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Gene 2

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    Considering its matching to different protein pieces, it is probably a pseudogene                   Back to main page

    Or a probable new protein product...

     

    ESTs support the following gene model:

    Exon.1: 16066-16224

    Exon.2: 16321-16440

    Exon.3: 16532-16669

    Exon.4: 17001-17075

    Exon.5: 18282-18629

    Exon.6: 19233-19292

    Exon.7: 19397-19594

     

    Protein Sequence:

    MVRALWLGGRAAAAARWCTCRRATVALCVANLVATLLVTRALYAPGSFAFAPKRGELKYS

    REHMRWVDESIWIRRAAEPVELIEAVIAVLQSSREEAAKAFAREEKTRKGLPLELKQKVS

    LETLQILHDLGEGSNTTEQQGMLKRALEFNWQMLLEDIGLWIPPTIWYLNDVDYYGGFEQ

    DELDELFEAMQSNYKAWCLGFAPLCVGGDMESVAVQEFSRTLFNIRPDIALNVAQTIFQS

    DVRSLLRHVSVPCHIVQSTKDLAVPVVVSEYLHRHLGGDSIVELLDTGFVGLIFSCFSED

    AQKVGKIQVTAFQSEGGQHHALPLAIAPVIDLDSSLSSSDNALTSHSALVEGMEQDTGDS

    RASKHNKV

     

    Function: Involved in hydrolase activity; Positive regulator required for energy stress activation of the sigma-B transcription factor. Could be required for rsbP phosphatase activity. 

    Conserved domain: Mov34/MPN/PAD-1 family: BRCC36, a subunit of BRCA1-A complex

    BRCC36 and BRCC36-like domains are members of JAMM/MPN+ deubiquitinases (DUBs), possibly with Zn2+-dependent ubiquitin isopeptidase activity. BRCC36 is part of the BRCA1/BRCA2/BARD1-containing nuclear complex that displays an E3 ubiquitin ligase activity. It is targeted to DNA damage foci after irradiation; RAP80 recruits the Abraxas-BRCC36-BRCA1-BARD1 complex to DNA double strand breaks (DSBs) for DNA repair through specific recognition of Lys 63-linked polyubiquitinated proteins by its tandem ubiquitin-interacting motifs. A new protein, MERIT40 (mediator of RAP80 interactions and targeting 40 kDa), also named NBA1 (new component of the BRCA1 A complex), exists in the same BRCA1-containing complex and is essential for the integrity of the complex. There are studies suggesting that MERIT40/NBA1 ties BRCA1 complex integrity, DSB recognition, and ubiquitin chain activities to the DNA damage response. It has also been shown that BRCA1-containing complex resembles the lid complex of the 26S proteasome.

     

    Annotation Process

    1. Comparison of the two gene models:

    GeneMark, 1083bp, 360aa FGENESH, 987bp, 328aa EST Evidence
    4 + 15754 18725 2 + 16066 19594      
    4_1 + 15754 15906              
    4_2 + 16006 16225 2_1 + 16066 16224 16049 16226 4
    4_3 + 16321 16440         16321 16417 4
    4_4 + 16530 16674 2_2 + 16532 16669 16529 16670 3
            2_3 + 17001 17075 16970 17065 >5
    4_5 + 18281 18725 2_4 + 18282 18629 18279 18741 >10
            2_5 + 19233 19292 19205 19294 >10
            2_6 + 19397 19594 19395 19589 >10

     

    Only the last two exons (GeneMark) match in blastp. However, once blastp is conducted using FGENESH predicted sequence, the C-terminal (240-328) matches to mov34/MPN/PAD-1 family protein: BRCC36. For this, we propose two possibilities: 1. this sigma factor sigB homology acquires partial function of BRCC36; 2. the assembly was not quite correct due to sequence fusion; 3. This is a new protein product.

     

    2. Blastn for EST matching (15751-19600): 

    G2_EST.bmp

     

    3. Comparison of the two predicted protein sequences:

    CLUSTAL 2.1 multiple sequence alignment
    
    
    FGENESH_                     --------------------------------------------------
    GMK_4|GeneMark.hmm|gene      MPVLLSATSRCPHSKGVPPPRRPPPHHALGSPRDPCPQPGCSDPSFPYYL 50
                                                                                   
    
    FGENESH_                     ---------------------MVRALWLGGRAAAAARWCTCRRATVALCV 29
    GMK_4|GeneMark.hmm|gene      KPRCRARRHSDPAPASSTRDAMVRALWLGGRAAAAARWCTCRRATVALCV 100
                                                      *****************************
    
