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SPIDR scaffolding protein involved in DNA repair [ Homo sapiens (human) ]

Gene ID: 23514, updated on 6-Jun-2017
Official Symbol
SPIDRprovided by HGNC
Official Full Name
scaffolding protein involved in DNA repairprovided by HGNC
Primary source
HGNC:HGNC:28971
See related
Ensembl:ENSG00000164808 MIM:615384; Vega:OTTHUMG00000164176
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
KIAA0146
Orthologs
Location:
8q11.21
Exon count:
29
Annotation release Status Assembly Chr Location
108 current GRCh38.p7 (GCF_000001405.33) 8 NC_000008.11 (47260878..47736001)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (48173489..48648563)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene Ig lambda chain V region 4A-like Neighboring gene ATPase H+ transporting V1 subunit G1 pseudogene 2 Neighboring gene uncharacterized LOC107986940 Neighboring gene NSFL1 cofactor pseudogene Neighboring gene ribosomal protein S4, Y-linked 2 pseudogene Neighboring gene ubiquitin conjugating enzyme E2 N pseudogene Neighboring gene RNA, U6 small nuclear 665, pseudogene Neighboring gene CCAAT/enhancer binding protein delta Neighboring gene protein kinase, DNA-activated, catalytic polypeptide Neighboring gene uncharacterized LOC105375818

  • 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 Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

  • DNA Double-Strand Break Repair, organism-specific biosystem (from REACTOME)
    DNA Double-Strand Break Repair, organism-specific biosystemNumerous types of DNA damage can occur within a cell due to the endogenous production of oxygen free radicals, normal alkylation reactions, or exposure to exogenous radiations and chemicals. Double-s...
  • DNA Repair, organism-specific biosystem (from REACTOME)
    DNA Repair, organism-specific biosystemDNA repair is a phenomenal multi-enzyme, multi-pathway system required to ensure the integrity of the cellular genome. Living organisms are constantly exposed to harmful metabolic by-products, enviro...
  • HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA), organism-specific biosystem (from REACTOME)
    HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA), organism-specific biosystemHomology directed repair (HDR) of replication-independent DNA double strand breaks (DSBs) via homologous recombination repair (HRR) or single strand annealing (SSA) requires the activation of ATM fol...
  • HDR through Homologous Recombination (HRR), organism-specific biosystem (from REACTOME)
    HDR through Homologous Recombination (HRR), organism-specific biosystemHomology directed repair (HDR) through homologous recombination is known as homologous recombination repair (HRR). HRR occurs after extensive resection of DNA double strand break (DSB) ends, which cr...
  • Homology Directed Repair, organism-specific biosystem (from REACTOME)
    Homology Directed Repair, organism-specific biosystemHomology directed repair (HDR) of DNA double strand breaks (DSBs) requires resection of DNA DSB ends. Resection creates 3'-ssDNA overhangs which then anneal with a homologous DNA sequence. This homol...
  • Resolution of D-Loop Structures, organism-specific biosystem (from REACTOME)
    Resolution of D-Loop Structures, organism-specific biosystemOnce repair synthesis has occurred, the D-loop structure may be resolved either through Holliday junction intermediates or through synthesis-dependent strand-annealing (SDSA) (Prado and Aguilera 2003...
  • Resolution of D-loop Structures through Holliday Junction Intermediates, organism-specific biosystem (from REACTOME)
    Resolution of D-loop Structures through Holliday Junction Intermediates, organism-specific biosystemD-loops generated after strand invasion and DNA repair synthesis during homologous recombination repair (HRR) can be resolved through Holliday junction intermediates.A D-loop can be cleaved by the co...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • FLJ35017, KIAA0146

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
nuclear chromosome IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
Preferred Names
DNA repair-scaffolding protein

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_001080394.3NP_001073863.1  DNA repair-scaffolding protein isoform 1

    See identical proteins and their annotated locations for NP_001073863.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC233269, BM981420, D63480
    Consensus CDS
    CCDS43737.1
    UniProtKB/Swiss-Prot
    Q14159
    Related
    ENSP00000297423.4, OTTHUMP00000226081, ENST00000297423.8, OTTHUMT00000377611
    Conserved Domains (2) summary
    pfam14950
    Location:11369
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:521905
    DUF4503; Domain of unknown function (DUF4503)
  2. NM_001282916.1NP_001269845.1  DNA repair-scaffolding protein isoform 2

