CuGenDBv2

Gene ID	HG10018330
Organism	Lagenaria siceraria cv. Hangzhou Gourd (Bottle gourd (Hangzhou Gourd) v1)
Description	DNA-directed RNA polymerase II subunit 4-like
Genome location	Chr04:3135049..3136683
RNA-Seq Expression	HG10018330
Synteny	HG10018330
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

KAG7033258.1 DNA-directed RNA polymerase II subunit 4 [Cucurbita argyrosperma subsp. argyrosperma]

6.1e-58

94.35

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Query:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQLCVLGNLCPETVEEATSIVPSLKT
        MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQ +EDP NQVSQVFEKSLQYVKRFSRYKNPDAVRQLCVLGNLCPETVEEA ++VPSLK 
Subjt:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQLCVLGNLCPETVEEATSIVPSLKT

Query:  KGRVHDDEAIEKMLNDLSLIKKFE
        KGRVHDDEAIEKMLNDLSLIKKFE
Subjt:  KGRVHDDEAIEKMLNDLSLIKKFE

TYK00568.1 DNA-directed RNA polymerase II subunit 4-like [Cucumis melo var. makuwa]

4.2e-59

91.79

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Query:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQ----------LCVLGNLCPETVEE
        MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQ+SQVFEKSLQYVKRFSRYKNPDAVRQ          LCVLGNLCPETVEE
Subjt:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQ----------LCVLGNLCPETVEE

Query:  ATSIVPSLKTKGRVHDDEAIEKMLNDLSLIKKFE
        ATSIVPSLKTKGRVHDDEAIEKMLNDLSLIKKFE
Subjt:  ATSIVPSLKTKGRVHDDEAIEKMLNDLSLIKKFE

XP_004141497.1 DNA-directed RNA polymerase II subunit 4 [Cucumis sativus]

2.8e-58

89.13

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Query:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQ--------------LCVLGNLCPE
        MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQ              LCVLGNLCPE
Subjt:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQ--------------LCVLGNLCPE

Query:  TVEEATSIVPSLKTKGRVHDDEAIEKMLNDLSLIKKFE
        TVEEATSIVPSLKTKGRVH+DEAIEKMLNDLSLIKKFE
Subjt:  TVEEATSIVPSLKTKGRVHDDEAIEKMLNDLSLIKKFE

XP_008459458.1 PREDICTED: DNA-directed RNA polymerase II subunit 4-like [Cucumis melo]

1.2e-58

89.13

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Query:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQ--------------LCVLGNLCPE
        MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQ+SQVFEKSLQYVKRFSRYKNPDAVRQ              LCVLGNLCPE
Subjt:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQ--------------LCVLGNLCPE

Query:  TVEEATSIVPSLKTKGRVHDDEAIEKMLNDLSLIKKFE
        TVEEATSIVPSLKTKGRVHDDEAIEKMLNDLSLIKKFE
Subjt:  TVEEATSIVPSLKTKGRVHDDEAIEKMLNDLSLIKKFE

XP_038890773.1 DNA-directed RNA polymerase II subunit 4-like [Benincasa hispida]

6.1e-58

88.41

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Query:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQ--------------LCVLGNLCPE
        MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQ              LCVLGNLCPE
Subjt:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQ--------------LCVLGNLCPE

Query:  TVEEATSIVPSLKTKGRVHDDEAIEKMLNDLSLIKKFE
        TVEEA S+VPSLKTKGRVHDDEAIEKMLNDLSLIKKFE
Subjt:  TVEEATSIVPSLKTKGRVHDDEAIEKMLNDLSLIKKFE

TrEMBL top hits

e value

%identity

Alignment

A0A0A0KXP7 RPOL4c domain-containing protein

3.0e-58

96.77

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Query:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQLCVLGNLCPETVEEATSIVPSLKT
        MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDA   LCVLGNLCPETVEEATSIVPSLKT
Subjt:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQLCVLGNLCPETVEEATSIVPSLKT

Query:  KGRVHDDEAIEKMLNDLSLIKKFE
        KGRVH+DEAIEKMLNDLSLIKKFE
Subjt:  KGRVHDDEAIEKMLNDLSLIKKFE

A0A1S3CA78 DNA-directed RNA polymerase II subunit 4-like

6.0e-59

89.13

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Query:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQ--------------LCVLGNLCPE
        MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQ+SQVFEKSLQYVKRFSRYKNPDAVRQ              LCVLGNLCPE
Subjt:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQ--------------LCVLGNLCPE