    FGENESH_                     ANLVATLLVTRALYAPGSFAFAPKR------------------------- 54
    GMK_4|GeneMark.hmm|gene      ANLVATLLVTRALYAPGSFAFAPKRGELKYSREHMRWVDESIWIRRAAEP 150
                                 *************************                         
    
    FGENESH_                     ---------------EEAAKAFAREEKTRKGLPLELKQKVSLETLQILHD 89
    GMK_4|GeneMark.hmm|gene      VELIEAVIAVLQSSCEEAAKAFAREEKTRKGLPLELKQKVSLETLQILHD 200
                                                ***********************************
    
    FGENESH_                     LGEGSNTTEQQGMLKRALEFNWQMLLEDIGLWIPPTIWYLNDVDYYGGFE 139
    GMK_4|GeneMark.hmm|gene      LGEGSNTTEQQGL-------------------------YLNDVDYYGGFE 225
                                 ************:                         ************
    
    FGENESH_                     QDELDELFEAMQSNYKAWCLGFAPLCVGGDMESVAVQEFSRTLFNIRPDI 189
    GMK_4|GeneMark.hmm|gene      QDELDELFEAMQSNYKAWCLGFAPLCVGGDMESVAVQEFSRTLFNIRPDI 275
                                 **************************************************
    
    FGENESH_                     ALNVAQTIFQSDVRSLLRHVSVPCHIVQSTKDLAVPVVVSEYLHRHLGGD 239
    GMK_4|GeneMark.hmm|gene      ALNVAQTIFQSDVRSLLRHVSVPCHIVQSTKDLAVPVVVSEYLHRHLGGD 325
                                 **************************************************
    
    FGENESH_                     SIVELLDTGFVGLIFSCFSEDAQKVGKIQVTAFQSEGGQHHALPLAIAPV 289
    GMK_4|GeneMark.hmm|gene      SIVEVMP---------------------------SEG----HLP------ 338
                                 ****::                            ***     **      
    
    FGENESH_                     IDLDSSLSSSDNALTSHSALVEGMEQDTGDSRASKHNKV 328
    GMK_4|GeneMark.hmm|gene      -----QLSSPD---IVTPVLLRHIQHDIAV--------- 360
                                      .***.*      ..*:. :::* .  

     

    4. Compare the FGENESH predicted protein with real sigma factor sigB regulation protein [Zea Mays]:

    CLUSTAL 2.1 multiple sequence alignment
    
    
    FGENESH           -----MVRALWLGGRAAAAARWCTCRRATVALCVANLVATLLVTRALYAPGSFAFAPKRE 55
    sigB[Z.mays]      MGIVEEAHNLRVVGEGKRGVIVLAHGFGTDQSVWKHLVPHLVADYRVVLFDTMGAGPTN- 59
                            .: * : *..  ..   :   .*      :**. *:.   :   .::. .*.. 
    
    FGENESH           EAAKAFAREEKTRKGLPLELKQKVSLETLQILHDLGEGSNTTEQQGMLKRALEFNWQMLL 115
    sigB[Z.mays]      PDYFDFSR-YATLEGYALDL--LAILQELGVQSCIYVGHSVSAIIGALA---SISRPDLF 113
                           *:*   * :* .*:*   . *: * :   :  * ..:   * *    .:.   *:
                                      Perfect match with sigB protein [Zea Mays]
    FGENESH           EDIGLWIPPTIWYLNDVDYYGGFEQDELDELFEAMQSNYKAWCLGFAPLCVGGDMESVAV 175
    sigB[Z.mays]      TKL-VLLSASPRYLNDVDYYGGFEQDELDELFEAMQSNYKAWCLGFAPLCVGGDMESVAV 172
                       .: : :..:  ************************************************
    
    FGENESH           QEFSRTLFNIRPDIALNVAQTIFQSDVRSLLRHVSVPCHIVQSTKDLAVPVVVSEYLHRH 235
    sigB[Z.mays]      QEFSRTLFNIRPDIALNVAQTIFQSDVRSLLPHVSVPCHIVQSTKDLAVPVVVSEYLHRH 232
                      ******************************* ****************************
                                           BRCC36 conserved domain
    FGENESH           LGGDSIVELLDTGFVGLIFSCFSEDAQKVGKIQVTAFQSEGGQHHALPLAIAPVIDLDSS 295
    sigB[Z.mays]      LGGDSIVEVMP---------------------------SEG----HLP-----------Q 250
                      ********::                            ***     **           .
    
    FGENESH           LSSSDNALTSHSALVEGMEQDTGDSRASKHNKV 328
    sigB[Z.mays]      LSSPD---IVTPVLLRHIQHDIAI--------- 271
                      ***.*      ..*:. :::* .  

