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

Gene ID: 23514, updated on 18-Aug-2020

Summary

Official Symbol
SPIDRprovided by HGNC
Official Full Name
scaffold protein involved in DNA repairprovided by HGNC
Primary source
HGNC:HGNC:28971
See related
Ensembl:ENSG00000164808 MIM:615384
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
Expression
Ubiquitous expression in lung (RPKM 8.1), thyroid (RPKM 7.9) and 25 other tissues See more
Orthologs

Genomic context

See SPIDR in Genome Data Viewer
Location:
8q11.21
Exon count:
31
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 8 NC_000008.11 (47260878..47736306)
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 ATPase H+ transporting V1 subunit G1 pseudogene 2 Neighboring gene immunoglobulin lambda variable 8/OR8-1 (pseudogene) 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 subunit Neighboring gene uncharacterized LOC105375818

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?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear chromosome IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
DNA repair-scaffolding protein
Names
scaffolding protein involved in DNA repair

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_001080394.4NP_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)
    AC023991, AC233269, BM981420, D63480
    Consensus CDS
    CCDS43737.1
    UniProtKB/Swiss-Prot
    Q14159
    Related
    ENSP00000297423.4, ENST00000297423.9
    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, ENST00000518074.5
    Conserved Domains (2) summary
    pfam14950
    Location:3309
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:461790
    DUF4503; Domain of unknown function (DUF4503)
  4. NM_001352931.1NP_001339860.1  DNA repair-scaffolding protein isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC023991, AC024451, AC024649, AC145060, AC233269
    Conserved Domains (2) summary
    pfam14950
    Location:11369
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:521850
    DUF4503; Domain of unknown function (DUF4503)
  5. NM_001352932.1NP_001339861.1  DNA repair-scaffolding protein isoform 5

    Status: VALIDATED

    Source sequence(s)
    AC023991, AC024451, AC024649, AC145060, AC233269
    Conserved Domains (2) summary
    pfam14950
    Location:11329
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:481865
    DUF4503; Domain of unknown function (DUF4503)
  6. NM_001352933.1NP_001339862.1  DNA repair-scaffolding protein isoform 6

    Status: VALIDATED

    Source sequence(s)
    AC023991, AC024451, AC024649, AC145060, AC233269
    Conserved Domains (2) summary
    pfam14950
    Location:3309
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:461845
    DUF4503; Domain of unknown function (DUF4503)
  7. NM_001352934.1NP_001339863.1  DNA repair-scaffolding protein isoform 8

    Status: VALIDATED

    Source sequence(s)
    AC023991, AC024451, AC024649, AC145060, AC233269
    Conserved Domains (2) summary
    pfam14950
    Location:11369
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:521814
    DUF4503; Domain of unknown function (DUF4503)
  8. NM_001352935.1NP_001339864.1  DNA repair-scaffolding protein isoform 9

    Status: VALIDATED

    Source sequence(s)
    AC023991, AC024451, AC024649, AC145060, AC233269
    Conserved Domains (2) summary
    pfam14950
    Location:25299
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:451780
    DUF4503; Domain of unknown function (DUF4503)
  9. NM_001352936.1NP_001339865.1  DNA repair-scaffolding protein isoform 10

    Status: VALIDATED

    Source sequence(s)
    AC023991, AC024451, AC024649, AC145060, AC233269
    Conserved Domains (2) summary
    pfam14950
    Location:25299
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:451710
    DUF4503; Domain of unknown function (DUF4503)
  10. NM_001352937.1NP_001339866.1  DNA repair-scaffolding protein isoform 11

    Status: VALIDATED

    Source sequence(s)
    AC023991, AC024451, AC024649, AC145060, AC233269
    Conserved Domains (2) summary
    pfam14950
    Location:3309
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:461754
    DUF4503; Domain of unknown function (DUF4503)
  11. NM_001352938.1NP_001339867.1  DNA repair-scaffolding protein isoform 12

    Status: VALIDATED

    Description
    Transcript Variant: This variant (13), as well as variants 14 and 15, encodes isoform 12.
    Source sequence(s)
    AC023991, AC024451, AC024649, AC145060, AC233269
    Conserved Domains (2) summary
    pfam14950
    Location:11205
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:357741
    DUF4503; Domain of unknown function (DUF4503)
  12. NM_001352939.1NP_001339868.1  DNA repair-scaffolding protein isoform 12

    Status: VALIDATED

    Description
    Transcript Variant: This variant (14), as well as variants 13 and 15, encodes isoform 12.
    Source sequence(s)
    AC023991, AC024451, AC024649, AC145060, AC233269
    Conserved Domains (2) summary
    pfam14950
    Location:11205
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:357741
    DUF4503; Domain of unknown function (DUF4503)
  13. NM_001352940.1NP_001339869.1  DNA repair-scaffolding protein isoform 12

    Status: VALIDATED

    Description
    Transcript Variant: This variant (15), as well as variants 13 and 14, encodes isoform 12.
    Source sequence(s)
    AC023991, AC024451, AC024649, AC145060, AC233269
    Conserved Domains (2) summary
    pfam14950
    Location:11205
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:357741
    DUF4503; Domain of unknown function (DUF4503)
  14. NM_001352941.1NP_001339870.1  DNA repair-scaffolding protein isoform 13

