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CARMIL1 capping protein regulator and myosin 1 linker 1 [ Homo sapiens (human) ]

Gene ID: 55604, updated on 7-Jan-2024

Summary

Official Symbol
CARMIL1provided by HGNC
Official Full Name
capping protein regulator and myosin 1 linker 1provided by HGNC
Primary source
HGNC:HGNC:21581
See related
Ensembl:ENSG00000079691 MIM:609593; AllianceGenome:HGNC:21581
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
CARMIL; LRRC16; LRRC16A; CARMIL1a; dJ501N12.1; dJ501N12.5
Summary
Involved in several processes, including actin filament network formation; plasma membrane bounded cell projection organization; and positive regulation of cellular component organization. Located in several cellular components, including lamellipodium; macropinosome; and nuclear speck. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in testis (RPKM 7.4), small intestine (RPKM 6.3) and 24 other tissues See more
Orthologs
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Genomic context

See CARMIL1 in Genome Data Viewer
Location:
6p22.2
Exon count:
41
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (25279374..25620530)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (25145130..25486328)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (25279602..25620758)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101928663 Neighboring gene katanin regulatory subunit B1 like 1 pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16995 Neighboring gene ribosomal protein L21 pseudogene 68 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:25292659-25293159 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:25311331-25311831 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:25315887-25316577 Neighboring gene uncharacterized LOC124901281 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:25342051-25342783 Neighboring gene RNA, U6 small nuclear 987, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24169 Neighboring gene uncharacterized LOC124901546 Neighboring gene NANOG hESC enhancer GRCh37_chr6:25462672-25463208 Neighboring gene MPRA-validated peak5738 silencer Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:25504114-25505313 Neighboring gene MPRA-validated peak5739 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:25627151-25627701 Neighboring gene NANOG hESC enhancer GRCh37_chr6:25635867-25636368 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:25660432-25661631 Neighboring gene uncharacterized LOC124901284 Neighboring gene PRELID1 pseudogene 2 Neighboring gene secretagogin, EF-hand calcium binding 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?

Phenotypes

EBI GWAS Catalog

Description
A meta-analysis and genome-wide association study of platelet count and mean platelet volume in african americans.
EBI GWAS Catalog
Meta-analysis of 28,141 individuals identifies common variants within five new loci that influence uric acid concentrations.
EBI GWAS Catalog
New gene functions in megakaryopoiesis and platelet formation.
EBI GWAS Catalog
Variants in TF and HFE explain approximately 40% of genetic variation in serum-transferrin levels.
EBI GWAS Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of leucine rich repeat containing 16A (LRRC16A) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • FLJ20048, FLJ43708

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein-containing complex binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
involved_in actin filament network formation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in actin filament organization NAS
Non-traceable Author Statement
more info
PubMed 
involved_in barbed-end actin filament uncapping ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in cell migration IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in cell migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in lamellipodium assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in macropinocytosis IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of barbed-end actin filament capping ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of actin filament polymerization ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of cell migration IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of cell migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of lamellipodium organization IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of stress fiber assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of substrate adhesion-dependent cell spreading IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of Arp2/3 complex-mediated actin nucleation IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in ruffle organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in urate metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
located_in cell leading edge IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
 
located_in cytosol TAS
Traceable Author Statement
more info
 
located_in extracellular exosome HDA PubMed 
part_of filamentous actin ISS
Inferred from Sequence or Structural Similarity
more info
 
is_active_in lamellipodium IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in lamellipodium IDA
Inferred from Direct Assay
more info
PubMed 
located_in macropinosome IDA
Inferred from Direct Assay
more info
PubMed 
located_in nuclear speck IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
F-actin-uncapping protein LRRC16A
Names
CARMIL homolog
capping protein regulator and myosin 1 linker protein 1
capping protein, Arp2/3 and myosin-I linker homolog 1
capping protein, Arp2/3 and myosin-I linker protein 1
capping protein, Arp2/3, and Myosin-I Linker homolog 1
leucine rich repeat containing 16
leucine rich repeat containing 16A
leucine-rich repeat-containing protein 16A
testicular tissue protein Li 107

