PODNL1 podocan like 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PODNL1provided by HGNC
Official Full Name: podocan like 1provided by HGNC
Primary source: HGNC:HGNC:26275
See related: Ensembl:ENSG00000132000 MIM:621043; 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: An extracellular matrix structural constituent. Is active in collagen-containing extracellular matrix. [provided by Alliance of Genome Resources, Dec 2024]
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

Location:: 19p13.12

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (13931187..13953383, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (14057347..14079667, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (14042000..14064195, complement)

Chromosome 19 - NC_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables extracellular matrix structural constituent	HDA more info	PubMed

Component	Evidence Code	Pubs
is_active_in collagen-containing extracellular matrix	HDA more info	PubMed
is_active_in extracellular matrix	HDA more info	PubMed
located_in extracellular matrix	HDA more info	PubMed
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)

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
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
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
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
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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000019.10 Reference GRCh38.p14 Primary Assembly

Range

13931187..13953383 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

NW_021160022.1 Reference GRCh38.p14 PATCHES

Range

143028..165224 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054332730.1 → XP_054188705.1 podocan-like protein 1 isoform X7
XM_054332724.1 → XP_054188699.1 podocan-like protein 1 isoform X1

UniProtKB/Swiss-Prot

B7Z564, Q6PEZ8, Q9H5G9
XM_054332726.1 → XP_054188701.1 podocan-like protein 1 isoform X3

UniProtKB/Swiss-Prot

B7Z564, Q6PEZ8, Q9H5G9

UniProtKB/TrEMBL

A8K3W6
XM_054332725.1 → XP_054188700.1 podocan-like protein 1 isoform X2
XM_054332729.1 → XP_054188704.1 podocan-like protein 1 isoform X6
XM_054332728.1 → XP_054188703.1 podocan-like protein 1 isoform X5
XM_054332731.1 → XP_054188706.1 podocan-like protein 1 isoform X8
XM_054332727.1 → XP_054188702.1 podocan-like protein 1 isoform X4
XM_054332732.1 → XP_054188707.1 podocan-like protein 1 isoform X9

UniProtKB/Swiss-Prot

B7Z564, Q6PEZ8, Q9H5G9

UniProtKB/TrEMBL

A8K3W6

Alternate T2T-CHM13v2.0

Genomic

NC_060943.1 Alternate T2T-CHM13v2.0

Range

14057347..14079667 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054322200.1 → XP_054178175.1 podocan-like protein 1 isoform X7
XM_054322194.1 → XP_054178169.1 podocan-like protein 1 isoform X1

UniProtKB/Swiss-Prot

B7Z564, Q6PEZ8, Q9H5G9
XM_054322196.1 → XP_054178171.1 podocan-like protein 1 isoform X3

UniProtKB/Swiss-Prot

B7Z564, Q6PEZ8, Q9H5G9

UniProtKB/TrEMBL

A8K3W6
XM_054322195.1 → XP_054178170.1 podocan-like protein 1 isoform X2
XM_054322199.1 → XP_054178174.1 podocan-like protein 1 isoform X6
XM_054322198.1 → XP_054178173.1 podocan-like protein 1 isoform X5
XM_054322201.1 → XP_054178176.1 podocan-like protein 1 isoform X8
XM_054322197.1 → XP_054178172.1 podocan-like protein 1 isoform X4
XM_054322202.1 → XP_054178177.1 podocan-like protein 1 isoform X9

UniProtKB/Swiss-Prot

B7Z564, Q6PEZ8, Q9H5G9

UniProtKB/TrEMBL

A8K3W6