    Status: VALIDATED

    Source sequence(s)
    AC023991, AC024451, AC024649, AC145060, AC233269
    Conserved Domains (2) summary
    pfam14950
    Location:11197
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:349733
    DUF4503; Domain of unknown function (DUF4503)
  15. NM_001352942.1NP_001339871.1  DNA repair-scaffolding protein isoform 14

    Status: VALIDATED

    Source sequence(s)
    AC023991, AC024451, AC024649, AC145060, AC233269
    Conserved Domains (2) summary
    pfam14950
    Location:1150
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:302686
    DUF4503; Domain of unknown function (DUF4503)
  16. NM_001352943.1NP_001339872.1  DNA repair-scaffolding protein isoform 15

    Status: VALIDATED

    Source sequence(s)
    AC023991, AC024451, AC024649, AC145060, AC233269
    Conserved Domains (2) summary
    pfam14950
    Location:11205
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:357616
    DUF4503; Domain of unknown function (DUF4503)
  17. NM_001352944.1NP_001339873.1  DNA repair-scaffolding protein isoform 16

    Status: VALIDATED

    Source sequence(s)
    AC023991, AC024451, AC024649, AC145060, AC233269
    Conserved Domains (2) summary
    pfam14950
    Location:11197
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:349608
    DUF4503; Domain of unknown function (DUF4503)
  18. NM_001352945.1NP_001339874.1  DNA repair-scaffolding protein isoform 17

    Status: VALIDATED

    Source sequence(s)
    AC023991, AC024451, AC024649, AC145060, AC233269
    Conserved Domains (2) summary
    pfam14950
    Location:43127
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:279663
    DUF4503; Domain of unknown function (DUF4503)
  19. NM_001352946.1NP_001339875.1  DNA repair-scaffolding protein isoform 18

    Status: VALIDATED

    Description
    Transcript Variant: This variant (21), as well as variants 22 and 23, encodes isoform 18.
    Source sequence(s)
    AC023991, AC024451, AC024649, AC145060, AC233269
    Conserved Domains (2) summary
    pfam14950
    Location:5119
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:271655
    DUF4503; Domain of unknown function (DUF4503)
  20. NM_001352947.1NP_001339876.1  DNA repair-scaffolding protein isoform 18

    Status: VALIDATED

    Description
    Transcript Variant: This variant (22), as well as variants 21 and 23, encodes isoform 18.
    Source sequence(s)
    AC023991, AC024451, AC024649, AC145060, AC233269
    Conserved Domains (2) summary
    pfam14950
    Location:5119
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:271655
    DUF4503; Domain of unknown function (DUF4503)
  21. NM_001352948.1NP_001339877.1  DNA repair-scaffolding protein isoform 18

    Status: VALIDATED

    Description
    Transcript Variant: This variant (23), as well as variants 21 and 22, encodes isoform 18.
    Source sequence(s)
    AC023991, AC024451, AC024649, AC145060, AC233269
    Conserved Domains (2) summary
    pfam14950
    Location:5119
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:271655
    DUF4503; Domain of unknown function (DUF4503)
  22. NM_001352949.1NP_001339878.1  DNA repair-scaffolding protein isoform 19

    Status: VALIDATED

    Source sequence(s)
    AC023991, AC024451, AC024649, AC145060, AC233269
    Conserved Domains (2) summary
    pfam14950
    Location:1150
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:302631
    DUF4503; Domain of unknown function (DUF4503)
  23. NM_001352950.1NP_001339879.1  DNA repair-scaffolding protein isoform 20

    Status: VALIDATED

    Source sequence(s)
    AC023991, AC024451, AC024649, AC145060, AC233269
    Conserved Domains (2) summary
    pfam14950
    Location:11205
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:357650
    DUF4503; Domain of unknown function (DUF4503)
  24. NM_001352951.1NP_001339880.1  DNA repair-scaffolding protein isoform 21

    Status: VALIDATED

    Source sequence(s)
    AC023991, AC024451, AC024649, AC145060, AC233269
    Conserved Domains (2) summary
    pfam14950
    Location:5119
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:271600
    DUF4503; Domain of unknown function (DUF4503)
  25. NM_001352952.1NP_001339881.1  DNA repair-scaffolding protein isoform 22

    Status: VALIDATED

    Description
    Transcript Variant: This variant (27), as well as variants 28, 29, and 30, encodes isoform 22.
    Source sequence(s)
    AC023991, AC024451, AC024649, AC145060, AC233269
    Conserved Domains (2) summary
    pfam14950
    Location:158
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:210594
    DUF4503; Domain of unknown function (DUF4503)
  26. NM_001352953.1NP_001339882.1  DNA repair-scaffolding protein isoform 22