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_001173977.2NP_001167448.1  F-actin-uncapping protein LRRC16A isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The resulting isoform (2) lacks an internal 6-aa segment near the C-terminus, compared to isoform 1.
    Source sequence(s)
    AL022170, AL024509, AL160037
    Consensus CDS
    CCDS93871.1
    UniProtKB/TrEMBL
    A0A8V8TRE2, B2RTQ5
    Related
    ENSP00000515137.1, ENST00000700669.1
    Conserved Domains (4) summary
    cd00116
    Location:229373
    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:484507
    LRR_RI; leucine-rich repeat [structural motif]
    sd00034
    Location:248277
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam16000
    Location:7861078
    CARMIL_C; CARMIL C-terminus
  2. NM_017640.6NP_060110.4  F-actin-uncapping protein LRRC16A isoform 1

    See identical proteins and their annotated locations for NP_060110.4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AL022170, AL024509, AL160037
    Consensus CDS
    CCDS54973.1
    UniProtKB/Swiss-Prot
    B8X1J0, Q5VZK9, Q6ZUH5, Q6ZW07, Q9NXU7
    UniProtKB/TrEMBL
    B2RTQ5
    Related
    ENSP00000331983.6, ENST00000329474.7
    Conserved Domains (4) summary
    cd00116
    Location:229373
    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:484507
    LRR_RI; leucine-rich repeat [structural motif]
    sd00034
    Location:248277
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam16000
    Location:7861078
    CARMIL_C; CARMIL C-terminus

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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    25279374..25620530
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017011008.2XP_016866497.1  F-actin-uncapping protein LRRC16A isoform X1

    UniProtKB/TrEMBL
    B2RTQ5
  2. XM_017011009.2XP_016866498.1  F-actin-uncapping protein LRRC16A isoform X2

    UniProtKB/TrEMBL
    B2RTQ5
  3. XM_017011015.2XP_016866504.1  F-actin-uncapping protein LRRC16A isoform X12

    UniProtKB/TrEMBL
    B2RTQ5
  4. XM_017011012.2XP_016866501.1  F-actin-uncapping protein LRRC16A isoform X5

    UniProtKB/TrEMBL
    B2RTQ5
  5. XM_024446484.2XP_024302252.1  F-actin-uncapping protein LRRC16A isoform X6

    UniProtKB/TrEMBL
    B2RTQ5
    Conserved Domains (5) summary
    sd00033
    Location:488511
    LRR_RI; leucine-rich repeat [structural motif]
    sd00034
    Location:248277
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam16000
    Location:7901088
    CARMIL_C; CARMIL C-terminus
    cl26161
    Location:229373
    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 ...
    cl28033
    Location:10991348
    Herpes_ICP4_C; Herpesvirus ICP4-like protein C-terminal region
  6. XM_024446485.2XP_024302253.1  F-actin-uncapping protein LRRC16A isoform X14

    UniProtKB/TrEMBL
    B2RTQ5
    Conserved Domains (5) summary
    sd00033
    Location:488511
    LRR_RI; leucine-rich repeat [structural motif]
    sd00034
    Location:248277
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam16000
    Location:7901088
    CARMIL_C; CARMIL C-terminus
    cl26161
    Location:229373
    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 ...
    cl28033
    Location:10991345
    Herpes_ICP4_C; Herpesvirus ICP4-like protein C-terminal region
  7. XM_017011011.2XP_016866500.1  F-actin-uncapping protein LRRC16A isoform X4

    UniProtKB/TrEMBL
    B2RTQ5
  8. XM_017011016.2XP_016866505.1  F-actin-uncapping protein LRRC16A isoform X13

    UniProtKB/TrEMBL
    B2RTQ5
  9. XM_017011013.2XP_016866502.1  F-actin-uncapping protein LRRC16A isoform X9

    UniProtKB/TrEMBL
    B2RTQ5
  10. XM_047418997.1XP_047274953.1  F-actin-uncapping protein LRRC16A isoform X15

    UniProtKB/TrEMBL
    B2RTQ5
  11. XM_017011010.2XP_016866499.1  F-actin-uncapping protein LRRC16A isoform X3

    UniProtKB/TrEMBL
    B2RTQ5
  12. XM_005249218.2XP_005249275.1  F-actin-uncapping protein LRRC16A isoform X7

    UniProtKB/TrEMBL
    B2RTQ5
    Conserved Domains (4) summary
    cd00116
    Location:229373
    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:484507
    LRR_RI; leucine-rich repeat [structural motif]
    sd00034
    Location:248277
    LRR_AMN1; leucine-rich repeat [structural motif]
    pfam16000
    Location:7861078
    CARMIL_C; CARMIL C-terminus
  13. XM_047418994.1XP_047274950.1  F-actin-uncapping protein LRRC16A isoform X8

