CuGenDBv2

Gene ID	Lcy06g011330
Organism	Luffa cylindrica cv. P93075 (Sponge gourd (P93075) v1)
Description	DNA-directed RNA polymerase II subunit 4
Genome location	Chr06:13222400..13224516
RNA-Seq Expression	Lcy06g011330
Synteny	Lcy06g011330
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

KAF3440471.1 hypothetical protein FNV43_RR18755 [Rhamnella rubrinervis]

1.8e-66

96.38

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Query:  MSGEEEENAAELKIGDEFLKVKCLMNCEVSLILEHKYEQLQQMSEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPE
        MSGEEEENAAELKIG+EFLK KCLMNCEVSLILEHKYEQLQQMSEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPE
Subjt:  MSGEEEENAAELKIGDEFLKVKCLMNCEVSLILEHKYEQLQQMSEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPE

Query:  TVEEAIAMVPSLKIKGRAHDDEAIKKMLNDLSLIKKFE
        TVEEAIAMVPS+K KGRAHDDEAI+KMLNDLSLIKKFE
Subjt:  TVEEAIAMVPSLKIKGRAHDDEAIKKMLNDLSLIKKFE

KAG8649808.1 hypothetical protein MANES_08G141900v8 [Manihot esculenta]

3.1e-66

95.65

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Query:  MSGEEEENAAELKIGDEFLKVKCLMNCEVSLILEHKYEQLQQMSEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPE
        MSGEEEENAAELKIGDEFLK KCLMNCEV+LILEHKYEQLQQMS+DPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPE
Subjt:  MSGEEEENAAELKIGDEFLKVKCLMNCEVSLILEHKYEQLQQMSEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPE

Query:  TVEEAIAMVPSLKIKGRAHDDEAIKKMLNDLSLIKKFE
        TVEEAIAMVPS+K KGRAHDDEAI+KMLNDLSLIKKFE
Subjt:  TVEEAIAMVPSLKIKGRAHDDEAIKKMLNDLSLIKKFE

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

3.6e-67

97.83

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Query:  MSGEEEENAAELKIGDEFLKVKCLMNCEVSLILEHKYEQLQQMSEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPE
        MSGEEEENAAELKIGDEFLK KCLMNCEVSLILEHKYEQLQQMSEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPE
Subjt:  MSGEEEENAAELKIGDEFLKVKCLMNCEVSLILEHKYEQLQQMSEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPE

Query:  TVEEAIAMVPSLKIKGRAHDDEAIKKMLNDLSLIKKFE
        TVEEAIAMVPSLK KGRAHDDEAI+KMLNDLSLIKKFE
Subjt:  TVEEAIAMVPSLKIKGRAHDDEAIKKMLNDLSLIKKFE

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

1.1e-66

97.1

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Query:  MSGEEEENAAELKIGDEFLKVKCLMNCEVSLILEHKYEQLQQMSEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPE
        MSGEEEENAAELKIGDEFLK KCLMNCEVSLILEHKYEQLQQMSEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPE
Subjt:  MSGEEEENAAELKIGDEFLKVKCLMNCEVSLILEHKYEQLQQMSEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPE

Query:  TVEEAIAMVPSLKIKGRAHDDEAIKKMLNDLSLIKKFE
        TVEEAIAMVPSLK KGR HDDEAI+KMLNDLSLIKKFE
Subjt:  TVEEAIAMVPSLKIKGRAHDDEAIKKMLNDLSLIKKFE

XP_030924038.1 DNA-directed RNA polymerase II subunit 4 [Quercus lobata]

1.4e-66

96.38

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Query:  MSGEEEENAAELKIGDEFLKVKCLMNCEVSLILEHKYEQLQQMSEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPE
        MSGEEEENAAELKIGDEFLK KCLMNCEV+LILEHKYEQLQQMSEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPE
Subjt:  MSGEEEENAAELKIGDEFLKVKCLMNCEVSLILEHKYEQLQQMSEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPE

Query:  TVEEAIAMVPSLKIKGRAHDDEAIKKMLNDLSLIKKFE
        TVEEAIAMVPS+K KGRAHDDEAI+KMLNDLSLIKKFE
Subjt:  TVEEAIAMVPSLKIKGRAHDDEAIKKMLNDLSLIKKFE

