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    PODNL1 podocan like 1 [ Homo sapiens (human) ]

    Gene ID: 79883, updated on 6-Jun-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    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

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001146254.2NP_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:193447
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      sd00033
      Location:98123
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:427480
      LRR_8; Leucine rich repeat
    2. NM_001146255.2NP_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:72303
      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:7597
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:149208
      LRR_8; Leucine rich repeat
    3. NM_001370095.3NP_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:152529
      PLN00113; leucine-rich repeat receptor-like protein kinase; Provisional
      sd00033
      Location:93118
      LRR_RI; leucine-rich repeat [structural motif]
      cd21340
      Location:67226
      PPP1R42; protein phosphatase 1 regulatory subunit 42
    4. NM_001411137.1NP_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_024825.5NP_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:93118
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:422475
      LRR_8; Leucine rich repeat
      cl26018
      Location:188442
      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_047439453.1XP_047295409.1  podocan-like protein 1 isoform X7

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

      UniProtKB/Swiss-Prot
      B7Z564, Q6PEZ8, Q9H5G9
      Conserved Domains (3) summary
      PRK15370
      Location:32180
      PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
      PLN00113
      Location:157534
      PLN00113; leucine-rich repeat receptor-like protein kinase; Provisional
      sd00033
      Location:98123
      LRR_RI; leucine-rich repeat [structural motif]
    3. XM_011528310.3XP_011526612.1  podocan-like protein 1 isoform X3

      UniProtKB/Swiss-Prot
      B7Z564, Q6PEZ8, Q9H5G9
      UniProtKB/TrEMBL
      A8K3W6
      Conserved Domains (3) summary
      cd00116
      Location:74297
      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:169187
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:186248
      LRR_8; Leucine rich repeat
    4. XM_011528309.3XP_011526611.1  podocan-like protein 1 isoform X2

      Conserved Domains (4) summary
      cd00116
      Location:217376
      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:224249
      LRR_RI; leucine-rich repeat [structural motif]
      pfam12799
      Location:77112
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:411473
      LRR_8; Leucine rich repeat
    5. XM_006722903.2XP_006722966.1  podocan-like protein 1 isoform X6

      Conserved Domains (3) summary
      cd00116
      Location:74305
      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:7799
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:340402
      LRR_8; Leucine rich repeat
    6. XM_006722902.2XP_006722965.1  podocan-like protein 1 isoform X5

      Conserved Domains (3) summary
      cd00116
      Location:74349
      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:7799
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:171233
      LRR_8; Leucine rich repeat
    7. XM_011528314.2XP_011526616.1  podocan-like protein 1 isoform X8

      Conserved Domains (3) summary
      cd00116
      Location:84297
      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:102120
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:119181
      LRR_8; Leucine rich repeat
    8. XM_011528311.2XP_011526613.1  podocan-like protein 1 isoform X4

      Conserved Domains (3) summary
      cd00116
      Location:202361
      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:209234
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:396458
      LRR_8; Leucine rich repeat
    9. XM_024451726.2XP_024307494.1  podocan-like protein 1 isoform X9

      UniProtKB/Swiss-Prot
      B7Z564, Q6PEZ8, Q9H5G9
      UniProtKB/TrEMBL
      A8K3W6
      Conserved Domains (2) summary
      sd00033
      Location:7799
      LRR_RI; leucine-rich repeat [structural motif]
      cl26018
      Location:121376
      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_054332730.1XP_054188705.1  podocan-like protein 1 isoform X7

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

      UniProtKB/Swiss-Prot
      B7Z564, Q6PEZ8, Q9H5G9
    3. XM_054332726.1XP_054188701.1  podocan-like protein 1 isoform X3

      UniProtKB/Swiss-Prot
      B7Z564, Q6PEZ8, Q9H5G9
      UniProtKB/TrEMBL
      A8K3W6
    4. XM_054332725.1XP_054188700.1  podocan-like protein 1 isoform X2

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

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

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

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

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

      UniProtKB/Swiss-Prot
      B7Z564, Q6PEZ8, Q9H5G9
      UniProtKB/TrEMBL
      A8K3W6

    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_054322200.1XP_054178175.1  podocan-like protein 1 isoform X7

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

      UniProtKB/Swiss-Prot
      B7Z564, Q6PEZ8, Q9H5G9
    3. XM_054322196.1XP_054178171.1  podocan-like protein 1 isoform X3

      UniProtKB/Swiss-Prot
      B7Z564, Q6PEZ8, Q9H5G9
      UniProtKB/TrEMBL
      A8K3W6
    4. XM_054322195.1XP_054178170.1  podocan-like protein 1 isoform X2

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

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

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

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

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

      UniProtKB/Swiss-Prot
      B7Z564, Q6PEZ8, Q9H5G9
      UniProtKB/TrEMBL
      A8K3W6