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CUX1 cut like homeobox 1 [ Homo sapiens (human) ]

Gene ID: 1523, updated on 6-Sep-2022

Summary

Official Symbol
CUX1provided by HGNC
Official Full Name
cut like homeobox 1provided by HGNC
Primary source
HGNC:HGNC:2557
See related
Ensembl:ENSG00000257923 MIM:116896; AllianceGenome:HGNC:2557
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
CDP; CUX; p75; CASP; CDP1; COY1; Clox; GDDI; p100; p110; p200; CUTL1; GOLIM6; CDP/Cut; Cux/CDP; Nbla10317
Summary
The protein encoded by this gene is a member of the homeodomain family of DNA binding proteins. It may regulate gene expression, morphogenesis, and differentiation and it may also play a role in the cell cycle progession. Several alternatively spliced transcript variants encoding different isoforms have been identified.[provided by RefSeq, Feb 2011]
Expression
Ubiquitous expression in endometrium (RPKM 11.3), thyroid (RPKM 8.5) and 25 other tissues See more
Orthologs
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Genomic context

See CUX1 in Genome Data Viewer
Location:
7q22.1
Exon count:
34
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (101816007..102283958)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (103136249..103601363)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (101459287..101927250)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986832 Neighboring gene myosin light chain 10 Neighboring gene Sharpr-MPRA regulatory region 716 Neighboring gene Sharpr-MPRA regulatory region 4286 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:101595769-101596968 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:101630224-101631423 Neighboring gene Sharpr-MPRA regulatory region 1808 Neighboring gene Sharpr-MPRA regulatory region 3063 Neighboring gene small nucleolar RNA SNORA48 Neighboring gene uncharacterized LOC124901711 Neighboring gene uncharacterized LOC107986717 Neighboring gene microRNA 4285 Neighboring gene SH2B adaptor protein 2

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

Associated conditions

Description Tests
Global developmental delay with or without impaired intellectual development
MedGen: C5193032 OMIM: 618330 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Possible association of CUX1 gene polymorphisms with antidepressant response in major depressive disorder.
EBI GWAS Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ31745

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in negative regulation of transcription by RNA polymerase II TAS
Traceable Author Statement
more info
PubMed 
involved_in positive regulation of dendrite morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
 
located_in chromatin ISA
Inferred from Sequence Alignment
more info
 
located_in cytosol TAS
Traceable Author Statement
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
protein CASP; Homeobox protein cut-like 1
Names
CCAAT displacement protein
CDP/Cux p200
CUX1 gene Alternatively Spliced Product
cut homolog
golgi integral membrane protein 6
homeobox protein cux-1
mutant CUX1
putative protein product of Nbla10317

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.

Genomic

  1. NG_029476.2 RefSeqGene

    Range
    5104..473055
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_1123

mRNA and Protein(s)

  1. NM_001202543.2NP_001189472.1  Homeobox protein cut-like 1 isoform d

    See identical proteins and their annotated locations for NP_001189472.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) encodes the longest isoform (d).
    Source sequence(s)
    AC005088, BC040199, BC066592, DC410774
    Consensus CDS
    CCDS56498.1
    UniProtKB/Swiss-Prot
    P39880
    Related
    ENSP00000353401.3, ENST00000360264.7
    Conserved Domains (5) summary
    pfam05887
    Location:13141412
    Trypan_PARP; Procyclic acidic repetitive protein (PARP)
    pfam00046
    Location:12581311
    Homeobox; Homeobox domain
    pfam00901
    Location:86361
    Orbi_VP5; Orbivirus outer capsid protein VP5
    pfam02376
    Location:11331210
    CUT; CUT domain
    pfam13851
    Location:131352
    GAS; Growth-arrest specific micro-tubule binding
  2. NM_001202544.3NP_001189473.1  protein CASP isoform e