TrEMBL top hits

e value

%identity

Alignment

A0A2N9G2U2 RPOL4c domain-containing protein

6.6e-67

96.38

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Query:  MSGEEEENAAELKIGDEFLKVKCLMNCEVSLILEHKYEQLQQMSEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPE
        MSGEEEENAAELKIGDEFLK KCLMNCEV+LILEHKYEQLQQMSEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPE
Subjt:  MSGEEEENAAELKIGDEFLKVKCLMNCEVSLILEHKYEQLQQMSEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPE

Query:  TVEEAIAMVPSLKIKGRAHDDEAIKKMLNDLSLIKKFE
        TVEEAIAMVPS+K KGRAHDDEAI+KMLNDLSLIKKFE
Subjt:  TVEEAIAMVPSLKIKGRAHDDEAIKKMLNDLSLIKKFE

A0A6A1VC16 DNA-directed RNA polymerase II subunit 4

6.6e-67

96.38

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Query:  MSGEEEENAAELKIGDEFLKVKCLMNCEVSLILEHKYEQLQQMSEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPE
        MSGEEEENAAELKIGDEFLK KCLMNCEV+LILEHKYEQLQQMSEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPE
Subjt:  MSGEEEENAAELKIGDEFLKVKCLMNCEVSLILEHKYEQLQQMSEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPE

Query:  TVEEAIAMVPSLKIKGRAHDDEAIKKMLNDLSLIKKFE
        TVEEAIAMVPS+K KGRAHDDEAI+KMLNDLSLIKKFE
Subjt:  TVEEAIAMVPSLKIKGRAHDDEAIKKMLNDLSLIKKFE

A0A6J1BWW4 DNA-directed RNA polymerase II subunit 4

1.7e-67

97.83

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Query:  MSGEEEENAAELKIGDEFLKVKCLMNCEVSLILEHKYEQLQQMSEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPE
        MSGEEEENAAELKIGDEFLK KCLMNCEVSLILEHKYEQLQQMSEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPE
Subjt:  MSGEEEENAAELKIGDEFLKVKCLMNCEVSLILEHKYEQLQQMSEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPE

Query:  TVEEAIAMVPSLKIKGRAHDDEAIKKMLNDLSLIKKFE
        TVEEAIAMVPSLK KGRAHDDEAI+KMLNDLSLIKKFE
Subjt:  TVEEAIAMVPSLKIKGRAHDDEAIKKMLNDLSLIKKFE

A0A6J1GS12 DNA-directed RNA polymerase II subunit 4

5.1e-67

97.1

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Query:  MSGEEEENAAELKIGDEFLKVKCLMNCEVSLILEHKYEQLQQMSEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPE
        MSGEEEENAAELKIGDEFLK KCLMNCEVSLILEHKYEQLQQMSEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPE
Subjt:  MSGEEEENAAELKIGDEFLKVKCLMNCEVSLILEHKYEQLQQMSEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPE

Query:  TVEEAIAMVPSLKIKGRAHDDEAIKKMLNDLSLIKKFE
        TVEEAIAMVPSLK KGR HDDEAI+KMLNDLSLIKKFE
Subjt:  TVEEAIAMVPSLKIKGRAHDDEAIKKMLNDLSLIKKFE

A0A6J1JHK7 DNA-directed RNA polymerase II subunit 4

5.1e-67

97.1

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Query:  MSGEEEENAAELKIGDEFLKVKCLMNCEVSLILEHKYEQLQQMSEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPE
        MSGEEEENAAELKIGDEFLK KCLMNCEVSLILEHKYEQLQQMSEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPE
Subjt:  MSGEEEENAAELKIGDEFLKVKCLMNCEVSLILEHKYEQLQQMSEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPE

Query:  TVEEAIAMVPSLKIKGRAHDDEAIKKMLNDLSLIKKFE
        TVEEAIAMVPSLK KGR HDDEAI+KMLNDLSLIKKFE
Subjt:  TVEEAIAMVPSLKIKGRAHDDEAIKKMLNDLSLIKKFE

SwissProt top hits

e value

%identity

Alignment

O15514 DNA-directed RNA polymerase II subunit RPB4

1.5e-20

39.42

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

Query:  VEEAIAMVPSLKIKGRAHDDEAIKKMLNDLSLIKKFE
         EE+ A++PSL  +GR  +DE ++++L+D+   + F+
Subjt:  VEEAIAMVPSLKIKGRAHDDEAIKKMLNDLSLIKKFE

