Cla009928 (gene) Watermelon (97103) v1 | Cucurbit Genomics Database (CuGenDB)

Overview


Name	Cla009928
Type	gene
Organism	Citrullus. lanatus (Watermelon (97103) v1)
Description	Sigma factor binding protein 1 (AHRD V1 ***- D1MWZ4_CITLA); contains Interpro domain(s) IPR008889 VQ
Location	Chr5 : 33544189 .. 33544629 (-)

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Gene Expression

Sequences

The following sequences are available for this feature:

Gene sequence (with intron)

Legend: CDS

Hold the cursor over a type above to highlight its positions in the sequence below.

ATGAATGTAACCGGCAAAAAACAGGCAAAAAGAAGCAGGAAATCGGCGGCAGCCGATTTCAAAGTCGTGTACATTTCGAGTCCGATGAAGGTGAAAACCAGCGCCTCGAAGTTCCGATCTCTCGTTCAGAAACTCACCGGTCAGGACTCCGATGCCAAAAGGTTCATGGAACTGACCGCCTCCGCCGCTAGTGATCGGAATCTTCAATCCTCGGCTTCGGCGACGTTCTTCGACTACCAACTCCTCGGCGACGACGATCTAGTGGTGGCAGGAAAGGTCGAAACAGCGGCGTACGAATCGTCGGTTGCGGCTCTCCCGCCGCAGGATGATTTGGCGGTTCTGCAGAATTTGGATACGAGTTTTGGAGGAATGTTCCATGGCTTTTGGTTTGATTCTTCTACGGCACAGGCTGAGATGCCAGGTTTAAATGCACTACTTTAG

mRNA sequence

ATGAATGTAACCGGCAAAAAACAGGCAAAAAGAAGCAGGAAATCGGCGGCAGCCGATTTCAAAGTCGTGTACATTTCGAGTCCGATGAAGGTGAAAACCAGCGCCTCGAAGTTCCGATCTCTCGTTCAGAAACTCACCGGTCAGGACTCCGATGCCAAAAGGTTCATGGAACTGACCGCCTCCGCCGCTAGTGATCGGAATCTTCAATCCTCGGCTTCGGCGACGTTCTTCGACTACCAACTCCTCGGCGACGACGATCTAGTGGTGGCAGGAAAGGTCGAAACAGCGGCGTACGAATCGTCGGTTGCGGCTCTCCCGCCGCAGGATGATTTGGCGGTTCTGCAGAATTTGGATACGAGTTTTGGAGGAATGTTCCATGGCTTTTGGTTTGATTCTTCTACGGCACAGGCTGAGATGCCAGGTTTAAATGCACTACTTTAG

Coding sequence (CDS)

ATGAATGTAACCGGCAAAAAACAGGCAAAAAGAAGCAGGAAATCGGCGGCAGCCGATTTCAAAGTCGTGTACATTTCGAGTCCGATGAAGGTGAAAACCAGCGCCTCGAAGTTCCGATCTCTCGTTCAGAAACTCACCGGTCAGGACTCCGATGCCAAAAGGTTCATGGAACTGACCGCCTCCGCCGCTAGTGATCGGAATCTTCAATCCTCGGCTTCGGCGACGTTCTTCGACTACCAACTCCTCGGCGACGACGATCTAGTGGTGGCAGGAAAGGTCGAAACAGCGGCGTACGAATCGTCGGTTGCGGCTCTCCCGCCGCAGGATGATTTGGCGGTTCTGCAGAATTTGGATACGAGTTTTGGAGGAATGTTCCATGGCTTTTGGTTTGATTCTTCTACGGCACAGGCTGAGATGCCAGGTTTAAATGCACTACTTTAG

Protein sequence

MNVTGKKQAKRSRKSAAADFKVVYISSPMKVKTSASKFRSLVQKLTGQDSDAKRFMELTASAASDRNLQSSASATFFDYQLLGDDDLVVAGKVETAAYESSVAALPPQDDLAVLQNLDTSFGGMFHGFWFDSSTAQAEMPGLNALL

Homology

[Close]

BLAST of Cla009928 vs. Swiss-Prot
Match: SIB1_ARATH (Sigma factor binding protein 1, chloroplastic OS=Arabidopsis thaliana GN=SIB1 PE=1 SV=1)

