoform 2. 1 PublicationVSP_003566

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF189773 mRNA. Translation: AAF17481.1.
AF189774 mRNA. Translation: AAF17482.1.
AF189775 mRNA. Translation: AAF17483.1.
AF189776 mRNA. Translation: AAF17484.1.
RefSeqiNP_001001316.1. NM_001001316.1. [Q9PTJ6-1]
UniGeneiGga.4190.

Genome annotation databases

EnsembliENSGALT00000009158; ENSGALP00000009144; ENSGALG00000005710. [Q9PTJ6-1]
GeneIDi408252.
KEGGigga:408252.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF189773 mRNA. Translation: AAF17481.1.
AF189774 mRNA. Translation: AAF17482.1.
AF189775 mRNA. Translation: AAF17483.1.
AF189776 mRNA. Translation: AAF17484.1.
RefSeqiNP_001001316.1. NM_001001316.1. [Q9PTJ6-1]
UniGeneiGga.4190.

3D structure databases

ProteinModelPortaliQ9PTJ6.
SMRiQ9PTJ6. Positions 82-263.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSGALT00000009158; ENSGALP00000009144; ENSGALG00000005710. [Q9PTJ6-1]
GeneIDi408252.
KEGGigga:408252.

Organism-specific databases

CTDi10217.

Phylogenomic databases

eggNOGiCOG5190.
GeneTreeiENSGT00390000017194.
HOGENOMiHOG000236379.
HOVERGENiHBG053298.
InParanoidiQ9PTJ6.
KOiK15731.
OrthoDBiEOG71P2C3.
PhylomeDBiQ9PTJ6.
TreeFamiTF313556.

Miscellaneous databases

NextBioi20818670.
PROiQ9PTJ6.

Gene expression databases

ExpressionAtlasiQ9PTJ6. baseline and differential.

Family and domain databases

Gene3Di3.40.50.1000. 1 hit.
InterProiIPR011948. Dullard_phosphatase.
IPR023214. HAD-like_dom.
IPR004274. NIF.
[Graphical view]
PfamiPF03031. NIF. 1 hit.
[Graphical view]
SMARTiSM00577. CPDc. 1 hit.
[Graphical view]
SUPFAMiSSF56784. SSF56784. 1 hit.
TIGRFAMsiTIGR02251. HIF-SF_euk. 1 hit.
PROSITEiPS50969. FCP1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "NLI/Ldb1/CLIM interacting factor."
    Mikhailik A., Dezelee P., Calothy G.
    Submitted (AUG-1999) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1; 2; 3 AND 4).
    Strain: Brown leghorn.
    Tissue: Neuroretina.

Entry informationi

Entry nameiCTDSL_CHICK
AccessioniPrimary (citable) accession number: Q9PTJ6
Secondary accession number(s): Q9PTJ7, Q9PTJ8, Q9PTJ9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 12, 2001
Last sequence update: December 12, 2001
Last modified: March 31, 2015
This is version 76 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.