O48890 DNA-directed RNA polymerase II subunit 4

1.7e-67

92.75

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Query:  MSGEEEENAAELKIGDEFLKVKCLMNCEVSLILEHKYEQLQQMSEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPE
        MSGEEEENAAELKIGDEFLK KCLMNCEVSLILEHK+EQLQQ+SEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSR+QL EFELCVLGNLCPE
Subjt:  MSGEEEENAAELKIGDEFLKVKCLMNCEVSLILEHKYEQLQQMSEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPE

Query:  TVEEAIAMVPSLKIKGRAHDDEAIKKMLNDLSLIKKFE
        TVEEA+AMVPSLK KGRAHDDEAI+KMLNDLSL+K+FE
Subjt:  TVEEAIAMVPSLKIKGRAHDDEAIKKMLNDLSLIKKFE

Q54S04 DNA-directed RNA polymerase II subunit rpb4

7.2e-18

37.41

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

Query:  LCVLGNLCPETVEEAIAMVPSLKIKGRAHDDEAIKKMLNDLSLIKKF
        +  L NLCPE  +EA +++PSLK   +  DDE ++ +L++LS ++KF
Subjt:  LCVLGNLCPETVEEAIAMVPSLKIKGRAHDDEAIKKMLNDLSLIKKF

Q9D7M8 DNA-directed RNA polymerase II subunit RPB4

1.5e-20

39.42

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

Query:  VEEAIAMVPSLKIKGRAHDDEAIKKMLNDLSLIKKFE
         EE+ A++PSL  +GR  +DE ++++L+D+   + F+
Subjt:  VEEAIAMVPSLKIKGRAHDDEAIKKMLNDLSLIKKFE

Q9VEA5 DNA-directed RNA polymerase II subunit Rpb4

3.0e-16

38.1

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

Query:  IAMVPSLKIKGRAHDDEAIKKMLNDL
         A++PSL  +GR  +DE ++++L+D+
Subjt:  IAMVPSLKIKGRAHDDEAIKKMLNDL

Arabidopsis top hits

e value

%identity

Alignment

AT4G15950.1 RNA polymerase II, Rpb4, core protein

2.6e-15

36.75

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

Query:  EAIKKMLNDLSLIKKFE
        + ++  L +LS +KK E
Subjt:  EAIKKMLNDLSLIKKFE

AT5G09920.1 RNA polymerase II, Rpb4, core protein

1.2e-68

92.75

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Query:  MSGEEEENAAELKIGDEFLKVKCLMNCEVSLILEHKYEQLQQMSEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPE
        MSGEEEENAAELKIGDEFLK KCLMNCEVSLILEHK+EQLQQ+SEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSR+QL EFELCVLGNLCPE
Subjt:  MSGEEEENAAELKIGDEFLKVKCLMNCEVSLILEHKYEQLQQMSEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPE

Query:  TVEEAIAMVPSLKIKGRAHDDEAIKKMLNDLSLIKKFE
        TVEEA+AMVPSLK KGRAHDDEAI+KMLNDLSL+K+FE
Subjt:  TVEEAIAMVPSLKIKGRAHDDEAIKKMLNDLSLIKKFE

Sequences

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CDS sequence

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ATGTCTGGTGAAGAGGAAGAAAATGCTGCAGAGCTTAAAATTGGGGATGAGTTCTTAAAGGTCAAGTGTTTAATGAATTGTGAAGTTTCTTTGATCCTTGAACAC
AAATATGAGCAGCTCCAGCAGATGTCTGAGGATCCAATGAATCAAGTTTCTCAAGTGTTCGAAAAGTCATTGCAGTACGTGAAACGTTTCAGCCGCTATAAAAAT
CCTGACGCTGTTAGACAAGTACGAGAAATTCTAAGCAGATATCAGTTGGCCGAGTTTGAGCTCTGTGTTCTTGGCAACCTTTGCCCTGAAACTGTGGAGGAAGCT
ATTGCCATGGTTCCATCTTTGAAGATTAAAGGGAGGGCGCATGATGATGAAGCAATCAAGAAGATGTTGAATGACCTCTCGTTAATCAAAAAGTTTGAGTAG

mRNA sequence

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Protein sequence

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MSGEEEENAAELKIGDEFLKVKCLMNCEVSLILEHKYEQLQQMSEDPMNQVSQVFEKSLQYVKRFSRYKNPDAVRQVREILSRYQLAEFELCVLGNLCPETVEEA
IAMVPSLKIKGRAHDDEAIKKMLNDLSLIKKFE

Lcy06g011330 (gene) of Sponge gourd (P93075) v1 genome