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ONTOLOGY REPORT - ANNOTATIONS

Term:DNA secondary structure binding
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Accession:GO:0000217 term browser browse the term
Definition:Binding to a DNA secondary structure element such as a four-way junction, a bubble, a loop, Y-form DNA, or a double-strand/single-strand junction.


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DNA secondary structure binding term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Clspn claspin enables ISO (PMID:5226314) RGD PMID:5226314 NCBI chr 5:138,850,119...138,885,037
Ensembl chr 5:138,850,128...138,885,034 		JBrowse link
G Rad51ap1 RAD51 associated protein 1 enables ISO (PMID:17996710) RGD PMID:17996710 NCBI chr 4:159,759,454...159,772,473
Ensembl chr 4:159,759,459...159,772,524 		JBrowse link
G Smc5 structural maintenance of chromosomes 5 enables ISO (PMID:28095508) RGD PMID:28095508 NCBI chr 1:220,769,366...220,839,138
Ensembl chr 1:220,769,366...220,839,096 		JBrowse link
G Smc6 structural maintenance of chromosomes 6 enables ISO (PMID:28095508) RGD PMID:28095508 NCBI chr 6:33,978,730...34,033,201
Ensembl chr 6:33,978,716...34,031,746 		JBrowse link
bubble DNA binding term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Abl1 ABL proto-oncogene 1, non-receptor tyrosine kinase enables ISO (PMID:9558345) RGD PMID:9558345 NCBI chr 3:14,979,853...15,083,065
Ensembl chr 3:14,979,853...15,083,065 		JBrowse link
G Blm BLM RecQ like helicase enables ISO (PMID:11433031), (PMID:11735402) RGD PMID:11433031 PMID:11735402 NCBI chr 1:134,409,832...134,496,073
Ensembl chr 1:134,409,857...134,484,312 		JBrowse link
G Ercc5 ERCC excision repair 5, endonuclease enables ISO (PMID:16246722), (PMID:32821917) RGD PMID:16246722 PMID:32821917 NCBI chr 9:46,309,477...46,354,478
Ensembl chr 9:46,309,389...46,354,472 		JBrowse link
G Hmgb1 high mobility group box 1 enables ISS GO_REF:0000024 AgBase GO_REF:0000024 NCBI chr12:5,972,950...5,979,658
Ensembl chr12:5,901,586...5,978,565
Ensembl chr16:5,901,586...5,978,565 		JBrowse link
G Hmgb1l2 high mobility group box 1 like 2 enables ISS GO_REF:0000024 AgBase GO_REF:0000024 NCBI chr  X:107,671,273...107,672,015
Ensembl chr  X:107,671,272...107,672,535 		JBrowse link
G Neil3 nei-like DNA glycosylase 3 enables ISO (PMID:20185759) RGD PMID:20185759 NCBI chr16:38,359,305...38,418,528
Ensembl chr16:38,359,371...38,418,527 		JBrowse link
G Recql4 RecQ like helicase 4 enables ISO (PMID:19177149) RGD PMID:19177149 NCBI chr 7:108,423,453...108,430,790
Ensembl chr 7:108,423,455...108,430,619 		JBrowse link
G Wrn WRN RecQ like helicase enables ISO (PMID:11433031), (PMID:11735402) RGD PMID:11433031 PMID:11735402 NCBI chr16:58,763,517...58,898,604
Ensembl chr16:58,763,504...58,895,450 		JBrowse link
crossed form four-way junction DNA binding term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Hmgb1 high mobility group box 1 enables IDA PMID:10962007 MGI PMID:10962007 RGD:8554262 NCBI chr12:5,972,950...5,979,658
Ensembl chr12:5,901,586...5,978,565