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks an in-frame exon in the 5' region and has an alternate 3' sequence including the coding region, as compared to variant 1. The resulting isoform (e) lacks an internal segment and has a shorter and distinct C-terminus, as compared to isoform d.
    Source sequence(s)
    AC091390, AK125097, BC012323, BC066592, DC410774, L12579
    Consensus CDS
    CCDS56500.1
    UniProtKB/Swiss-Prot
    P39880, Q13948
    Related
    ENSP00000449371.2, ENST00000547394.6
    Conserved Domains (3) summary
    pfam00901
    Location:70345
    Orbi_VP5; Orbivirus outer capsid protein VP5
    pfam08172
    Location:407622
    CASP_C; CASP C terminal
    pfam13851
    Location:115336
    GAS; Growth-arrest specific micro-tubule binding
  3. NM_001202545.3NP_001189474.1  protein CASP isoform f

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) lacks an in-frame exon in the 5' region and has an alternate 3' sequence including the coding region, as compared to variant 1. The resulting isoform (f) lacks an internal segment and has a shorter and distinct C-terminus, as compared to isoform d.
    Source sequence(s)
    AC091390, AK122726, BC012323, DC410774, L12579
    Consensus CDS
    CCDS56499.1
    UniProtKB/Swiss-Prot
    P39880, Q13948
    Related
    ENSP00000409745.2, ENST00000425244.6
    Conserved Domains (3) summary
    pfam07851
    Location:261336
    TMPIT; TMPIT-like protein
    pfam08172
    Location:377592
    CASP_C; CASP C terminal
    pfam15290
    Location:101240
    Syntaphilin; Golgi-localized syntaxin-1-binding clamp
  4. NM_001202546.3NP_001189475.1  protein CASP isoform g

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) lacks an in-frame exon in the 5' region and has an alternate 3' sequence including the coding region, as compared to variant 1. The resulting isoform (g) lacks an internal segment and has a shorter and distinct C-terminus, as compared to isoform d.
    Source sequence(s)
    AC005096, AC091390, AK303151, BC012323, L12579
    Consensus CDS
    CCDS59071.1
    UniProtKB/Swiss-Prot
    Q13948
    Related
    ENSP00000377410.3, ENST00000393824.7
    Conserved Domains (3) summary
    pfam00901
    Location:49322
    Orbi_VP5; Orbivirus outer capsid protein VP5
    pfam08172
    Location:384599
    CASP_C; CASP C terminal
    pfam13851
    Location:94313
    GAS; Growth-arrest specific micro-tubule binding
  5. NM_001913.5NP_001904.2  protein CASP isoform b

    See identical proteins and their annotated locations for NP_001904.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has an alternate 3' sequence including the coding region, as compared to variant 4. The resulting isoform (b) has a shorter and distinct C-terminus, as compared to isoform d.
    Source sequence(s)
    AC091390, AK222832, BC012323, DC410774, L12579
    Consensus CDS
    CCDS5720.1
    UniProtKB/Swiss-Prot
    Q13948, Q8TBS3
    Related
    ENSP00000484760.2, ENST00000622516.6
    Conserved Domains (3) summary
    pfam00901
    Location:86361
    Orbi_VP5; Orbivirus outer capsid protein VP5
    pfam08172
    Location:423638
    CASP_C; CASP C terminal
    pfam13851
    Location:131352
    GAS; Growth-arrest specific micro-tubule binding
  6. NM_181500.4NP_852477.1  protein CASP isoform c

    See identical proteins and their annotated locations for NP_852477.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks a 6 nt segment at an alternate splice site and has an alternate 3' sequence including the coding region, as compared to variant 4. The resulting isoform (c) lacks two internal amino acids and has a shorter and distinct C-terminus, as compared to isoform d.
    Source sequence(s)
    AB075522, AC091390, BC012323, BC025422, BC066592, DC410774
    Consensus CDS
    CCDS47672.1
    UniProtKB/Swiss-Prot
    P39880, Q13948
    UniProtKB/TrEMBL
    Q3LIA3
    Related
    ENSP00000414091.5, ENST00000437600.9
    Conserved Domains (2) summary
    pfam00901
    Location:86359
    Orbi_VP5; Orbivirus outer capsid protein VP5
    pfam08172
    Location:421636
    CASP_C; CASP C terminal
  7. NM_181552.4NP_853530.2  Homeobox protein cut-like 1 isoform a

