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PODNL1 podocan like 1 [ Homo sapiens (human) ]

Gene ID: 79883, updated on 3-Apr-2024

Summary

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Official Symbol
PODNL1provided by HGNC
Official Full Name
podocan like 1provided by HGNC
Primary source
HGNC:HGNC:26275
See related
Ensembl:ENSG00000132000 AllianceGenome:HGNC:26275
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SLRR5B
Summary
Predicted to be located in collagen-containing extracellular matrix. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in placenta (RPKM 1.8), skin (RPKM 0.8) and 19 other tissues See more
Orthologs
mouse all
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Genomic context

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See PODNL1 in Genome Data Viewer
Location:
19p13.12
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (13931187..13953383, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (14057347..14079667, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (14042000..14064195, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13993737-13994582 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14000391-14000892 Neighboring gene break repair meiotic recombinase recruitment factor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10218 Neighboring gene coiled-coil and C2 domain containing 1A Neighboring gene MPRA-validated peak3378 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14046993-14047750 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14150 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10219 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14069830-14070403 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14070404-14070976 Neighboring gene DDB1 and CUL4 associated factor 15 Neighboring gene regulatory factor X1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14090312-14090838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14090839-14091365 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:14091366-14091891 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14093768-14094294 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14096053-14096944 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14151 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:14097836-14098726 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:14116358-14116886 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:14116887-14117414 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:14117415-14117942 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:14134324-14134824 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:14134825-14135325 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14152 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10222 Neighboring gene relaxin 3

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. PODNL1 promotes cell proliferation and migration in glioma via regulating Akt/mTOR pathway. Geng Y, et al. J Cancer, 2020. PMID 33033506, Free PMC Article
  2. PODNL1 Methylation Serves as a Prognostic Biomarker and Associates with Immune Cell Infiltration and Immune Checkpoint Blockade Response in Lower-Grade Glioma. Noor H, et al. Int J Mol Sci, 2021 Nov 22. PMID 34830454, Free PMC Article
  3. Cullin 1 (CUL1) Promotes Primary Ciliogenesis through the Induction of Ubiquitin-Proteasome-Dependent Dvl2 Degradation. Kim SO, et al. Int J Mol Sci, 2021 Jul 15. PMID 34299191, Free PMC Article
  4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
  5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. PODNL1 Methylation Serves as a Prognostic Biomarker and Associates with Immune Cell Infiltration and Immune Checkpoint Blockade Response in Lower-Grade Glioma.
    Title: PODNL1 Methylation Serves as a Prognostic Biomarker and Associates with Immune Cell Infiltration and Immune Checkpoint Blockade Response in Lower-Grade Glioma.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Homology

Clone Names

  • FLJ23447

Gene Ontology Provided by GOA

Component Evidence Code Pubs
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
podocan-like protein 1

NCBI Reference Sequences (RefSeq)

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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_001146254.2 → NP_001139726.1  podocan-like protein 1 isoform 2 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) encodes the longest isoform (2).
    Source sequence(s)
    AC020916, AI219486, AK027100, AK296101, AK298489, BC052610
    Consensus CDS
    CCDS54226.1
    UniProtKB/Swiss-Prot
    B7Z564, Q6PEZ8, Q9H5G9
    Related
    ENSP00000442553.1, ENST00000538371.6
    Conserved Domains (3) summary
    PRK15370
    Location:193 → 447
    PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
    sd00033
    Location:98 → 123
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:427 → 480
    LRR_8; Leucine rich repeat

  2. NM_001146255.2 → NP_001139727.1  podocan-like protein 1 isoform 3 precursor

    See identical proteins and their annotated locations for NP_001139727.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks two consecutive alternate exons in the 5' coding region, compared to variant 2. It encodes isoform 3, which lacks an internal in-frame segment and is shorter, compared to isoform 2.
    Source sequence(s)
    AC020916, AI219486, AK027100, AK298489, BC052610
    Consensus CDS
    CCDS54225.1
    UniProtKB/Swiss-Prot
    B7Z564, Q6PEZ8, Q9H5G9
    UniProtKB/TrEMBL
    A8K3W6
    Related
    ENSP00000440080.1, ENST00000538517.6
    Conserved Domains (3) summary
    cd00116
    Location:72 → 303
    LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
    sd00033
    Location:75 → 97
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:149 → 208
    LRR_8; Leucine rich repeat

  3. NM_001370095.3 → NP_001357024.2  podocan-like protein 1 isoform 4 precursor

    Status: VALIDATED

    Source sequence(s)
    AC020916
    Consensus CDS
    CCDS92539.1
    UniProtKB/Swiss-Prot
    B7Z564, Q6PEZ8, Q9H5G9
    UniProtKB/TrEMBL
    K7EPI2
    Related
    ENSP00000467395.2, ENST00000588872.3
    Conserved Domains (3) summary
    PLN00113
    Location:152 → 529
    PLN00113; leucine-rich repeat receptor-like protein kinase; Provisional
    sd00033
    Location:93 → 118
    LRR_RI; leucine-rich repeat [structural motif]
    cd21340
    Location:67 → 226
    PPP1R42; protein phosphatase 1 regulatory subunit 42

  4. NM_001411137.1 → NP_001398066.1  podocan-like protein 1 isoform 5

    Status: VALIDATED

    Source sequence(s)
    AC020916
    Consensus CDS
    CCDS92538.1
    UniProtKB/TrEMBL
    B7Z3M0
    Related
    ENSP00000254320.3, ENST00000254320.7

