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PPFIBP1 PPFIA binding protein 1 [ Homo sapiens (human) ]

Gene ID: 8496, updated on 13-Mar-2020

Summary

Official Symbol
PPFIBP1provided by HGNC
Official Full Name
PPFIA binding protein 1provided by HGNC
Primary source
HGNC:HGNC:9249
See related
Ensembl:ENSG00000110841 MIM:603141
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
L2; SGT2; hSGT2; hSgt2p
Summary
The protein encoded by this gene is a member of the LAR protein-tyrosine phosphatase-interacting protein (liprin) family. Liprins interact with members of LAR family of transmembrane protein tyrosine phosphatases, which are known to be important for axon guidance and mammary gland development. It has been proposed that liprins are multivalent proteins that form complex structures and act as scaffolds for the recruitment and anchoring of LAR family of tyrosine phosphatases. This protein was found to interact with S100A4, a calcium-binding protein related to tumor invasiveness and metastasis. In vitro experiment demonstrated that the interaction inhibited the phosphorylation of this protein by protein kinase C and protein kinase CK2. Alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in ovary (RPKM 22.3), heart (RPKM 16.3) and 24 other tissues See more
Orthologs

Genomic context

See PPFIBP1 in Genome Data Viewer
Location:
12p11.23-p11.22
Exon count:
34
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (27524126..27695564)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (27677045..27848497)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene aryl hydrocarbon receptor nuclear translocator like 2 Neighboring gene ARNTL2 antisense RNA 1 Neighboring gene single-pass membrane protein with coiled-coil domains 2 Neighboring gene arginyl-tRNA synthetase 1 pseudogene 1 Neighboring gene uncharacterized protein C12orf71-like Neighboring gene uncharacterized LOC107984461 Neighboring gene high mobility group box 1 pseudogene 49 Neighboring gene RAB15 effector protein

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

Replication interactions

Interaction Pubs
Screening in Jurkat T-cells with a short-hairpin-RNA (shRNA) library identifies protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein, binding protein 1, beta 1 (PPFIBP1) is important for HIV-1 replication PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
cadherin binding HDA PubMed 
Process Evidence Code Pubs
cell adhesion TAS
Traceable Author Statement
more info
PubMed 
neuromuscular junction development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
synapse organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
cytosol TAS
Traceable Author Statement
more info
 
focal adhesion HDA PubMed 
plasma membrane NAS
Non-traceable Author Statement
more info
PubMed 
presynaptic active zone IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
liprin-beta-1
Names
PTPRF interacting protein, binding protein 1 (liprin beta 1)
PTPRF-interacting protein-binding protein 1
liprin related protein
protein-tyrosine phosphatase receptor-type f polypeptide-interacting protein-binding protein 1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001198915.2NP_001185844.1  liprin-beta-1 isoform 3

    See identical proteins and their annotated locations for NP_001185844.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 2. The resulting isoform (3) is shorter at the N-terminus compared to isoform 2.
    Source sequence(s)
    AC009509, AC068794, AC087257
    Consensus CDS
    CCDS55814.1
    UniProtKB/Swiss-Prot
    Q86W92
    UniProtKB/TrEMBL
    A0A024RB02
    Related
    ENSP00000445425.1, ENST00000537927.5
    Conserved Domains (5) summary
    cd09563
    Location:491554
    SAM_liprin-beta1,2_repeat1; SAM domain of liprin-beta1,2 proteins repeat 1
    cd09566
    Location:565627
    SAM_liprin-beta1,2_repeat2; SAM domain of liprin-beta1,2 proteins repeat 2
    cd09569
    Location:650721
    SAM_liprin-beta1,2_repeat3; SAM domain of liprin-beta proteins repeat 3
    smart00454
    Location:491555
    SAM; Sterile alpha motif
    cl19219
    Location:50128
    DUF342; Protein of unknown function (DUF342)
  2. NM_001198916.2NP_001185845.2  liprin-beta-1 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an alternate in-frame exon compared to variant 2. The resulting isoform (4) has the same N- and C-termini but is shorter compared to isoform 2.
    Source sequence(s)
    AC009509, AC068794, AC087257
    Consensus CDS
    CCDS55813.1
    Related
    ENSP00000443442.1, ENST00000542629.5
  3. NM_003622.4NP_003613.4  liprin-beta-1 isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) has multiple differences in the coding sequence compared to variant 2. The resulting isoform (1) has the same N- and C-termini but is 6 aa shorter compared to isoform 2.
    Source sequence(s)
    AC009509, AC068794, AC087257
    Consensus CDS
    CCDS8713.1
    Related
    ENSP00000228425.6, ENST00000228425.11
    Conserved Domains (4) summary
    cd09563
    Location:638701
    SAM_liprin-beta1,2_repeat1; SAM domain of liprin-beta1,2 proteins repeat 1
    cd09566
    Location:712774
    SAM_liprin-beta1,2_repeat2; SAM domain of liprin-beta1,2 proteins repeat 2
    cd09569
    Location:797868
    SAM_liprin-beta1,2_repeat3; SAM domain of liprin-beta proteins repeat 3
    cl25732
    Location:103322
    SMC_N; RecF/RecN/SMC N terminal domain
  4. NM_177444.3NP_803193.3  liprin-beta-1 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) represents the longest transcript and encodes the longest isoform (2).
    Source sequence(s)
    AC009509, AC068794, AC087257
    Consensus CDS
    CCDS55812.1
    Related
    ENSP00000314724.8, ENST00000318304.12

