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Basic Information Integrated Annotations

Tag Content
iUUCD ID IUUC-Rno-104844
Ensembl Protein ID ENSRNOP00000021629.4
UniProt Accession Q4KMA2; Q0D2G8; Q5CZZ8; Q6IRD5; RD23B_RAT
Genbank Protein ID AAH70960.1; AAH90351.1; AAH98674.1; AAI11407.1
Protein Name UV excision repair protein RAD23 homolog B
Genbank Nucleotide ID BC070960; BC090351; BC098674; BC111406
Gene Name Rad23b
Ensembl Information
Ensembl Gene ID Ensembl Transcript ID Ensembl Protein ID
ENSRNOG00000016137.6 ENSRNOT00000021629.6 ENSRNOP00000021629.4
Annotation
Single Nucleotide Polymorphisms (SNP)
dbSNP
mRNA Expression
GEOArrayExpress
DNA & RNA Element
microRNATRANSFACmiRecordsmiRNAMap
RAID2
Protein-protein Interaction
IIDiRefIndexPINAHINT
Mentha
Post-translational Modifications (PTMs)
CPLMdbPAFPhosphositePlusdbPTM
UniProt
Protein Expression/Proteomics
GPMDB
Status Unreviewed
Classification
Family E-Value Score Start End
UBD/Alpha-Helix/UBA 2.10e-19 69.4 190 227
ULD/UDP/UBQ/UBQ_PIM 1.70e-27 95.6 1 78
Active Site
Position(s) Description Evidence
N/A N/A N/A
Domain Profile

   UBD/Alpha-Helix/UBA

   S: 3    dedkleqlveMGFdreealqaLraannnleaAveyLld 40
    +e ++ ++++MG++re+++ aLra++nn+++AveyLl
   Q: 190 YENMVTEIMSMGYEREQVIAALRASFNNPDRAVEYLLM 227
    5789********************************95 PP
   


   ULD/UDP/UBQ/UBQ_PIM

   S: 1    mkltvktlkgkefelevseddtveelKekiakesg...vppeqqkLIyaGkiLkDdttLselgikdgsvvhlvvkksk 75
    m++t+ktl++++f++++++++tv++lKeki++e+g +p++ qkLIyaGkiL+Ddt L+e++i+++++v+++v+k+k
   Q: 1 MQVTLKTLQQQTFKIDIDPEETVKALKEKIESEKGkdaFPVAGQKLIYAGKILSDDTALKEYKIDEKNFVVVMVTKPK 78
    99*************************************************************************997 PP
   

Organism Rattus norvegicus
Functional Description
(View)

Functional Description



     The XPC complex is proposed to represent the first factor bound at the sites of DNA damage and together with other core recognition factors, Xpa, RPA and the TFIIH complex, is part of the pre-incision (or initial recognition) complex. The XPC complex recognizes a wide spectrum of damaged DNA characterized by distortions of the DNA helix such as single-stranded loops, mismatched bubbles or single-stranded overhangs. The orientation of XPC complex binding appears to be crucial for inducing a productive NER. XPC complex is proposed to recognize and to interact with unpaired bases on the undamaged DNA strand which is followed by recruitment of the TFIIH complex and subsequent scanning for lesions in the opposite strand in a 5'-to-3' direction by the NER machinery. Cyclobutane pyrimidine dimers (CPDs) which are formed upon UV-induced DNA damage esacpe detection by the XPC complex due to a low degree of structural perurbation. Instead they are detected by the UV-DDB complex which in turn recruits and cooperates with the XPC complex in the respective DNA repair. In vitro, the XPC:RAD23B dimer is sufficient to initiate NER; it preferentially binds to cisplatin and UV-damaged double-stranded DNA and also binds to a variety of chemically and structurally diverse DNA adducts. XPC:RAD23B contacts DNA both 5' and 3' of a cisplatin lesion with a preference for the 5' side. Xpc:Rad22b induces a bend in DNA upon binding. Xpc:Rad23b stimulates the activity of DNA glycosylases Tdg and Smug1 (By similarity).
The XPC complex is proposed to represent the first factor bound at the sites of DNA damage and together with other core recognition factors, Xpa, RPA and the TFIIH complex, is part of the pre-incision (or initial recognition) complex. The XPC complex recognizes a wide spectrum of damaged DNA characterized by distortions of the DNA helix such as single-stranded loops, mismatched bubbles or single-stranded overhangs. The orientation of XPC complex binding appears to be crucial for inducing a productive NER. XPC complex is proposed to recognize and to interact with unpaired bases on the undamaged DNA strand which is followed by recruitment of the TFIIH complex and subsequent scanning for lesions in the opposite strand in a 5'-to-3' direction by the NER machinery. Cyclobutane pyrimidine dimers (CPDs) which are formed upon UV-induced DNA damage esacpe detection by the XPC complex due to a low degree of structural perurbation. Instead they are detected by the UV-DDB complex which in turn recruits and cooperates with the XPC complex in the respective DNA repair. In vitro, the XPC:RAD23B dimer is sufficient to initiate NER; it preferentially binds to cisplatin and UV-damaged double-stranded DNA and also binds to a variety of chemically and structurally diverse DNA adducts. XPC:RAD23B contacts DNA both 5' and 3' of a cisplatin lesion with a preference for the 5' side. Xpc:Rad22b induces a bend in DNA upon binding. Xpc:Rad23b stimulates the activity of DNA glycosylases Tdg and Smug1 (By similarity).
Protein Sequence
(Fasta)
MQVTLKTLQQ QTFKIDIDPE ETVKALKEKI ESEKGKDAFP VAGQKLIYAG KILSDDTALK 60
EYKIDEKNFV VVMVTKPKAV TSAVPATTQQ SSSPSTTTVS SSPAAAVAQA PAPTPALAPT 120
It may take some time, please wait.