Ensembl chr16:5,901,586...5,978,565 		JBrowse link
D-loop DNA binding term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Hmga1 high mobility group AT-hook 1 enables ISO (PMID:15893306) RGD PMID:15893306 NCBI chr20:5,611,088...5,618,755
Ensembl chr20:5,611,694...5,618,752 		JBrowse link
G Rad51ap1 RAD51 associated protein 1 enables ISO (PMID:17996711) RGD PMID:17996711 NCBI chr 4:159,759,454...159,772,473
Ensembl chr 4:159,759,459...159,772,524 		JBrowse link
DNA hairpin binding term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Nr0b1 nuclear receptor subfamily 0, group B, member 1 enables IEA
ISO
ISS		 GO_REF:0000107
(PMID:9384387)
GO_REF:0000024		 Ensembl
RGD
HGNC-UCL		 PMID:9384387 GO_REF:0000024 GO_REF:0000107 NCBI chr  X:50,756,886...50,761,014
Ensembl chr  X:50,756,886...50,761,011 		JBrowse link
four-way junction DNA binding term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Abl1 ABL proto-oncogene 1, non-receptor tyrosine kinase enables ISO (PMID:9558345) RGD PMID:9558345 NCBI chr 3:14,979,853...15,083,065
Ensembl chr 3:14,979,853...15,083,065 		JBrowse link
G Blm BLM RecQ like helicase enables ISO (PMID:11735402), (PMID:20639533), (PMID:25901030) RGD PMID:11735402 PMID:20639533 PMID:25901030 NCBI chr 1:134,409,832...134,496,073
Ensembl chr 1:134,409,857...134,484,312 		JBrowse link
G Fancm FA complementation group M enables IBA GO_REF:0000033 GO_Central GO_REF:0000033 NCBI chr 6:83,126,903...83,180,455
Ensembl chr 6:83,127,093...83,180,028 		JBrowse link
G Gen1 GEN1 Holliday junction 5' flap endonuclease enables ISO
IBA		 (PMID:26578604), (PMID:26682650), (PMID:28049850)
GO_REF:0000033		 RGD
GO_Central		 PMID:26578604 PMID:26682650 PMID:28049850 GO_REF:0000033 NCBI chr 6:33,947,599...33,978,461
Ensembl chr 6:33,948,206...33,978,401 		JBrowse link
G Hmgb1 high mobility group box 1 enables IDA
ISS		 GO_REF:0000024 AgBase
RGD		 PMID:1547772 GO_REF:0000024, RGD:2316829 NCBI chr12:5,972,950...5,979,658
Ensembl chr12:5,901,586...5,978,565
Ensembl chr16:5,901,586...5,978,565 		JBrowse link
G Hmgb1l2 high mobility group box 1 like 2 enables ISS GO_REF:0000024 AgBase GO_REF:0000024 NCBI chr  X:107,671,273...107,672,015
Ensembl chr  X:107,671,272...107,672,535 		JBrowse link
G Mecp2 methyl CpG binding protein 2 IDA RGD PMID:16314321 RGD:1601323 NCBI chr  X:151,781,177...151,844,687
Ensembl chr  X:151,789,930...151,844,689 		JBrowse link
G Men1 menin 1 enables ISO
IEA		 (PMID:15331604)
GO_REF:0000107		 RGD
Ensembl		 PMID:15331604 GO_REF:0000107 NCBI chr 1:203,638,905...203,644,871
Ensembl chr 1:203,639,000...203,644,871 		JBrowse link
G Msh2 mutS homolog 2 contributes_to
enables		 ISO
IEA		 (PMID:12034830)
GO_REF:0000107		 RGD
Ensembl		 PMID:12034830 GO_REF:0000107 NCBI chr 6:6,813,793...6,872,960
Ensembl chr 6:6,813,795...6,872,938 		JBrowse link
G Msh6 mutS homolog 6 contributes_to ISO (PMID:12034830) RGD PMID:12034830 NCBI chr 6:6,562,631...6,579,995
Ensembl chr 6:6,562,632...6,579,956 		JBrowse link
G Rad51b RAD51 paralog B contributes_to ISO
IBA		 (PMID:20207730)
GO_REF:0000033		 RGD