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p13 Primary Assembly

    Range
    27524126..27695564
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017020059.2XP_016875548.1  liprin-beta-1 isoform X7

    Conserved Domains (7) summary
    cd09563
    Location:658721
    SAM_liprin-beta1,2_repeat1; SAM domain of liprin-beta1,2 proteins repeat 1
    cd09566
    Location:732794
    SAM_liprin-beta1,2_repeat2; SAM domain of liprin-beta1,2 proteins repeat 2
    cd09569
    Location:817888
    SAM_liprin-beta1,2_repeat3; SAM domain of liprin-beta proteins repeat 3
    smart00454
    Location:658722
    SAM; Sterile alpha motif
    pfam01519
    Location:105156
    DUF16; Protein of unknown function DUF16
    pfam03528
    Location:103506
    Rabaptin; Rabaptin
    cl19219
    Location:203308
    DUF342; Protein of unknown function (DUF342)
  2. XM_017020063.2XP_016875552.1  liprin-beta-1 isoform X11

  3. XM_017020073.2XP_016875562.1  liprin-beta-1 isoform X21

  4. XM_017020068.2XP_016875557.1  liprin-beta-1 isoform X16

  5. XM_017020062.2XP_016875551.1  liprin-beta-1 isoform X10

    Conserved Domains (6) summary
    cd09563
    Location:647710
    SAM_liprin-beta1,2_repeat1; SAM domain of liprin-beta1,2 proteins repeat 1
    cd09566
    Location:721783
    SAM_liprin-beta1,2_repeat2; SAM domain of liprin-beta1,2 proteins repeat 2
    cd09569
    Location:806877
    SAM_liprin-beta1,2_repeat3; SAM domain of liprin-beta proteins repeat 3
    smart00454
    Location:647711
    SAM; Sterile alpha motif
    pfam01519
    Location:105156
    DUF16; Protein of unknown function DUF16
    cl19219
    Location:203281
    DUF342; Protein of unknown function (DUF342)
  6. XM_017020074.2XP_016875563.1  liprin-beta-1 isoform X23

    Related
    ENSP00000444304.1, ENST00000540114.5
  7. XM_017020078.1XP_016875567.1  liprin-beta-1 isoform X27

  8. XM_017020065.2XP_016875554.1  liprin-beta-1 isoform X13

  9. XM_017020071.2XP_016875560.1  liprin-beta-1 isoform X19

  10. XM_017020064.2XP_016875553.1  liprin-beta-1 isoform X12

    Conserved Domains (8) summary
    cd09563
    Location:635698
    SAM_liprin-beta1,2_repeat1; SAM domain of liprin-beta1,2 proteins repeat 1
    cd09566
    Location:709771
    SAM_liprin-beta1,2_repeat2; SAM domain of liprin-beta1,2 proteins repeat 2
    cd09569
    Location:794865
    SAM_liprin-beta1,2_repeat3; SAM domain of liprin-beta proteins repeat 3
    smart00454
    Location:635699
    SAM; Sterile alpha motif
    pfam01519
    Location:105156
    DUF16; Protein of unknown function DUF16
    pfam14662
    Location:106313
    KASH_CCD; Coiled-coil region of CCDC155 or KASH
    cl23720
    Location:134270
    RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
    cl23750
    Location:218330
    vATP-synt_E; ATP synthase (E/31 kDa) subunit
  11. XM_017020070.2XP_016875559.1  liprin-beta-1 isoform X18