Protein Fasta Sequence



>IUUC-Rno-104844|UBD,UBA;ULD,UBQ_PIM|Rattus norvegicus
Please wait for a moment...
Nucleotide Sequence
(Fasta)
CTCGGCGAGT CACGGTGATG GCGGCCACCA TCCTGTGGTG AGGTAGCGGA TTCTCTGCGT 60
CTCTCCGGGA GTCCCTCGCG CCTCCTGCGG GCCCGGTGTC TGGCGCGTGA GGAAGCACCG 120
It may take some time, please wait.

Nucleotide Fasta Sequence



>IUUC-Rno-104844|UBD,UBA;ULD,UBQ_PIM|Rattus norvegicus
Please wait for a moment...
Sequence Source Ensembl
Keyword

KW-0181--Complete proteome
KW-0963--Cytoplasm
KW-0903--Direct protein sequencing
KW-0227--DNA damage
KW-0234--DNA repair
KW-0539--Nucleus
KW-0597--Phosphoprotein
KW-0647--Proteasome
KW-1185--Reference proteome
KW-0677--Repeat
KW-0833--Ubl conjugation pathway

Interpro

IPR004806--Rad23
IPR006636--STI1_HS-bd
IPR015940--UBA
IPR009060--UBA-like
IPR029071--Ubiquitin-rel_dom
IPR000626--Ubiquitin_dom
IPR015360--XPC-bd

PROSITE

PS50030--UBA
PS50053--UBIQUITIN_2

Pfam

PF00627--UBA
PF00240--ubiquitin
PF09280--XPC-binding

PRINTS

PR01839--RAD23PROTEIN

SMART

SM00727--STI1
SM00165--UBA
SM00213--UBQ

Gene Ontology

GO:0005829--C:cytosol
GO:0005654--C:nucleoplasm
GO:0000502--C:proteasome complex
GO:0071942--C:XPC complex
GO:0003684--F:damaged DNA binding
GO:0048568--P:embryonic organ development
GO:0000715--P:nucleotide-excision repair, DNA damage recognition
GO:0043161--P:proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0032434--P:regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:0007283--P:spermatogenesis