  5. NM_024825.5 → NP_079101.4  podocan-like protein 1 isoform 1 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) includes an alternate 5' terminal exon, resulting in a different 5' UTR and 5' coding region, compared to variant 2. It encodes isoform 1, which is shorter and has a distinct N-terminus, compared to isoform 2.
    Source sequence(s)
    AC020916, AK290731, BC052610, BC057786, CA411674
    Consensus CDS
    CCDS12300.2
    UniProtKB/Swiss-Prot
    B7Z564, Q6PEZ8, Q9H5G9
    UniProtKB/TrEMBL
    A0A2U3TZJ2
    Related
    ENSP00000345175.5, ENST00000339560.10
    Conserved Domains (3) summary
    sd00033
    Location:93 → 118
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:422 → 475
    LRR_8; Leucine rich repeat
    cl26018
    Location:188 → 442
    NEL; C-terminal novel E3 ligase, LRR-interacting

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    13931187..13953383 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047439453.1 → XP_047295409.1  podocan-like protein 1 isoform X7

  2. XM_011528308.1 → XP_011526610.1  podocan-like protein 1 isoform X1

    UniProtKB/Swiss-Prot
    B7Z564, Q6PEZ8, Q9H5G9
    Conserved Domains (3) summary
    PRK15370
    Location:32 → 180
    PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
    PLN00113
    Location:157 → 534
    PLN00113; leucine-rich repeat receptor-like protein kinase; Provisional
    sd00033
    Location:98 → 123
    LRR_RI; leucine-rich repeat [structural motif]

  3. XM_011528310.3 → XP_011526612.1  podocan-like protein 1 isoform X3

    UniProtKB/Swiss-Prot
    B7Z564, Q6PEZ8, Q9H5G9
    UniProtKB/TrEMBL
    A8K3W6
    Conserved Domains (3) summary
    cd00116
    Location:74 → 297
    LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
    sd00033
    Location:169 → 187
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:186 → 248
    LRR_8; Leucine rich repeat

  4. XM_011528309.3 → XP_011526611.1  podocan-like protein 1 isoform X2

    Conserved Domains (4) summary
    cd00116
    Location:217 → 376
    LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
    sd00033
    Location:224 → 249
    LRR_RI; leucine-rich repeat [structural motif]
    pfam12799
    Location:77 → 112
    LRR_4; Leucine Rich repeats (2 copies)
    pfam13855
    Location:411 → 473
    LRR_8; Leucine rich repeat

  5. XM_006722903.2 → XP_006722966.1  podocan-like protein 1 isoform X6

    Conserved Domains (3) summary
    cd00116
    Location:74 → 305
    LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
    sd00033
    Location:77 → 99
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:340 → 402
    LRR_8; Leucine rich repeat

  6. XM_006722902.2 → XP_006722965.1  podocan-like protein 1 isoform X5

    Conserved Domains (3) summary
    cd00116
    Location:74 → 349
    LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
    sd00033
    Location:77 → 99
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:171 → 233
    LRR_8; Leucine rich repeat

  7. XM_011528314.2 → XP_011526616.1  podocan-like protein 1 isoform X8

    Conserved Domains (3) summary
    cd00116
    Location:84 → 297
    LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
    sd00033
    Location:102 → 120
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:119 → 181
    LRR_8; Leucine rich repeat

  8. XM_011528311.2 → XP_011526613.1  podocan-like protein 1 isoform X4

    Conserved Domains (3) summary
    cd00116
    Location:202 → 361
    LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
    sd00033
    Location:209 → 234
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:396 → 458
    LRR_8; Leucine rich repeat

  9. XM_024451726.2 → XP_024307494.1  podocan-like protein 1 isoform X9

    UniProtKB/Swiss-Prot
    B7Z564, Q6PEZ8, Q9H5G9
    UniProtKB/TrEMBL
    A8K3W6
    Conserved Domains (2) summary
    sd00033
    Location:77 → 99
    LRR_RI; leucine-rich repeat [structural motif]
    cl26018
    Location:121 → 376
    NEL; C-terminal novel E3 ligase, LRR-interacting

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_021160022.1 Reference GRCh38.p14 PATCHES

    Range
    143028..165224 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054332730.1 → XP_054188705.1  podocan-like protein 1 isoform X7

  2. XM_054332724.1 → XP_054188699.1  podocan-like protein 1 isoform X1

  3. XM_054332726.1 → XP_054188701.1  podocan-like protein 1 isoform X3

  4. XM_054332725.1 → XP_054188700.1  podocan-like protein 1 isoform X2

  5. XM_054332729.1 → XP_054188704.1  podocan-like protein 1 isoform X6

  6. XM_054332728.1 → XP_054188703.1  podocan-like protein 1 isoform X5

  7. XM_054332731.1 → XP_054188706.1  podocan-like protein 1 isoform X8

  8. XM_054332727.1 → XP_054188702.1  podocan-like protein 1 isoform X4

  9. XM_054332732.1 → XP_054188707.1  podocan-like protein 1 isoform X9

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    14057347..14079667 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054322200.1 → XP_054178175.1  podocan-like protein 1 isoform X7

  2. XM_054322194.1 → XP_054178169.1  podocan-like protein 1 isoform X1

  3. XM_054322196.1 → XP_054178171.1  podocan-like protein 1 isoform X3

  4. XM_054322195.1 → XP_054178170.1  podocan-like protein 1 isoform X2

  5. XM_054322199.1 → XP_054178174.1  podocan-like protein 1 isoform X6

  6. XM_054322198.1 → XP_054178173.1  podocan-like protein 1 isoform X5

  7. XM_054322201.1 → XP_054178176.1  podocan-like protein 1 isoform X8

  8. XM_054322197.1 → XP_054178172.1  podocan-like protein 1 isoform X4

  9. XM_054322202.1 → XP_054178177.1  podocan-like protein 1 isoform X9

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6PEZ8.2 GenPept UniProtKB/Swiss-Prot:Q6PEZ8

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