     

    Query from FGENSH, blastp:

    GENE ID: 100284983 LOC100284983 | sigma factor sigB regulation protein rsbQ
    [Zea mays] (10 or fewer PubMed links)
     
     Score =   245 bits (625),  Expect = 5e-81, Method: Compositional matrix adjust.
     Identities = 115/120 (96%), Positives = 118/120 (98%), Gaps = 0/120 (0%)
     
    Query  128  YLNDVDYYGGFEQDELDELFEAMQSNYKAWCLGFAPLCVGGDMESVAVQEFSRTLFNIRP  187
                YLNDVDYYGGFEQDELDELFEAMQSNYKAWCLGFAPLCVGGDMESVAVQEFSRTLFNIRP
    Sbjct  125  YLNDVDYYGGFEQDELDELFEAMQSNYKAWCLGFAPLCVGGDMESVAVQEFSRTLFNIRP  184
     
    Query  188  DIALNVAQTIFQSDVRSLLRHVSVPCHIVQSTKDLAVPVVVSEYLHRHLGGDSIVELLDT  247
                DIALNVAQTIFQSDVRSLL HVSVPCHIVQSTKDLAVPVVVSEYLHRHLGGDSIVE++ +
    Sbjct  185  DIALNVAQTIFQSDVRSLLPHVSVPCHIVQSTKDLAVPVVVSEYLHRHLGGDSIVEVMPS  244
     
     
    GENE ID: 100283593 LOC100283593 | mov34/MPN/PAD-1 family protein [Zea mays]
    (10 or fewer PubMed links)
     
     Score =   149 bits (376),  Expect = 5e-43, Method: Compositional matrix adjust.
     Identities = 83/89 (93%), Positives = 86/89 (97%), Gaps = 0/89 (0%)
     
    Query  240  SIVELLDTGFVGLIFSCFSEDAQKVGKIQVTAFQSEGGQHHALPLAIAPVIDLDSSLSSS  299
                ++ +LLDTGFVGLIFSCFSEDAQKVGKIQVTAFQSEGGQ HALPLAIAPVIDLDSSLSSS
    Sbjct  113  AMFQLLDTGFVGLIFSCFSEDAQKVGKIQVTAFQSEGGQQHALPLAIAPVIDLDSSLSSS  172
     
    Query  300  DNALTSHSALVEGMEQDTGDSRASKHNKV  328
                DNALTSHSALVEGMEQDTGDSRASKHNK 
    Sbjct  173  DNALTSHSALVEGMEQDTGDSRASKHNKA  201

     

    Query from GeneMark, blastp:

    GENE ID: 100284983 LOC100284983 | sigma factor sigB regulation protein rsbQ
    [Zea mays] (10 or fewer PubMed links)
     
     Score =   303 bits (776),  Expect = 1e-102, Method: Compositional matrix adjust.
     Identities = 145/147 (99%), Positives = 146/147 (99%), Gaps = 0/147 (0%)
     
    Query  214  YLNDVDYYGGFEQDELDELFEAMQSNYKAWCLGFAPLCVGGDMESVAVQEFSRTLFNIRP  273
                YLNDVDYYGGFEQDELDELFEAMQSNYKAWCLGFAPLCVGGDMESVAVQEFSRTLFNIRP
    Sbjct  125  YLNDVDYYGGFEQDELDELFEAMQSNYKAWCLGFAPLCVGGDMESVAVQEFSRTLFNIRP  184
     
    Query  274  DIALNVAQTIFQSDVRSLLRHVSVPCHIVQSTKDLAVPVVVSEYLHRHLGGDSIVEVMPS  333
                DIALNVAQTIFQSDVRSLL HVSVPCHIVQSTKDLAVPVVVSEYLHRHLGGDSIVEVMPS
    Sbjct  185  DIALNVAQTIFQSDVRSLLPHVSVPCHIVQSTKDLAVPVVVSEYLHRHLGGDSIVEVMPS  244
     
    Query  334  EGHLPQLSSPDIVTPVLLRHIQHDIAV  360
                EGHLPQLSSPDIVTPVLLRHIQHDIA+
    Sbjct  245  EGHLPQLSSPDIVTPVLLRHIQHDIAI  271
     
    G2.bmp
                                                                                                                       sigB regulation protein
     
    5. Gene model combination:
    Since there are considerable differences between the predicted gene models and fragmental Blast hits, we inspected further the possible better model. ESTs actually support a 7-exon gene model and the correspondingly translated protein can get a better blast hit. 
     

    Blastp with new sequence:

    G2_new.bmp

                                 Transmembrane signal peptide       sigB regulation protein    BRCC36 conserved domain

    InterProScan for potential function:

    G2_interpro.bmp

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     G2.bmp
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    881.42 kB21:05, 24 Oct 2012cui19Actions
     G2_EST.bmp
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     G2_interpro.bmp
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