Query:  TVEEATSIVPSLKTKGRVHDDEAIEKMLNDLSLIKKFE
        TVEEATSIVPSLKTKGRVHDDEAIEKMLNDLSLIKKFE
Subjt:  TVEEATSIVPSLKTKGRVHDDEAIEKMLNDLSLIKKFE

A0A5A7T811 DNA-directed RNA polymerase II subunit 4-like

6.0e-59

89.13

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Query:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQ--------------LCVLGNLCPE
        MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQ+SQVFEKSLQYVKRFSRYKNPDAVRQ              LCVLGNLCPE
Subjt:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQ--------------LCVLGNLCPE

Query:  TVEEATSIVPSLKTKGRVHDDEAIEKMLNDLSLIKKFE
        TVEEATSIVPSLKTKGRVHDDEAIEKMLNDLSLIKKFE
Subjt:  TVEEATSIVPSLKTKGRVHDDEAIEKMLNDLSLIKKFE

A0A5D3BN95 DNA-directed RNA polymerase II subunit 4-like

2.1e-59

91.79

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Query:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQ----------LCVLGNLCPETVEE
        MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQ+SQVFEKSLQYVKRFSRYKNPDAVRQ          LCVLGNLCPETVEE
Subjt:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQ----------LCVLGNLCPETVEE

Query:  ATSIVPSLKTKGRVHDDEAIEKMLNDLSLIKKFE
        ATSIVPSLKTKGRVHDDEAIEKMLNDLSLIKKFE
Subjt:  ATSIVPSLKTKGRVHDDEAIEKMLNDLSLIKKFE

A0A6J1JVN3 DNA-directed RNA polymerase II subunit 4-like

1.6e-56

86.23

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Query:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQ--------------LCVLGNLCPE
        MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQ +EDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQ              LCVLGNLCPE
Subjt:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQ--------------LCVLGNLCPE

Query:  TVEEATSIVPSLKTKGRVHDDEAIEKMLNDLSLIKKFE
        TVEEA S+VPSLKTKGR HDDEAIEKMLNDLSLIKKFE
Subjt:  TVEEATSIVPSLKTKGRVHDDEAIEKMLNDLSLIKKFE

SwissProt top hits

e value

%identity

Alignment

O15514 DNA-directed RNA polymerase II subunit RPB4

4.6e-16

37.23

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Query:  SGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVR--------------QLCVLGNLCPET
        +G+ EE+A++L    EF  A+ L+N EV ++LEH+ +Q  + AED   ++S+VF K+L Y  RFSR+KN + +               +L  L NLCPET
Subjt:  SGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVR--------------QLCVLGNLCPET

Query:  VEEATSIVPSLKTKGRVHDDEAIEKMLNDLSLIKKFE
         EE+ +++PSL  +GR  D+E ++++L+D+   + F+
Subjt:  VEEATSIVPSLKTKGRVHDDEAIEKMLNDLSLIKKFE

O48890 DNA-directed RNA polymerase II subunit 4

5.4e-57

82.61

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Query:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQ--------------LCVLGNLCPE
        MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHK+EQLQQ +EDP NQVSQVFEKSLQYVKRFSRYKNPDAVRQ              LCVLGNLCPE
Subjt:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQ--------------LCVLGNLCPE

Query:  TVEEATSIVPSLKTKGRVHDDEAIEKMLNDLSLIKKFE
        TVEEA ++VPSLKTKGR HDDEAIEKMLNDLSL+K+FE
Subjt:  TVEEATSIVPSLKTKGRVHDDEAIEKMLNDLSLIKKFE

Q54S04 DNA-directed RNA polymerase II subunit rpb4

1.8e-12

31.97

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Query:  EEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAED-------------PTNQVSQVFEKSLQYVKRFSRYKNPDAVRQ--------------
        +EEE+   LK   +   AK L+N EV+++LEH+    +    +               N + + F K+L Y ++FSRYKN  +++Q              
Subjt:  EEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAED-------------PTNQVSQVFEKSLQYVKRFSRYKNPDAVRQ--------------

