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Smarcal1 Swi/SNF related matrix associated, actin dependent regulator of chromatin, subfamily a-like 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 316477, updated on 2-Oct-2018

Summary

Symbol
Smarcal1provided by RGD
Full Name
Swi/SNF related matrix associated, actin dependent regulator of chromatin, subfamily a-like 1provided by RGD
Primary source
RGD:1306134
See related
Ensembl:ENSRNOG00000016503
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Expression
Biased expression in Thymus (RPKM 78.9), Spleen (RPKM 63.6) and 9 other tissues See more
Orthologs

Genomic context

See Smarcal1 in Genome Data Viewer
Location:
9q33
Exon count:
19
Annotation release Status Assembly Chr Location
106 current Rnor_6.0 (GCF_000001895.5) 9 NC_005108.4 (79943775..79990230)
104 previous assembly Rnor_5.0 (GCF_000001895.4) 9 NC_005108.3 (79716012..79762216)

Chromosome 9 - NC_005108.4Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102555358 Neighboring gene membrane associated ring-CH-type finger 4 Neighboring gene cyclin-dependent kinases regulatory subunit 2 pseudogene Neighboring gene ribosomal protein L37a Neighboring gene uncharacterized LOC102547940

Genomic regions, transcripts, and products

Expression

  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

General gene information

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
DNA-dependent ATPase activity ISO
Inferred from Sequence Orthology
more info
 
DNA-dependent ATPase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
annealing helicase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
annealing helicase activity ISO
Inferred from Sequence Orthology
more info
 
annealing helicase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
helicase activity IEA
Inferred from Electronic Annotation
more info
 
molecular_function ND
No biological Data available
more info
 
Process Evidence Code Pubs
DNA metabolic process ISO
Inferred from Sequence Orthology
more info
 
DNA metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
DNA repair IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA rewinding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA strand renaturation IEA
Inferred from Electronic Annotation
more info
 
biological_process ND
No biological Data available
more info
 
cellular response to DNA damage stimulus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cellular response to DNA damage stimulus ISO
Inferred from Sequence Orthology
more info
 
cellular response to DNA damage stimulus ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
 
replication fork processing IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
replication fork processing ISO
Inferred from Sequence Orthology
more info
 
replication fork processing ISS
Inferred from Sequence or Structural Similarity
more info
 
replication fork protection IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
colocalizes_with DNA replication factor A complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
colocalizes_with DNA replication factor A complex ISO
Inferred from Sequence Orthology
more info
 
colocalizes_with DNA replication factor A complex ISS
Inferred from Sequence or Structural Similarity
more info
 
cellular_component ND
No biological Data available
more info
 
nuclear replication fork IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleoplasm IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus ISO
Inferred from Sequence Orthology
more info
 
nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 
site of double-strand break ISO
Inferred from Sequence Orthology
more info
 
site of double-strand break ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1
Names
hepA-related protein
sucrose nonfermenting protein 2-like 1
NP_001101692.1
XP_006245274.1
XP_006245275.1
XP_008765457.1
XP_008765458.1
XP_017451963.1

NCBI Reference Sequences (RefSeq)

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_001108222.1NP_001101692.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1

    See identical proteins and their annotated locations for NP_001101692.1

    Status: PROVISIONAL

    Source sequence(s)
    CH474004
    UniProtKB/Swiss-Prot
    B4F769
    Related
    ENSRNOP00000064323.1, ENSRNOT00000071856.3
    Conserved Domains (5) summary
    COG0553
    Location:392836
    HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]
    cd00046
    Location:411539
    DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
    pfam00271
    Location:668778
    Helicase_C; Helicase conserved C-terminal domain
    pfam07443
    Location:300353
    HARP; HepA-related protein (HARP)
    pfam15265
    Location:33172
    FAM196; FAM196 family

RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

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

Reference Rnor_6.0 Primary Assembly

Genomic

  1. NC_005108.4 Reference Rnor_6.0 Primary Assembly

    Range
    79943775..79990230
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006245212.3XP_006245274.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 isoform X1

    See identical proteins and their annotated locations for XP_006245274.1

    UniProtKB/Swiss-Prot
    B4F769
    Related
    ENSRNOP00000022459.4, ENSRNOT00000022459.5
    Conserved Domains (5) summary
    COG0553
    Location:392836
    HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]
    cd00046
    Location:411539
    DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
    pfam00271
    Location:668778
    Helicase_C; Helicase conserved C-terminal domain
    pfam07443
    Location:300353
    HARP; HepA-related protein (HARP)
    pfam15265
    Location:33172
    FAM196; FAM196 family
  2. XM_008767236.2XP_008765458.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 isoform X2

    Conserved Domains (5) summary
    COG0553
    Location:355799
    HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]
    cd00046
    Location:374502
    DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
    pfam00271
    Location:631741
    Helicase_C; Helicase conserved C-terminal domain
    pfam07443
    Location:263316
    HARP; HepA-related protein (HARP)
    pfam15265
    Location:33172
    FAM196; FAM196 family
  3. XM_017596474.1XP_017451963.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 isoform X1

    UniProtKB/Swiss-Prot
    B4F769
    Conserved Domains (5) summary
    COG0553
    Location:392836
    HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]
    cd00046
    Location:411539
    DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
    pfam00271
    Location:668778
    Helicase_C; Helicase conserved C-terminal domain
    pfam07443
    Location:300353
    HARP; HepA-related protein (HARP)
    pfam15265
    Location:33172
    FAM196; FAM196 family
  4. XM_006245213.3XP_006245275.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 isoform X1

    See identical proteins and their annotated locations for XP_006245275.1

    UniProtKB/Swiss-Prot
    B4F769
    Conserved Domains (5) summary
    COG0553
    Location:392836
    HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]
    cd00046
    Location:411539
    DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
    pfam00271
    Location:668778
    Helicase_C; Helicase conserved C-terminal domain
    pfam07443
    Location:300353
    HARP; HepA-related protein (HARP)
    pfam15265
    Location:33172
    FAM196; FAM196 family
  5. XM_008767235.1XP_008765457.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 isoform X1

    See identical proteins and their annotated locations for XP_008765457.1

    UniProtKB/Swiss-Prot
    B4F769
    Conserved Domains (5) summary
    COG0553
    Location:392836
    HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]
    cd00046
    Location:411539
    DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
    pfam00271
    Location:668778
    Helicase_C; Helicase conserved C-terminal domain
    pfam07443
    Location:300353
    HARP; HepA-related protein (HARP)
    pfam15265
    Location:33172
    FAM196; FAM196 family

Alternate Rn_Celera

Genomic

  1. AC_000077.1 Alternate Rn_Celera

    Range
    71834400..71880797
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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