KEGG rno:298012
Orthology
iUUCD ID Species Identity E-value Score
IUUC-Aml-001195 Ailuropoda melanoleuca 87.89 9.00e-91 327.00
IUUC-Apl-003371 Anas platyrhynchos 70.84 2.00e-118 419.00
IUUC-Aca-004599 Anolis carolinensis 80.62 5.00e-91 327.00
IUUC-Aly-005498 Arabidopsis lyrata 39.30 3.00e-39 155.00
IUUC-Ath-006676 Arabidopsis thaliana 40.07 6.00e-41 161.00
IUUC-Afu-008877 Aspergillus fumigatus 44.29 5.00e-18 85.10
IUUC-Ate-010458 Aspergillus terreus 39.76 8.00e-31 127.00
IUUC-Ame-011107 Astyanax mexicanus 62.25 4.00e-55 208.00
IUUC-Bta-012922 Bos taurus 92.12 3.00e-94 338.00
IUUC-Bci-013933 Botrytis cinerea 47.14 9.00e-19 87.80
IUUC-Bdi-014253 Brachypodium distachyon 34.90 3.00e-33 135.00
IUUC-Bol-016493 Brassica oleracea 35.57 4.00e-35 142.00
IUUC-Bra-017582 Brassica rapa 35.94 3.00e-35 142.00
IUUC-Cja-018772 Callithrix jacchus 87.02 2.00e-133 468.00
IUUC-Cfa-020683 Canis familiaris 87.87 4.00e-98 351.00
IUUC-Cpo-022145 Cavia porcellus 85.54 3.00e-135 474.00
IUUC-Cre-022810 Chlamydomonas reinhardtii 36.32 4.00e-29 122.00
IUUC-Csa-023714 Chlorocebus sabaeus 88.70 2.00e-148 518.00
IUUC-Cho-024814 Choloepus hoffmanni 70.45 2.00e-81 296.00
IUUC-Cin-025741 Ciona intestinalis 40.62 2.00e-36 146.00
IUUC-Csv-025823 Ciona savignyi 38.98 8.00e-43 166.00
IUUC-Cgl-026495 Colletotrichum gloeosporioides 52.00 1.00e-16 80.50
IUUC-Cne-027056 Cryptococcus neoformans 46.15 7.00e-15 75.10
IUUC-Cme-027260 Cyanidioschyzon merolae 28.31 3.00e-24 106.00
IUUC-Dre-028369 Danio rerio 69.70 2.00e-82 299.00
IUUC-Dno-029543 Dasypus novemcinctus 84.86 2.00e-130 458.00
IUUC-Dor-031041 Dipodomys ordii 65.09 6.00e-55 207.00
IUUC-Dse-031336 Dothistroma septosporum 45.39 6.00e-17 82.00
IUUC-Dme-032027 Drosophila melanogaster 37.28 3.00e-63 235.00
IUUC-Ete-032583 Echinops telfairi 76.35 4.00e-64 238.00
IUUC-Eca-034243 Equus caballus 92.53 6.00e-93 334.00
IUUC-Eeu-034721 Erinaceus europaeus 84.75 3.00e-72 265.00
IUUC-Fca-035679 Felis catus 90.37 1.00e-95 343.00
IUUC-Fal-037148 Ficedula albicollis 78.66 2.00e-90 325.00
IUUC-Gmo-039080 Gadus morhua 61.79 8.00e-59 220.00
IUUC-Gga-040544 Gallus gallus 70.96 9.00e-121 426.00
IUUC-Gma-043937 Glycine max 35.69 1.00e-39 157.00
IUUC-Ggo-045125 Gorilla gorilla 91.05 4.00e-97 348.00
IUUC-Hsa-046519 Homo sapiens 91.05 4.00e-97 348.00
IUUC-Hvu-047832 Hordeum vulgare 35.29 2.00e-33 136.00
IUUC-Itr-048295 Ictidomys tridecemlineatus 86.75 7.00e-126 443.00
IUUC-Kpa-049314 Komagataella pastoris 35.83 7.00e-29 121.00
IUUC-Lch-050553 Latimeria chalumnae 63.05 2.00e-97 349.00
IUUC-Lpe-051087 Leersia perrieri 34.75 2.00e-35 143.00
IUUC-Loc-051748 Lepisosteus oculatus 74.27 5.00e-75 274.00
IUUC-Lma-053328 Leptosphaeria maculans 48.68 2.00e-13 67.00
IUUC-Laf-054293 Loxodonta africana 88.58 2.00e-117 415.00
IUUC-Mcc-055600 Macaca mulatta 90.77 3.00e-103 368.00
IUUC-Meu-056082 Macropus eugenii 65.12 2.00e-68 252.00
IUUC-Mor-057287 Magnaporthe oryzae 50.00 2.00e-16 79.70
IUUC-Mpo-057609 Magnaporthe poae 44.44 1.00e-14 73.90
IUUC-Mtr-058148 Medicago truncatula 35.85 1.00e-41 163.00