    Status: VALIDATED

    Description
    Transcript Variant: This variant (28), as well as variants 27, 29, and 30, encodes isoform 22.
    Source sequence(s)
    AC023991, AC024451, AC024649, AC145060, AC233269
    Conserved Domains (2) summary
    pfam14950
    Location:158
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:210594
    DUF4503; Domain of unknown function (DUF4503)
  27. NM_001352955.1NP_001339884.1  DNA repair-scaffolding protein isoform 22

    Status: VALIDATED

    Description
    Transcript Variant: This variant (29), as well as variants 27, 28, and 30, encodes isoform 22.
    Source sequence(s)
    AC023991, AC024451, AC024649, AC145060, AC233269
    Conserved Domains (2) summary
    pfam14950
    Location:158
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:210594
    DUF4503; Domain of unknown function (DUF4503)
  28. NM_001352956.1NP_001339885.1  DNA repair-scaffolding protein isoform 22

    Status: VALIDATED

    Description
    Transcript Variant: This variant (30), as well as variants 27, 28, and 29, encodes isoform 22.
    Source sequence(s)
    AC023991, AC024451, AC024649, AC145060, AC233269
    Conserved Domains (2) summary
    pfam14950
    Location:158
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:210594
    DUF4503; Domain of unknown function (DUF4503)
  29. NM_001352957.1NP_001339886.1  DNA repair-scaffolding protein isoform 23

    Status: VALIDATED

    Source sequence(s)
    AC023991, AC024451, AC024649, AC145060, AC233269
    Related
    ENSP00000429193.1, ENST00000519401.5
    Conserved Domains (2) summary
    pfam14950
    Location:158
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:210503
    DUF4503; Domain of unknown function (DUF4503)
  30. NM_001352958.1NP_001339887.1  DNA repair-scaffolding protein isoform 24

    Status: VALIDATED

    Source sequence(s)
    AC023991, AC024451, AC024649, AC145060, AC233269
    Conserved Domains (1) summary
    pfam14951
    Location:105489
    DUF4503; Domain of unknown function (DUF4503)
  31. NM_001352959.1NP_001339888.1  DNA repair-scaffolding protein isoform 25

    Status: VALIDATED

    Source sequence(s)
    AC023991
    Related
    ENST00000519141.5
    Conserved Domains (1) summary
    pfam14951
    Location:26410
    DUF4503; Domain of unknown function (DUF4503)
  32. NM_001352960.1NP_001339889.1  DNA repair-scaffolding protein isoform 26

    Status: VALIDATED

    Source sequence(s)
    AC023991
    Consensus CDS
    CCDS87607.1
    Related
    ENSP00000427889.1, ENST00000517693.5
    Conserved Domains (1) summary
    pfam14951
    Location:1380
    DUF4503; Domain of unknown function (DUF4503)
  33. NM_001352961.1NP_001339890.1  DNA repair-scaffolding protein isoform 7

    Status: VALIDATED

    Source sequence(s)
    AC023991, AC024451, AC024649, AC145060, AC233269
    Conserved Domains (2) summary
    pfam14950
    Location:11369
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:521780
    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
  2. NR_148202.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC023991, AC024451, AC024649, AC145060, AC233269
  3. NR_148203.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC023991, AC024451, AC024649, AC145060, AC233269
  4. NR_148204.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC023991, AC024451, AC024649, AC145060, AC233269
    Related
    ENST00000522117.5
  5. NR_148205.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC023991, AC024451, AC024649, AC145060, AC233269

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20200815

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p13 Primary Assembly

    Range
    47260878..47736306
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017013281.1XP_016868770.1  DNA repair-scaffolding protein isoform X10

  2. XM_017013280.1XP_016868769.1  DNA repair-scaffolding protein isoform X10

  3. XM_017013273.1XP_016868762.1  DNA repair-scaffolding protein isoform X6

  4. XM_024447116.1XP_024302884.1  DNA repair-scaffolding protein isoform X11

    Conserved Domains (2) summary
    pfam14950
    Location:158
    DUF4502; Domain of unknown function (DUF4502)
    pfam14951
    Location:210539
    DUF4503; Domain of unknown function (DUF4503)
  5. XM_017013274.2XP_016868763.1  DNA repair-scaffolding protein isoform X7

  6. XM_017013268.2XP_016868757.1  DNA repair-scaffolding protein isoform X1

  7. XM_011517497.3XP_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)
  8. XM_017013269.2XP_016868758.1  DNA repair-scaffolding protein isoform X2

  9. XM_017013270.2XP_016868759.1  DNA repair-scaffolding protein isoform X3

  10. XM_017013279.2XP_016868768.1  DNA repair-scaffolding protein isoform X9

  11. XM_017013271.2XP_016868760.1  DNA repair-scaffolding protein isoform X5

    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)
  12. XM_017013289.1XP_016868778.1  DNA repair-scaffolding protein isoform X12

  13. XM_017013276.1XP_016868765.1  DNA repair-scaffolding protein isoform X8

  14. XM_024447117.1XP_024302885.1  DNA repair-scaffolding protein isoform X13

    Conserved Domains (1) summary
    pfam14951
    Location:1380
    DUF4503; Domain of unknown function (DUF4503)

RNA

  1. XR_001745508.2 RNA Sequence

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