HSP 1 Score: 53.5 bits (127), Expect = 2.2e-06
Identity = 41/127 (32.28%), Postives = 67/127 (52.76%), Query Frame = 1


Query: 6   KKQAKRSRKSAAAD--FKVVYISSPMKVKTSASKFRSLVQKLTGQDSDAKRFMELTASAA 65
           +K  K+ +K+ + +   KV YIS+PM+V+T ASKFR LVQ+LTGQD+   +   + + ++
Sbjct: 24  RKSPKQKKKTTSTNKPIKVRYISNPMRVQTCASKFRELVQELTGQDAVDLQPEPIYSPSS 83

Query: 66  SDRNLQSSASATFFDYQLLGDDDLVVAGKVETAAYESSVAALPPQDDLAVLQNLDTSFGG 125
            D NL  S  A     ++L  +     G+ ++  YE   A     +D+ +   +   F G
Sbjct: 84  DDHNL--SPPAENLAPRVLHQEPF---GERDSDCYEPLNA-----EDMFLPDQMSAGFSG 140

Query: 126 MF-HGFW 130
            F +GF+
Sbjct: 144 FFSNGFY 140

[Close]

BLAST of Cla009928 vs. TrEMBL
Match: D1MWZ4_CITLA (Sigma factor binding protein 1 OS=Citrullus lanatus subsp. vulgaris GN=CitSIB PE=2 SV=1)

HSP 1 Score: 271.9 bits (694), Expect = 4.4e-70
Identity = 140/146 (95.89%), Postives = 142/146 (97.26%), Query Frame = 1


Query: 1   MNVTGKKQAKRSRKSAAADFKVVYISSPMKVKTSASKFRSLVQKLTGQDSDAKRFMELTA 60
           MNVTGKKQAKRSRKSAAADFKVVYISSPMKVKTSASKFRSLVQ+LTGQDSDA+RFMELTA
Sbjct: 1   MNVTGKKQAKRSRKSAAADFKVVYISSPMKVKTSASKFRSLVQRLTGQDSDAERFMELTA 60

Query: 61  SAASDRNLQSSASATFFDYQLLGDDDLVVAGKVETAAYESSVAALPPQDDLAVLQNLDTS 120
           SAASDRNLQSSASATFFDYQLLGDDDLVVAGKVETAAYESSVAALPP DDLAVL NLD S
Sbjct: 61  SAASDRNLQSSASATFFDYQLLGDDDLVVAGKVETAAYESSVAALPPPDDLAVLHNLDAS 120

Query: 121 FGGMFHGFWFDSSTAQAEMPGLNALL 147
           FGGMFHGFWFDS TAQAEMPGLNALL
Sbjct: 121 FGGMFHGFWFDSFTAQAEMPGLNALL 146

[Close]

BLAST of Cla009928 vs. TrEMBL
Match: A0A0A0KTR9_CUCSA (Uncharacterized protein OS=Cucumis sativus GN=Csa_5G623915 PE=4 SV=1)

HSP 1 Score: 180.6 bits (457), Expect = 1.3e-42
Identity = 97/146 (66.44%), Postives = 118/146 (80.82%), Query Frame = 1


Query: 1   MNVTGKKQAKRSRKSAAADFKVVYISSPMKVKTSASKFRSLVQKLTGQDSDAKRFMELTA 60
           M VTGKKQAKRS+KSA A FKVVYISSPMKVKTSASKFRSLVQKLTGQDSDA+RFME+ A
Sbjct: 1   MIVTGKKQAKRSKKSAGAGFKVVYISSPMKVKTSASKFRSLVQKLTGQDSDAERFMEM-A 60

Query: 61  SAASDRNLQSSASATFFDYQLLGDDDLVVAGKVETAAYESSVAALPPQDDLAVLQNLDTS 120
           S  SD N +  ASA+F D+Q++G++D++V GKV     E+ V  + P D+LA LQNLD +
Sbjct: 61  SGGSDGNGEWWASASFVDHQVMGEEDVMVGGKV-----EAGVGGVSPLDELAFLQNLDGN 120

Query: 121 FGGMFHGFWFDSSTAQAEMPGLNALL 147
           +  M +GFW DSSTA++EMPGL+ALL
Sbjct: 121 YAEMLNGFWHDSSTAESEMPGLSALL 140