    UniProtKB/TrEMBL
    B2RTQ5
  14. XM_047418995.1XP_047274951.1  F-actin-uncapping protein LRRC16A isoform X10

    UniProtKB/TrEMBL
    B2RTQ5
  15. XM_047418996.1XP_047274952.1  F-actin-uncapping protein LRRC16A isoform X11

    UniProtKB/TrEMBL
    B2RTQ5
  16. XM_047418998.1XP_047274954.1  F-actin-uncapping protein LRRC16A isoform X16

    UniProtKB/TrEMBL
    B2RTQ5
  17. XM_047418999.1XP_047274955.1  F-actin-uncapping protein LRRC16A isoform X17

    UniProtKB/TrEMBL
    B2RTQ5
  18. XM_017011017.2XP_016866506.1  F-actin-uncapping protein LRRC16A isoform X18

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    25145130..25486328
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054355815.1XP_054211790.1  F-actin-uncapping protein LRRC16A isoform X1

    UniProtKB/TrEMBL
    B2RTQ5
  2. XM_054355816.1XP_054211791.1  F-actin-uncapping protein LRRC16A isoform X2

    UniProtKB/TrEMBL
    B2RTQ5
  3. XM_054355828.1XP_054211803.1  F-actin-uncapping protein LRRC16A isoform X12

    UniProtKB/TrEMBL
    B2RTQ5
  4. XM_054355819.1XP_054211794.1  F-actin-uncapping protein LRRC16A isoform X5

    UniProtKB/TrEMBL
    B2RTQ5
  5. XM_054355820.1XP_054211795.1  F-actin-uncapping protein LRRC16A isoform X6

    UniProtKB/TrEMBL
    B2RTQ5
  6. XM_054355830.1XP_054211805.1  F-actin-uncapping protein LRRC16A isoform X14

    UniProtKB/TrEMBL
    B2RTQ5
  7. XM_054355818.1XP_054211793.1  F-actin-uncapping protein LRRC16A isoform X4

    UniProtKB/TrEMBL
    B2RTQ5
  8. XM_054355829.1XP_054211804.1  F-actin-uncapping protein LRRC16A isoform X13

    UniProtKB/TrEMBL
    B2RTQ5
  9. XM_054355823.1XP_054211798.1  F-actin-uncapping protein LRRC16A isoform X9

    UniProtKB/TrEMBL
    B2RTQ5
  10. XM_054355831.1XP_054211806.1  F-actin-uncapping protein LRRC16A isoform X15

    UniProtKB/TrEMBL
    B2RTQ5
  11. XM_054355817.1XP_054211792.1  F-actin-uncapping protein LRRC16A isoform X3

    UniProtKB/TrEMBL
    B2RTQ5
  12. XM_054355821.1XP_054211796.1  F-actin-uncapping protein LRRC16A isoform X7

    UniProtKB/TrEMBL
    B2RTQ5
  13. XM_054355822.1XP_054211797.1  F-actin-uncapping protein LRRC16A isoform X8

    UniProtKB/TrEMBL
    B2RTQ5
  14. XM_054355824.1XP_054211799.1  F-actin-uncapping protein LRRC16A isoform X10

    UniProtKB/TrEMBL
    B2RTQ5
  15. XM_054355825.1XP_054211800.1  F-actin-uncapping protein LRRC16A isoform X19

    UniProtKB/TrEMBL
    B2RTQ5
  16. XM_054355826.1XP_054211801.1  F-actin-uncapping protein LRRC16A isoform X20

    UniProtKB/TrEMBL
    B2RTQ5
  17. XM_054355827.1XP_054211802.1  F-actin-uncapping protein LRRC16A isoform X11

    UniProtKB/TrEMBL
    B2RTQ5
  18. XM_054355832.1XP_054211807.1  F-actin-uncapping protein LRRC16A isoform X16

    UniProtKB/TrEMBL
    B2RTQ5
  19. XM_054355833.1XP_054211808.1  F-actin-uncapping protein LRRC16A isoform X17

    UniProtKB/TrEMBL
    B2RTQ5
  20. XM_054355834.1XP_054211809.1  F-actin-uncapping protein LRRC16A isoform X18