CuGenDBv2

Gene ID	Cucsat.G5890
Organism	Cucumis sativus L. var. sativus cv. B10 (Cucumber (B10) v3)
Description	DNA-directed RNA polymerase II subunit 4
Genome location	ctg1402:1668713..1672394
RNA-Seq Expression	Cucsat.G5890
Synteny	Cucsat.G5890
Gene Ontology terms	GO:0000288 - nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (biological process) GO:0006367 - transcription initiation from RNA polymerase II promoter (biological process) GO:0031990 - mRNA export from nucleus in response to heat stress (biological process) GO:0034402 - recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex (biological process) GO:0045948 - positive regulation of translational initiation (biological process) GO:0000932 - P-body (cellular component) GO:0005665 - RNA polymerase II, core complex (cellular component) GO:0000166 - nucleotide binding (molecular function) GO:0003899 - DNA-directed 5'-3' RNA polymerase activity (molecular function) GO:0031369 - translation initiation factor binding (molecular function)
InterPro domains	IPR005574 - RNA polymerase subunit RPB4/RPC9 IPR006590 - RNA polymerase Rpb4/RPC9, core IPR010997 - HRDC-like superfamily IPR038324 - Rpb4/RPC9 superfamily

Homology

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GenBank top hits

e value

%identity

Alignment

XP_004138390.1 DNA-directed RNA polymerase II subunit 4 [Cucumis sativus]

1.68e-90

100

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Query:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPE
        MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPE
Subjt:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPE

Query:  TVEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRFE
        TVEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRFE
Subjt:  TVEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRFE

XP_022133507.1 DNA-directed RNA polymerase II subunit 4 [Momordica charantia]

2.30e-88

97.1

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Query:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPE
        MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDP NQVSQVFEKSLQYVKRFSRYKNPDAVRQVRE+LSRYQLAEFELCVLGNLCPE
Subjt:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPE

Query:  TVEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRFE
        TVEEAIAMVPSLKTKGR HDDEAIEKMLNDLSLIK+FE
Subjt:  TVEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRFE

XP_022939401.1 DNA-directed RNA polymerase II subunit 4-like [Cucurbita moschata]

8.01e-89

97.1

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Query:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPE
        MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVRE+LSRYQLAEFELCVLGNLCPE
Subjt:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPE

Query:  TVEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRFE
        TVEEAI+MVPSLKTKGR HDDEAIEKMLNDLSLIK+FE
Subjt:  TVEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRFE

XP_022954766.1 DNA-directed RNA polymerase II subunit 4 [Cucurbita moschata]

3.27e-88

97.1

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Query:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPE
        MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDP NQVSQVFEKSLQYVKRFSRYKNPDAVRQVRE+LSRYQLAEFELCVLGNLCPE
Subjt:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPE

Query:  TVEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRFE
        TVEEAIAMVPSLK KGRVHDDEAIEKMLNDLSLIK+FE
Subjt:  TVEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRFE

XP_038884885.1 DNA-directed RNA polymerase II subunit 4 [Benincasa hispida]

2.39e-90

99.28

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Query:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPE
        MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVRE+LSRYQLAEFELCVLGNLCPE
Subjt:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPE

Query:  TVEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRFE
        TVEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRFE
Subjt:  TVEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRFE

TrEMBL top hits

e value

%identity

Alignment

A0A0A0K7V5 RPOL4c domain-containing protein

8.15e-91

100

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Query:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPE
        MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPE
Subjt:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPE

Query:  TVEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRFE
        TVEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRFE
Subjt:  TVEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRFE

A0A1S3C4R9 DNA-directed RNA polymerase II subunit 4

8.15e-91

100

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Query:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPE
        MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPE
Subjt:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPE

Query:  TVEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRFE
        TVEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRFE
Subjt:  TVEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRFE

A0A5D3C019 DNA-directed RNA polymerase II subunit 4

8.15e-91

100

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Query:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPE
        MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPE
Subjt:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPE

Query:  TVEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRFE
        TVEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRFE
Subjt:  TVEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRFE

A0A6J1FFS7 DNA-directed RNA polymerase II subunit 4-like

3.88e-89

97.1

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Query:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPE
        MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVRE+LSRYQLAEFELCVLGNLCPE
Subjt:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPE

Query:  TVEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRFE
        TVEEAI+MVPSLKTKGR HDDEAIEKMLNDLSLIK+FE
Subjt:  TVEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRFE

A0A6J1JVN3 DNA-directed RNA polymerase II subunit 4-like

3.88e-89

97.1

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Query:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPE
        MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVRE+LSRYQLAEFELCVLGNLCPE
Subjt:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPE

Query:  TVEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRFE
        TVEEAI+MVPSLKTKGR HDDEAIEKMLNDLSLIK+FE
Subjt:  TVEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRFE

SwissProt top hits

e value

%identity

Alignment

O15514 DNA-directed RNA polymerase II subunit RPB4

3.1e-21

40.88

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Query:  SGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPET
        +G+ EE+A++L    EF  A+ L+N EV ++LEH+ +Q +  S +   ++S+VF K+L Y  RFSR+KN + +  VR +L + +L +FEL  L NLCPET
Subjt:  SGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPET

Query:  VEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRFE
         EE+ A++PSL  +GR  D+E ++++L+D+   + F+
Subjt:  VEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRFE

O48890 DNA-directed RNA polymerase II subunit 4

2.0e-68

93.48

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Query:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPE
        MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHK+EQLQQ+SEDP NQVSQVFEKSLQYVKRFSRYKNPDAVRQVRE+LSR+QL EFELCVLGNLCPE
Subjt:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPE

Query:  TVEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRFE
        TVEEA+AMVPSLKTKGR HDDEAIEKMLNDLSL+KRFE
Subjt:  TVEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRFE

Q54S04 DNA-directed RNA polymerase II subunit rpb4

1.9e-18

37.41

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Query:  EEEENAAELKIGDEFLKAKCLMNCEVSLILEHK----------YEQ---LQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFE
        +EEE+   LK   +   AK L+N EV+++LEH+          + Q   L  +  +  N + + F K+L Y ++FSRYKN  +++QVR  LS+  L EFE
Subjt:  EEEENAAELKIGDEFLKAKCLMNCEVSLILEHK----------YEQ---LQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFE

Query:  LCVLGNLCPETVEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRF
        +  L NLCPE  +EA +++PSLK   ++ DDE ++ +L++LS +++F
Subjt:  LCVLGNLCPETVEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRF

Q9D7M8 DNA-directed RNA polymerase II subunit RPB4

3.1e-21

40.88

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Query:  SGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPET
        +G+ EE+A++L    EF  A+ L+N EV ++LEH+ +Q +  S +   ++S+VF K+L Y  RFSR+KN + +  VR +L + +L +FEL  L NLCPET
Subjt:  SGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPET

Query:  VEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRFE
         EE+ A++PSL  +GR  D+E ++++L+D+   + F+
Subjt:  VEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRFE

Q9VEA5 DNA-directed RNA polymerase II subunit Rpb4

1.4e-16

38.89

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Query:  EENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPETVEEA
        +E+AA+L+   EF  A+ L+  EV ++L+H+  + Q  S D   + S+VF K+  Y   F ++KN + +   R +L + +L +FEL  LGNLCPE  EEA
Subjt:  EENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPETVEEA

Query:  IAMVPSLKTKGRVHDDEAIEKMLNDL
         A++PSL  +GR  D+E + ++L+D+
Subjt:  IAMVPSLKTKGRVHDDEAIEKMLNDL

Arabidopsis top hits

e value

%identity

Alignment

AT4G15950.1 RNA polymerase II, Rpb4, core protein

2.1e-17

38.14

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Query:  AKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKTKGRVHD
        A+C+M+CE   IL+    QL  +SEDP+ ++   ++++L YV+    Y NP +VR+V E L  Y +++ E+CV+ N   E+V+E +A +PSLKTK  V  
Subjt:  AKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPETVEEAIAMVPSLKTKGRVHD

Query:  DEAIEKMLNDLSLIKRFE
        ++ ++  L +LS +K+ E
Subjt:  DEAIEKMLNDLSLIKRFE

AT5G09920.1 RNA polymerase II, Rpb4, core protein

1.4e-69

93.48

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Query:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPE
        MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHK+EQLQQ+SEDP NQVSQVFEKSLQYVKRFSRYKNPDAVRQVRE+LSR+QL EFELCVLGNLCPE
Subjt:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPE

Query:  TVEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRFE
        TVEEA+AMVPSLKTKGR HDDEAIEKMLNDLSL+KRFE
Subjt:  TVEEAIAMVPSLKTKGRVHDDEAIEKMLNDLSLIKRFE

Sequences

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CDS sequence

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ATGTCCGGGGAGGAGGAAGAAAATGCTGCTGAGCTTAAAATTGGAGATGAGTTCTTAAAAGCCAAATGTTTAATGAATTGTGAAGTTTCTCTAATCCTTGAACATAAATA
TGAGCAACTTCAACAGATGTCCGAGGATCCAACAAATCAAGTTTCCCAAGTGTTTGAAAAGTCACTTCAATATGTGAAACGCTTCAGCCGTTATAAGAATCCCGATGCTG
TTAGACAAGTTCGAGAAGTTCTAAGCAGGTATCAGTTGGCGGAGTTTGAGCTTTGTGTTCTTGGCAACCTTTGCCCTGAAACTGTGGAAGAAGCCATTGCCATGGTACCA
TCATTGAAGACCAAGGGAAGGGTGCATGACGATGAAGCAATTGAGAAGATGTTGAATGATCTTTCATTAATCAAAAGATTTGAGTAG

mRNA sequence

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Protein sequence

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MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQMSEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREVLSRYQLAEFELCVLGNLCPETVEEAIAMVP
SLKTKGRVHDDEAIEKMLNDLSLIKRFE

Cucsat.G5890 (gene) of Cucumber (B10) v3 genome