IUUC-Mla-058961 Melampsora laricipopulina 44.60 3.00e-24 106.00
IUUC-Mga-060060 Meleagris gallopavo 45.62 9.00e-16 77.40
IUUC-Mvi-060220 Microbotryum violaceum 42.65 4.00e-21 96.30
IUUC-Mmr-061159 Microcebus murinus 92.74 2.00e-94 338.00
IUUC-Mdo-061967 Monodelphis domestica 81.34 1.00e-118 419.00
IUUC-Mmu-063258 Mus musculus 96.63 3.00e-162 564.00
IUUC-Mpu-066389 Mustela putorius furo 87.89 4.00e-91 328.00
IUUC-Mlu-067999 Myotis lucifugus 90.74 2.00e-95 342.00
IUUC-Nfi-068390 Neosartorya fischeri 44.29 5.00e-18 85.10
IUUC-Ncr-068685 Neurospora crassa 42.86 2.00e-23 103.00
IUUC-Nle-069655 Nomascus leucogenys 88.22 3.00e-142 498.00
IUUC-Opr-070234 Ochotona princeps 82.10 5.00e-29 121.00
IUUC-Ont-072484 Oreochromis niloticus 58.69 9.00e-105 373.00
IUUC-Oan-073258 Ornithorhynchus anatinus 89.36 2.00e-50 191.00
IUUC-Ocu-074831 Oryctolagus cuniculus 88.56 1.00e-92 333.00
IUUC-Obr-076909 Oryza brachyantha 36.05 2.00e-36 146.00
IUUC-Osa-086112 Oryza sativa 33.98 4.00e-33 135.00
IUUC-Ola-086540 Oryzias latipes 63.28 2.00e-64 239.00
IUUC-Olu-087843 Ostreococcus lucimarinus 40.95 5.00e-38 151.00
IUUC-Oga-088023 Otolemur garnettii 87.53 3.00e-134 471.00
IUUC-Oar-089964 Ovis aries 92.12 1.00e-92 333.00
IUUC-Ptr-091165 Pan troglodytes 91.05 6.00e-97 347.00
IUUC-Pan-092009 Papio anubis 88.07 4.00e-142 497.00
IUUC-Psi-093477 Pelodiscus sinensis 81.59 1.00e-85 310.00
IUUC-Pfo-097385 Poecilia formosa 65.57 4.00e-70 258.00
IUUC-Pab-097868 Pongo abelii 91.05 3.00e-96 344.00
IUUC-Pca-100652 Procavia capensis 89.86 3.00e-66 245.00
IUUC-Pva-102137 Pteropus vampyrus 92.37 7.00e-98 350.00
IUUC-Ptt-103717 Puccinia triticina 43.26 1.00e-24 107.00
IUUC-Pte-104303 Pyrenophora teres 47.89 4.00e-19 89.00
IUUC-Pyt-104580 Pyrenophora triticirepentis 47.55 5.00e-19 88.60
IUUC-Sce-106214 Saccharomyces cerevisiae 35.82 6.00e-13 68.60
IUUC-Sha-107073 Sarcophilus harrisii 88.43 4.00e-86 311.00
IUUC-Ssl-108382 Sclerotinia sclerotiorum 41.53 3.00e-16 79.30
IUUC-Sar-112925 Sorex araneus 81.55 1.00e-85 309.00
IUUC-Sbi-113871 Sorghum bicolor 35.41 6.00e-33 134.00
IUUC-Sre-114894 Sporisorium reilianum 52.46 3.00e-11 63.20
IUUC-Ssc-116329 Sus scrofa 90.74 6.00e-98 350.00
IUUC-Tgu-116918 Taeniopygia guttata 77.61 2.00e-91 329.00
IUUC-Tru-118651 Takifugu rubripes 60.47 2.00e-72 266.00
IUUC-Tsy-118836 Tarsius syrichta 93.66 5.00e-47 181.00
IUUC-Tni-120493 Tetraodon nigroviridis 60.56 3.00e-72 265.00
IUUC-Tvi-122617 Trichoderma virens 52.56 2.00e-18 86.30
IUUC-Tme-127092 Tuber melanosporum 37.23 5.00e-27 115.00
IUUC-Tbe-127493 Tupaia belangeri 78.18 2.00e-64 239.00
IUUC-Ttr-128464 Tursiops truncatus 90.37 9.00e-98 350.00
IUUC-Uma-129484 Ustilago maydis 47.54 1.00e-11 64.70
IUUC-Vda-129946 Verticillium dahliae 45.00 7.00e-17 81.60
IUUC-Vpa-130357 Vicugna pacos 85.67 2.00e-84 305.00
IUUC-Vvi-131039 Vitis vinifera 34.87 9.00e-40 157.00
IUUC-Xtr-132679 Xenopus tropicalis 84.80 3.00e-70 259.00
IUUC-Yli-134615 Yarrowia lipolytica 41.89 7.00e-37 147.00
Created Date 25-Jun-2017

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