[Close]

BLAST of Cla009928 vs. TrEMBL
Match: A0A067L8W8_JATCU (Uncharacterized protein OS=Jatropha curcas GN=JCGZ_24548 PE=4 SV=1)

HSP 1 Score: 80.5 bits (197), Expect = 1.9e-12
Identity = 44/71 (61.97%), Postives = 56/71 (78.87%), Query Frame = 1


Query: 1  MNVTGKKQAKRSRKSAAADFKVVYISSPMKVKTSASKFRSLVQKLTGQDSDAKRFMELTA 60
          +N+  K+QAKRS+K+     KVVYISSPMKV+TSASKFR+LVQ+LTG+DSDA RFM++  
Sbjct: 6  VNMKNKRQAKRSKKA----IKVVYISSPMKVQTSASKFRALVQELTGKDSDAARFMDVN- 65

Query: 61 SAASDRNLQSS 72
              D+NL SS
Sbjct: 66 --GGDQNLNSS 69

[Close]

BLAST of Cla009928 vs. TrEMBL
Match: A0A061FST3_THECC (Sigma factor binding protein 1, putative OS=Theobroma cacao GN=TCM_045032 PE=4 SV=1)

HSP 1 Score: 73.2 bits (178), Expect = 3.0e-10
Identity = 54/122 (44.26%), Postives = 74/122 (60.66%), Query Frame = 1


Query: 6   KKQAKRSRKSAAADFKVVYISSPMKVKTSASKFRSLVQKLTGQDSDAK-RFMELTASAAS 65
           KK +KRS  ++  D KVVYISSPMKVKT AS+FR+LVQ+LTG+DSD   +FM+   +  S
Sbjct: 13  KKHSKRS--NSKKDIKVVYISSPMKVKTCASQFRALVQELTGKDSDVSVQFMD---NYGS 72

Query: 66  DRNLQSSASATFFDYQLLGDDDLVVAG-KVETAAYESSVAALPPQDDLAVLQNLDTSFGG 125
             N  + +  T    + + DDD VV G  +  + +E SV    P DD  +++    SF G
Sbjct: 73  SENSPTHSDVTTTTTERVVDDDRVVRGLPLGNSNHEFSV--FEPFDDGLIMEG---SFLG 124

[Close]

BLAST of Cla009928 vs. TrEMBL
Match: M5XE50_PRUPE (Uncharacterized protein OS=Prunus persica GN=PRUPE_ppa013276mg PE=4 SV=1)

HSP 1 Score: 72.8 bits (177), Expect = 3.9e-10
Identity = 36/52 (69.23%), Postives = 44/52 (84.62%), Query Frame = 1


Query: 6  KKQAKRSRKSAAADFKVVYISSPMKVKTSASKFRSLVQKLTGQDSDAKRFME 58
          K   K+S++  +   KVVYISSPMKVKTSASKFR+LVQ+LTG+DSDA+RFME
Sbjct: 10 KSPPKQSKRRKSKGVKVVYISSPMKVKTSASKFRALVQELTGRDSDAERFME 61

[Close]

BLAST of Cla009928 vs. NCBI nr
Match: gi|270309002|dbj|BAI52954.1| (sigma factor binding protein 1 [Citrullus lanatus subsp. vulgaris])

HSP 1 Score: 271.9 bits (694), Expect = 6.3e-70
Identity = 140/146 (95.89%), Postives = 142/146 (97.26%), Query Frame = 1


Query: 1   MNVTGKKQAKRSRKSAAADFKVVYISSPMKVKTSASKFRSLVQKLTGQDSDAKRFMELTA 60
           MNVTGKKQAKRSRKSAAADFKVVYISSPMKVKTSASKFRSLVQ+LTGQDSDA+RFMELTA
Sbjct: 1   MNVTGKKQAKRSRKSAAADFKVVYISSPMKVKTSASKFRSLVQRLTGQDSDAERFMELTA 60

Query: 61  SAASDRNLQSSASATFFDYQLLGDDDLVVAGKVETAAYESSVAALPPQDDLAVLQNLDTS 120
           SAASDRNLQSSASATFFDYQLLGDDDLVVAGKVETAAYESSVAALPP DDLAVL NLD S
Sbjct: 61  SAASDRNLQSSASATFFDYQLLGDDDLVVAGKVETAAYESSVAALPPPDDLAVLHNLDAS 120