GO_Central		 PMID:20207730 GO_REF:0000033 NCBI chr 6:98,096,525...98,640,988
Ensembl chr 6:98,098,868...98,640,979 		JBrowse link
G Rad51c RAD51 paralog C contributes_to ISO
IBA		 (PMID:20207730)
GO_REF:0000033		 RGD
GO_Central		 PMID:20207730 GO_REF:0000033 NCBI chr10:72,205,032...72,231,643
Ensembl chr10:72,205,032...72,231,248 		JBrowse link
G Rad51d RAD51 paralog D contributes_to ISO
IBA		 (PMID:20207730)
GO_REF:0000033		 RGD
GO_Central		 PMID:20207730 GO_REF:0000033 NCBI chr10:67,805,720...67,824,452
Ensembl chr10:67,740,712...67,824,434 		JBrowse link
G Rffl ring finger and FYVE-like domain containing E3 ubiquitin protein ligase contributes_to IBA GO_REF:0000033 GO_Central GO_REF:0000033 NCBI chr10:67,740,711...67,803,669
Ensembl chr10:67,740,712...67,824,434 		JBrowse link
G Wrn WRN RecQ like helicase enables ISO (PMID:11735402) RGD PMID:11735402 NCBI chr16:58,763,517...58,898,604
Ensembl chr16:58,763,504...58,895,450 		JBrowse link
G Xrcc2 X-ray repair cross complementing 2 contributes_to ISO
IBA		 (PMID:20207730)
GO_REF:0000033		 RGD
GO_Central		 PMID:20207730 GO_REF:0000033 NCBI chr 4:9,423,873...9,502,980
Ensembl chr 4:9,423,898...9,442,482 		JBrowse link
G Xrcc3 X-ray repair cross complementing 3 contributes_to ISO
IBA		 (PMID:20207730)
GO_REF:0000033		 RGD
GO_Central		 PMID:20207730 GO_REF:0000033 NCBI chr 6:130,863,405...130,873,765
Ensembl chr 6:130,863,959...130,872,444 		JBrowse link
G Yy1 YY1 transcription factor enables ISO (PMID:18026119) RGD PMID:18026119 NCBI chr 6:127,706,739...127,736,499
Ensembl chr 6:127,707,596...127,732,747 		JBrowse link
minor groove of adenine-thymine-rich DNA binding term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G H1f0 H1.0 linker histone enables ISO (PMID:11413144) RGD PMID:11413144 NCBI chr 7:110,592,834...110,594,694
Ensembl chr 7:110,592,208...110,594,694 		JBrowse link
G Hand2 heart and neural crest derivatives expressed 2 enables ISO
IEA		 (PMID:15486975)
GO_REF:0000107		 RGD
Ensembl		 PMID:15486975 GO_REF:0000107 NCBI chr16:32,917,448...32,920,791
Ensembl chr16:32,917,823...32,919,891 		JBrowse link
G Hmga1 high mobility group AT-hook 1 enables ISO (PMID:9253416)
(PMID:19389484)		 RGD PMID:9253416 PMID:19389484 NCBI chr20:5,611,088...5,618,755
Ensembl chr20:5,611,694...5,618,752 		JBrowse link
G Hmga2 high mobility group AT-hook 2 enables ISO
ISS		 (PMID:14627817), (PMID:17078040), (PMID:17426251), (PMID:18832382), (PMID:20108983), (PMID:21533145)
(PMID:16109425)
GO_REF:0000024		 RGD
UniProt		 PMID:14627817 PMID:16109425 PMID:17078040 PMID:17426251 PMID:18832382 More... GO_REF:0000024 NCBI chr 7:55,877,145...55,998,813
Ensembl chr 7:55,880,112...55,994,784 		JBrowse link
G Hnrnpd heterogeneous nuclear ribonucleoprotein D IDA RGD PMID:18413351 RGD:10041067 NCBI chr14:9,615,375...9,638,975
Ensembl chr14:9,615,479...9,633,786 		JBrowse link
G Lin54 lin-54 DREAM MuvB core complex component enables ISO
IEA		 (PMID:27465258)
GO_REF:0000107		 RGD
Ensembl		 PMID:27465258 GO_REF:0000107 NCBI chr14:9,129,775...9,188,244
Ensembl chr14:9,130,336...9,187,790 		JBrowse link
G Mef2c myocyte enhancer factor 2C enables ISO