    Conserved Domains (8) summary
    cd09563
    Location:624687
    SAM_liprin-beta1,2_repeat1; SAM domain of liprin-beta1,2 proteins repeat 1
    cd09566
    Location:698760
    SAM_liprin-beta1,2_repeat2; SAM domain of liprin-beta1,2 proteins repeat 2
    cd09569
    Location:783854
    SAM_liprin-beta1,2_repeat3; SAM domain of liprin-beta proteins repeat 3
    smart00454
    Location:624688
    SAM; Sterile alpha motif
    pfam01519
    Location:105156
    DUF16; Protein of unknown function DUF16
    pfam14662
    Location:106313
    KASH_CCD; Coiled-coil region of CCDC155 or KASH
    cl23720
    Location:134270
    RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
    cl23750
    Location:218330
    vATP-synt_E; ATP synthase (E/31 kDa) subunit
  12. XM_017020061.2XP_016875550.1  liprin-beta-1 isoform X9

  13. XM_017020056.2XP_016875545.1  liprin-beta-1 isoform X1

    Conserved Domains (4) summary
    cd09563
    Location:669732
    SAM_liprin-beta1,2_repeat1; SAM domain of liprin-beta1,2 proteins repeat 1
    cd09566
    Location:743805
    SAM_liprin-beta1,2_repeat2; SAM domain of liprin-beta1,2 proteins repeat 2
    cd09569
    Location:828899
    SAM_liprin-beta1,2_repeat3; SAM domain of liprin-beta proteins repeat 3
    cl25732
    Location:47352
    SMC_N; RecF/RecN/SMC N terminal domain
  14. XM_006719159.4XP_006719222.1  liprin-beta-1 isoform X22

    Conserved Domains (5) summary
    cd09563
    Location:516579
    SAM_liprin-beta1,2_repeat1; SAM domain of liprin-beta1,2 proteins repeat 1
    cd09566
    Location:590652
    SAM_liprin-beta1,2_repeat2; SAM domain of liprin-beta1,2 proteins repeat 2
    cd09569
    Location:675746
    SAM_liprin-beta1,2_repeat3; SAM domain of liprin-beta proteins repeat 3
    smart00454
    Location:516580
    SAM; Sterile alpha motif
    cl19219
    Location:50155
    DUF342; Protein of unknown function (DUF342)
  15. XM_024449232.1XP_024305000.1  liprin-beta-1 isoform X1

    Conserved Domains (4) summary
    cd09563
    Location:669732
    SAM_liprin-beta1,2_repeat1; SAM domain of liprin-beta1,2 proteins repeat 1
    cd09566
    Location:743805
    SAM_liprin-beta1,2_repeat2; SAM domain of liprin-beta1,2 proteins repeat 2
    cd09569
    Location:828899
    SAM_liprin-beta1,2_repeat3; SAM domain of liprin-beta proteins repeat 3
    cl25732
    Location:47352
    SMC_N; RecF/RecN/SMC N terminal domain
  16. XM_024449237.1XP_024305005.1  liprin-beta-1 isoform X8

    Conserved Domains (4) summary
    cd09563
    Location:648711
    SAM_liprin-beta1,2_repeat1; SAM domain of liprin-beta1,2 proteins repeat 1
    cd09566
    Location:722784
    SAM_liprin-beta1,2_repeat2; SAM domain of liprin-beta1,2 proteins repeat 2
    cd09569
    Location:807878
    SAM_liprin-beta1,2_repeat3; SAM domain of liprin-beta proteins repeat 3
    cl25732
    Location:47352
    SMC_N; RecF/RecN/SMC N terminal domain
  17. XM_024449234.1XP_024305002.1  liprin-beta-1 isoform X3

    Conserved Domains (4) summary
    cd09563
    Location:659722
    SAM_liprin-beta1,2_repeat1; SAM domain of liprin-beta1,2 proteins repeat 1
    cd09566
    Location:733795
    SAM_liprin-beta1,2_repeat2; SAM domain of liprin-beta1,2 proteins repeat 2
    cd09569
    Location:818889
    SAM_liprin-beta1,2_repeat3; SAM domain of liprin-beta proteins repeat 3
    cl25732
    Location:47352
    SMC_N; RecF/RecN/SMC N terminal domain
  18. XM_024449233.1XP_024305001.1  liprin-beta-1 isoform X2