Query:  LCVLGNLCPETVEEATSIVPSLKTKGRVHDDEAIEKMLNDLSLIKKF
        +  L NLCPE  +EA S++PSLK   ++ DDE ++ +L++LS ++KF
Subjt:  LCVLGNLCPETVEEATSIVPSLKTKGRVHDDEAIEKMLNDLSLIKKF

Q9D7M8 DNA-directed RNA polymerase II subunit RPB4

4.6e-16

37.23

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Query:  SGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVR--------------QLCVLGNLCPET
        +G+ EE+A++L    EF  A+ L+N EV ++LEH+ +Q  + AED   ++S+VF K+L Y  RFSR+KN + +               +L  L NLCPET
Subjt:  SGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVR--------------QLCVLGNLCPET

Query:  VEEATSIVPSLKTKGRVHDDEAIEKMLNDLSLIKKFE
         EE+ +++PSL  +GR  D+E ++++L+D+   + F+
Subjt:  VEEATSIVPSLKTKGRVHDDEAIEKMLNDLSLIKKFE

Q9VEA5 DNA-directed RNA polymerase II subunit Rpb4

1.5e-11

33.33

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Query:  EENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVR--------------QLCVLGNLCPETVEEA
        +E+AA+L+   EF  A+ L+  EV ++L+H+  + Q  + D   + S+VF K+  Y   F ++KN + +               +L  LGNLCPE  EEA
Subjt:  EENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVR--------------QLCVLGNLCPETVEEA

Query:  TSIVPSLKTKGRVHDDEAIEKMLNDL
         +++PSL  +GR  D+E + ++L+D+
Subjt:  TSIVPSLKTKGRVHDDEAIEKMLNDL

Arabidopsis top hits

e value

%identity

Alignment

AT4G15950.1 RNA polymerase II, Rpb4, core protein

1.6e-11

33.05

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Query:  AKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVR--------------QLCVLGNLCPETVEEATSIVPSLKTKGRVHD
        A+C+M+CE   IL+    QL   +EDP+ ++   ++++L YV+    Y NP +VR              ++CV+ N   E+V+E  + +PSLKTK  V  
Subjt:  AKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVR--------------QLCVLGNLCPETVEEATSIVPSLKTKGRVHD

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

AT5G09920.1 RNA polymerase II, Rpb4, core protein

3.8e-58

82.61

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Query:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQ--------------LCVLGNLCPE
        MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHK+EQLQQ +EDP NQVSQVFEKSLQYVKRFSRYKNPDAVRQ              LCVLGNLCPE
Subjt:  MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQ--------------LCVLGNLCPE

Query:  TVEEATSIVPSLKTKGRVHDDEAIEKMLNDLSLIKKFE
        TVEEA ++VPSLKTKGR HDDEAIEKMLNDLSL+K+FE
Subjt:  TVEEATSIVPSLKTKGRVHDDEAIEKMLNDLSLIKKFE

Sequences

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CDS sequence

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ATGTCTGGAGAAGAAGAAGAAAATGCTGCGGAGCTTAAAATTGGGGATGAGTTCTTAAAAGCCAAGTGTTTAATGAATTGCGAAGTTTCTTTGATCCTTGAACACAAGTA
TGAGCAGCTTCAACAAAGGGCCGAGGATCCAACAAATCAAGTTTCTCAAGTGTTTGAAAAGTCATTGCAGTATGTGAAACGCTTCAGTCGCTATAAGAACCCTGATGCTG
TTAGACAACTATGTGTTCTTGGCAACCTTTGCCCTGAAACTGTGGAGGAAGCTACATCCATAGTTCCATCTTTGAAGACTAAAGGAAGGGTGCATGACGATGAAGCTATA
GAGAAGATGTTGAATGATCTTTCATTAATAAAAAAGTTTGAGTAG

mRNA sequence

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Protein sequence

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MSGEEEENAAELKIGDEFLKAKCLMNCEVSLILEHKYEQLQQRAEDPTNQVSQVFEKSLQYVKRFSRYKNPDAVRQLCVLGNLCPETVEEATSIVPSLKTKGRVHDDEAI
EKMLNDLSLIKKFE

HG10018330 (gene) of Bottle gourd (Hangzhou Gourd) v1 genome