    See identical proteins and their annotated locations for NP_001269845.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an in-frame exon in the 5' coding region which results in the use of a downstream start codon, compred to variant 1. The encoded isoform (2) is shorter and has a distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AC023991, AC233269, AK294275, BM981420
    Consensus CDS
    CCDS64891.1
    UniProtKB/Swiss-Prot
    Q14159
    Related
    ENSP00000444061.1, ENST00000541342.2
    Conserved Domains (2) summary
    pfam14950
    Location:25299
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:451835
    DUF4503; Domain of unknown function (DUF4503)
  3. NM_001282919.1NP_001269848.1  DNA repair-scaffolding protein isoform 3

    See identical proteins and their annotated locations for NP_001269848.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site in the 5' coding and lacks an exon in the 3' coding region. These differences cause translation initiation at a downstream AUG and a frameshift in the 3' coding egion . The resulting isoform (3) is shorter and has a distinct N-and C-termini, compared to isoform 1.
    Source sequence(s)
    AK303579, BM981420, HY012281
    Consensus CDS
    CCDS64890.1
    UniProtKB/Swiss-Prot
    Q14159
    Related
    ENSP00000429487.1, OTTHUMP00000226084, ENST00000518074.5, OTTHUMT00000377614
    Conserved Domains (2) summary
    pfam14950
    Location:3309
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:461790
    DUF4503; Domain of unknown function (DUF4503)

RNA

  1. NR_104581.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks several exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC233269, BC031627, BM981420
    Related
    ENST00000524126.5, OTTHUMT00000377618

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

Reference GRCh38.p7 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p7 Primary Assembly

    Range
    47260878..47736001
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017013281.1XP_016868770.1  DNA repair-scaffolding protein isoform X19

  2. XM_017013280.1XP_016868769.1  DNA repair-scaffolding protein isoform X19

  3. XM_005251198.4XP_005251255.1  DNA repair-scaffolding protein isoform X21

    See identical proteins and their annotated locations for XP_005251255.1

    Conserved Domains (2) summary
    pfam14950
    Location:5119
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:271655
    DUF4503; Domain of unknown function (DUF4503)
  4. XM_017013273.1XP_016868762.1  DNA repair-scaffolding protein isoform X12

  5. XM_006716444.3XP_006716507.1  DNA repair-scaffolding protein isoform X21

    See identical proteins and their annotated locations for XP_006716507.1

    Conserved Domains (2) summary
    pfam14950
    Location:5119
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:271655
    DUF4503; Domain of unknown function (DUF4503)
  6. XM_017013285.1XP_016868774.1  DNA repair-scaffolding protein isoform X24

  7. XM_017013277.1XP_016868766.1  DNA repair-scaffolding protein isoform X16

  8. XM_017013270.1XP_016868759.1  DNA repair-scaffolding protein isoform X3

  9. XM_011517500.2XP_011515802.1  DNA repair-scaffolding protein isoform X7

    Conserved Domains (2) summary
    pfam14950
    Location:11329
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:481865
    DUF4503; Domain of unknown function (DUF4503)
  10. XM_017013278.1XP_016868767.1  DNA repair-scaffolding protein isoform X17

    Conserved Domains (2) summary
    pfam14950
    Location:11205
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:357741
    DUF4503; Domain of unknown function (DUF4503)
  11. XM_017013274.1XP_016868763.1  DNA repair-scaffolding protein isoform X13

  12. XM_005251195.4XP_005251252.1  DNA repair-scaffolding protein isoform X17

    Conserved Domains (2) summary
    pfam14950
    Location:11205
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:357741
    DUF4503; Domain of unknown function (DUF4503)
  13. XM_017013284.1XP_016868773.1  DNA repair-scaffolding protein isoform X23