IEA		 (PMID:15486975)
GO_REF:0000107		 RGD
Ensembl		 PMID:15486975 GO_REF:0000107 NCBI chr 2:13,973,299...14,136,065
Ensembl chr 2:13,993,438...14,132,880 		JBrowse link
G Pax6 paired box 6 IDA RGD PMID:12370174 RGD:632189 NCBI chr 3:92,128,772...92,157,022
Ensembl chr 3:92,135,637...92,157,014 		JBrowse link
G Pou3f4 POU class 3 homeobox 4 IDA RGD PMID:9372951 RGD:1599157 NCBI chr  X:75,858,646...75,859,923
Ensembl chr  X:75,858,646...75,859,923 		JBrowse link
open form four-way junction DNA binding term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Hmgb1 high mobility group box 1 enables IDA PMID:10962007 MGI PMID:10962007 RGD:8554262 NCBI chr12:5,972,950...5,979,658
Ensembl chr12:5,901,586...5,978,565
Ensembl chr16:5,901,586...5,978,565 		JBrowse link
telomeric D-loop binding term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Blm BLM RecQ like helicase enables ISO (PMID:19734539) RGD PMID:19734539 NCBI chr 1:134,409,832...134,496,073
Ensembl chr 1:134,409,857...134,484,312 		JBrowse link
G Pot1 protection of telomeres 1 enables ISO (PMID:19734539) RGD PMID:19734539 NCBI chr 4:54,205,330...54,263,137
Ensembl chr 4:54,205,332...54,263,042 		JBrowse link
G Recql4 RecQ like helicase 4 enables ISO (PMID:22039056) RGD PMID:22039056 NCBI chr 7:108,423,453...108,430,790
Ensembl chr 7:108,423,455...108,430,619 		JBrowse link
G Wrn WRN RecQ like helicase enables ISO (PMID:19734539), (PMID:26420422) RGD PMID:19734539 PMID:26420422 NCBI chr16:58,763,517...58,898,604
Ensembl chr16:58,763,504...58,895,450 		JBrowse link
Y-form DNA binding term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Blm BLM RecQ like helicase enables ISO (PMID:11735402) RGD PMID:11735402 NCBI chr 1:134,409,832...134,496,073
Ensembl chr 1:134,409,857...134,484,312 		JBrowse link
G Men1 menin 1 enables ISO
IBA
IEA		 (PMID:15331604)
GO_REF:0000033
GO_REF:0000107		 RGD
GO_Central
Ensembl		 PMID:15331604 GO_REF:0000033 GO_REF:0000107 NCBI chr 1:203,638,905...203,644,871
Ensembl chr 1:203,639,000...203,644,871 		JBrowse link
G Rad18 RAD18 E3 ubiquitin protein ligase enables ISO (PMID:18363965) RGD PMID:18363965 NCBI chr 4:145,735,654...145,821,102
Ensembl chr 4:145,735,654...145,821,069 		JBrowse link
G Wrn WRN RecQ like helicase enables ISO (PMID:11735402), (PMID:17715146), (PMID:26420422) RGD PMID:11735402 PMID:17715146 PMID:26420422 NCBI chr16:58,763,517...58,898,604
Ensembl chr16:58,763,504...58,895,450 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  molecular_function 20626
    binding 17717
      organic cyclic compound binding 6134
        nucleic acid binding 3844
          DNA binding 2276
            DNA secondary structure binding 37
              D-loop DNA binding + 6
              DNA hairpin binding 1
              Y-form DNA binding 4
              bubble DNA binding 8
              double-strand/single-strand DNA junction binding + 0
              four-way junction DNA binding + 18
              heteroduplex DNA loop binding 0
              minor groove of adenine-thymine-rich DNA binding 9
paths to the root