    See identical proteins and their annotated locations for NP_853530.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) has an alternate 5' exon, as compared to variant 4. The resulting isoform (a) has a shorter and distinct N-terminus, as compared to isoform d.
    Source sequence(s)
    AC005088, AC005096, BC040199, BC066592, M74099
    Consensus CDS
    CCDS5721.1
    UniProtKB/Swiss-Prot
    P39880, Q9UEV5
    Related
    ENSP00000292535.7, ENST00000292535.12
    Conserved Domains (5) summary
    pfam05887
    Location:13031401
    Trypan_PARP; Procyclic acidic repetitive protein (PARP)
    pfam00046
    Location:12471300
    Homeobox; Homeobox domain
    pfam00901
    Location:75350
    Orbi_VP5; Orbivirus outer capsid protein VP5
    pfam02376
    Location:11221199
    CUT; CUT domain
    pfam13851
    Location:120341
    GAS; Growth-arrest specific micro-tubule binding

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    101816007..102283958
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047419908.1XP_047275864.1  Homeobox protein cut-like 1 isoform X5

  2. XM_047419912.1XP_047275868.1  Homeobox protein cut-like 1 isoform X10

    Related
    ENSP00000496653.1, ENST00000645010.1
  3. XM_047419913.1XP_047275869.1  Homeobox protein cut-like 1 isoform X11

  4. XM_011515825.3XP_011514127.1  Homeobox protein cut-like 1 isoform X13

    Conserved Domains (5) summary
    PHA03247
    Location:656842
    PHA03247; large tegument protein UL36; Provisional
    PHA03307
    Location:12231296
    PHA03307; transcriptional regulator ICP4; Provisional
    TIGR02169
    Location:18368
    SMC_prok_A; chromosome segregation protein SMC, primarily archaeal type
    pfam00046
    Location:11561210
    Homeobox; Homeobox domain
    pfam02376
    Location:10311104
    CUT; CUT domain
  5. XM_047419914.1XP_047275870.1  Homeobox protein cut-like 1 isoform X14

  6. XM_047419916.1XP_047275872.1  Homeobox protein cut-like 1 isoform X16

    Related
    ENSP00000494610.1, ENST00000646649.1
  7. XM_047419917.1XP_047275873.1  Homeobox protein cut-like 1 isoform X17

  8. XM_047419909.1XP_047275865.1  Homeobox protein cut-like 1 isoform X6

  9. XM_047419910.1XP_047275866.1  Homeobox protein cut-like 1 isoform X7

  10. XM_017011760.3XP_016867249.1  Homeobox protein cut-like 1 isoform X12

    Conserved Domains (5) summary
    PHA03247
    Location:734920
    PHA03247; large tegument protein UL36; Provisional
    PHA03307
    Location:13011374
    PHA03307; transcriptional regulator ICP4; Provisional
    TIGR02168
    Location:18362
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type
    pfam00046
    Location:12341288
    Homeobox; Homeobox domain
    pfam02376
    Location:11091182
    CUT; CUT domain
  11. XM_047419915.1XP_047275871.1  Homeobox protein cut-like 1 isoform X15

  12. XM_005250154.4XP_005250211.2  protein CASP isoform X18

    Related
    ENST00000560541.5
  13. XM_005250150.4XP_005250207.2  Homeobox protein cut-like 1 isoform X1

  14. XM_006715854.3XP_006715917.2  Homeobox protein cut-like 1 isoform X4

    Related
    ENSP00000446630.2, ENST00000549414.6
  15. XM_047419906.1XP_047275862.1  Homeobox protein cut-like 1 isoform X2

  16. XM_047419907.1XP_047275863.1  Homeobox protein cut-like 1 isoform X3

  17. XM_024446668.2XP_024302436.2  Homeobox protein cut-like 1 isoform X8

  18. XM_047419911.1XP_047275867.1  Homeobox protein cut-like 1 isoform X9

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    103136249..103601363
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)