  14. XM_017013282.1XP_016868771.1  DNA repair-scaffolding protein isoform X20

  15. XM_006716443.3XP_006716506.1  DNA repair-scaffolding protein isoform X8

    Conserved Domains (2) summary
    pfam14950
    Location:3309
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:461845
    DUF4503; Domain of unknown function (DUF4503)
  16. XM_017013268.1XP_016868757.1  DNA repair-scaffolding protein isoform X1

  17. XM_011517497.2XP_011515799.1  DNA repair-scaffolding protein isoform X4

    Conserved Domains (2) summary
    pfam14950
    Location:11369
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:521870
    DUF4503; Domain of unknown function (DUF4503)
  18. XM_005251193.3XP_005251250.1  DNA repair-scaffolding protein isoform X10

    Conserved Domains (2) summary
    pfam14950
    Location:11369
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:521814
    DUF4503; Domain of unknown function (DUF4503)
  19. XM_005251191.3XP_005251248.1  DNA repair-scaffolding protein isoform X9

    Conserved Domains (2) summary
    pfam14950
    Location:11369
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:521780
    DUF4503; Domain of unknown function (DUF4503)
  20. XM_017013269.1XP_016868758.1  DNA repair-scaffolding protein isoform X2

  21. XM_005251189.3XP_005251246.1  DNA repair-scaffolding protein isoform X5

    See identical proteins and their annotated locations for XP_005251246.1

    Conserved Domains (2) summary
    pfam14950
    Location:11369
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:521850
    DUF4503; Domain of unknown function (DUF4503)
  22. XM_017013287.1XP_016868776.1  DNA repair-scaffolding protein isoform X27

  23. XM_017013271.1XP_016868760.1  DNA repair-scaffolding protein isoform X6

    UniProtKB/Swiss-Prot
    Q14159
    Conserved Domains (2) summary
    pfam14950
    Location:3309
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:461790
    DUF4503; Domain of unknown function (DUF4503)
  24. XM_017013291.1XP_016868780.1  DNA repair-scaffolding protein isoform X31

    Conserved Domains (1) summary
    pfam14951
    Location:105489
    DUF4503; Domain of unknown function (DUF4503)
  25. XM_017013279.1XP_016868768.1  DNA repair-scaffolding protein isoform X18

  26. XM_017013286.1XP_016868775.1  DNA repair-scaffolding protein isoform X25

  27. XM_005251199.4XP_005251256.1  DNA repair-scaffolding protein isoform X26

    Conserved Domains (2) summary
    pfam14950
    Location:158
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:210594
    DUF4503; Domain of unknown function (DUF4503)
  28. XM_017013290.1XP_016868779.1  DNA repair-scaffolding protein isoform X30

    Related
    ENSP00000429193.1, OTTHUMP00000226095, ENST00000519401.5, OTTHUMT00000377630
  29. XM_017013283.1XP_016868772.1  DNA repair-scaffolding protein isoform X22

  30. XM_017013289.1XP_016868778.1  DNA repair-scaffolding protein isoform X29

  31. XM_017013288.1XP_016868777.1  DNA repair-scaffolding protein isoform X28

    Conserved Domains (1) summary
    pfam14951
    Location:165549
    DUF4503; Domain of unknown function (DUF4503)
  32. XM_017013272.1XP_016868761.1  DNA repair-scaffolding protein isoform X11

  33. XM_017013276.1XP_016868765.1  DNA repair-scaffolding protein isoform X15

  34. XM_017013275.1XP_016868764.1  DNA repair-scaffolding protein isoform X14

  35. XM_011517507.2XP_011515809.1  DNA repair-scaffolding protein isoform X32

    See identical proteins and their annotated locations for XP_011515809.1

    UniProtKB/TrEMBL
    B3KP42
    Related
    ENSP00000427889.1, OTTHUMP00000226097, ENST00000517693.5, OTTHUMT00000377632
    Conserved Domains (1) summary
    pfam14951
    Location:1380
    DUF4503; Domain of unknown function (DUF4503)

RNA

  1. XR_001745507.1 RNA Sequence

  2. XR_001745508.1 RNA Sequence

Alternate CHM1_1.1

Genomic

  1. NC_018919.2 Alternate CHM1_1.1

    Range
    48225078..48700450
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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