    Conserved Domains (4) summary
    cd09563
    Location:666729
    SAM_liprin-beta1,2_repeat1; SAM domain of liprin-beta1,2 proteins repeat 1
    cd09566
    Location:740802
    SAM_liprin-beta1,2_repeat2; SAM domain of liprin-beta1,2 proteins repeat 2
    cd09569
    Location:825896
    SAM_liprin-beta1,2_repeat3; SAM domain of liprin-beta proteins repeat 3
    cl25732
    Location:100352
    SMC_N; RecF/RecN/SMC N terminal domain
  19. XM_017020058.2XP_016875547.1  liprin-beta-1 isoform X5

  20. XM_024449235.1XP_024305003.1  liprin-beta-1 isoform X4

    Conserved Domains (4) summary
    cd09563
    Location:658721
    SAM_liprin-beta1,2_repeat1; SAM domain of liprin-beta1,2 proteins repeat 1
    cd09566
    Location:732794
    SAM_liprin-beta1,2_repeat2; SAM domain of liprin-beta1,2 proteins repeat 2
    cd09569
    Location:817888
    SAM_liprin-beta1,2_repeat3; SAM domain of liprin-beta proteins repeat 3
    cl25732
    Location:47341
    SMC_N; RecF/RecN/SMC N terminal domain
  21. XM_024449236.1XP_024305004.1  liprin-beta-1 isoform X6

    Conserved Domains (4) summary
    cd09563
    Location:655718
    SAM_liprin-beta1,2_repeat1; SAM domain of liprin-beta1,2 proteins repeat 1
    cd09566
    Location:729791
    SAM_liprin-beta1,2_repeat2; SAM domain of liprin-beta1,2 proteins repeat 2
    cd09569
    Location:814885
    SAM_liprin-beta1,2_repeat3; SAM domain of liprin-beta proteins repeat 3
    cl25732
    Location:47341
    SMC_N; RecF/RecN/SMC N terminal domain
  22. XM_017020066.2XP_016875555.1  liprin-beta-1 isoform X14

  23. XM_017020067.2XP_016875556.1  liprin-beta-1 isoform X15

    Conserved Domains (6) summary
    cd09563
    Location:627690
    SAM_liprin-beta1,2_repeat1; SAM domain of liprin-beta1,2 proteins repeat 1
    cd09566
    Location:701763
    SAM_liprin-beta1,2_repeat2; SAM domain of liprin-beta1,2 proteins repeat 2
    cd09569
    Location:786857
    SAM_liprin-beta1,2_repeat3; SAM domain of liprin-beta proteins repeat 3
    smart00454
    Location:627691
    SAM; Sterile alpha motif
    pfam01519
    Location:105156
    DUF16; Protein of unknown function DUF16
    cl23720
    Location:134270
    RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
  24. XM_017020072.2XP_016875561.1  liprin-beta-1 isoform X20

  25. XM_017020069.2XP_016875558.1  liprin-beta-1 isoform X17

    Conserved Domains (6) summary
    cd09563
    Location:624687
    SAM_liprin-beta1,2_repeat1; SAM domain of liprin-beta1,2 proteins repeat 1
    cd09566
    Location:698760
    SAM_liprin-beta1,2_repeat2; SAM domain of liprin-beta1,2 proteins repeat 2
    cd09569
    Location:783854
    SAM_liprin-beta1,2_repeat3; SAM domain of liprin-beta proteins repeat 3
    smart00454
    Location:624688
    SAM; Sterile alpha motif
    pfam01519
    Location:105156
    DUF16; Protein of unknown function DUF16
    cl23720
    Location:134270
    RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
  26. XM_024449238.1XP_024305006.1  liprin-beta-1 isoform X26

    Conserved Domains (1) summary
    cl25732
    Location:100352
    SMC_N; RecF/RecN/SMC N terminal domain
  27. XM_017020075.2XP_016875564.1  liprin-beta-1 isoform X24

  28. XM_017020057.2XP_016875546.1  liprin-beta-1 isoform X1

    Conserved Domains (4) summary
    cd09563
    Location:669732
    SAM_liprin-beta1,2_repeat1; SAM domain of liprin-beta1,2 proteins repeat 1
    cd09566
    Location:743805
    SAM_liprin-beta1,2_repeat2; SAM domain of liprin-beta1,2 proteins repeat 2
    cd09569
    Location:828899
    SAM_liprin-beta1,2_repeat3; SAM domain of liprin-beta proteins repeat 3
    cl25732
    Location:47352
    SMC_N; RecF/RecN/SMC N terminal domain
  29. XM_017020076.2XP_016875565.1  liprin-beta-1 isoform X25

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