Query: 121 FGGMFHGFWFDSSTAQAEMPGLNALL 147
           FGGMFHGFWFDS TAQAEMPGLNALL
Sbjct: 121 FGGMFHGFWFDSFTAQAEMPGLNALL 146

[Close]

BLAST of Cla009928 vs. NCBI nr
Match: gi|659092245|ref|XP_008446972.1| (PREDICTED: sigma factor binding protein 1, chloroplastic-like [Cucumis melo])

HSP 1 Score: 191.8 bits (486), Expect = 8.3e-46
Identity = 105/146 (71.92%), Postives = 117/146 (80.14%), Query Frame = 1


Query: 1   MNVTGKKQAKRSRKSAAADFKVVYISSPMKVKTSASKFRSLVQKLTGQDSDAKRFMELTA 60
           MNVTGKKQAKRS+KS AADFKVVYISSPMKVKTSASKFRSLVQKLTGQDSDA+RFME+ A
Sbjct: 1   MNVTGKKQAKRSKKSTAADFKVVYISSPMKVKTSASKFRSLVQKLTGQDSDAERFMEM-A 60

Query: 61  SAASDRNLQSSASATFFDYQLLGDDDLVVAGKVETAAYESSVAALPPQDDLAVLQNLDTS 120
           S ASD N QS ASA+F D QL+G++D+VV GK E A        + P DDL  LQNLD +
Sbjct: 61  SGASDGNGQSWASASFLDQQLMGEEDVVVGGKEEAA-----FGGVNPADDLVFLQNLDGN 120

Query: 121 FGGMFHGFWFDSSTAQAEMPGLNALL 147
           F  MF+GFW DSSTAQ EM GL+ALL
Sbjct: 121 FAEMFNGFWHDSSTAQTEMTGLSALL 140

[Close]

BLAST of Cla009928 vs. NCBI nr
Match: gi|449449264|ref|XP_004142385.1| (PREDICTED: uncharacterized protein LOC101217123 [Cucumis sativus])

HSP 1 Score: 180.6 bits (457), Expect = 1.9e-42
Identity = 97/146 (66.44%), Postives = 118/146 (80.82%), Query Frame = 1


Query: 1   MNVTGKKQAKRSRKSAAADFKVVYISSPMKVKTSASKFRSLVQKLTGQDSDAKRFMELTA 60
           M VTGKKQAKRS+KSA A FKVVYISSPMKVKTSASKFRSLVQKLTGQDSDA+RFME+ A
Sbjct: 1   MIVTGKKQAKRSKKSAGAGFKVVYISSPMKVKTSASKFRSLVQKLTGQDSDAERFMEM-A 60

Query: 61  SAASDRNLQSSASATFFDYQLLGDDDLVVAGKVETAAYESSVAALPPQDDLAVLQNLDTS 120
           S  SD N +  ASA+F D+Q++G++D++V GKV     E+ V  + P D+LA LQNLD +
Sbjct: 61  SGGSDGNGEWWASASFVDHQVMGEEDVMVGGKV-----EAGVGGVSPLDELAFLQNLDGN 120

Query: 121 FGGMFHGFWFDSSTAQAEMPGLNALL 147
           +  M +GFW DSSTA++EMPGL+ALL
Sbjct: 121 YAEMLNGFWHDSSTAESEMPGLSALL 140

[Close]

BLAST of Cla009928 vs. NCBI nr
Match: gi|802574171|ref|XP_012068696.1| (PREDICTED: uncharacterized protein LOC105631246 [Jatropha curcas])

HSP 1 Score: 80.5 bits (197), Expect = 2.7e-12
Identity = 44/71 (61.97%), Postives = 56/71 (78.87%), Query Frame = 1


Query: 1  MNVTGKKQAKRSRKSAAADFKVVYISSPMKVKTSASKFRSLVQKLTGQDSDAKRFMELTA 60
          +N+  K+QAKRS+K+     KVVYISSPMKV+TSASKFR+LVQ+LTG+DSDA RFM++  
Sbjct: 6  VNMKNKRQAKRSKKA----IKVVYISSPMKVQTSASKFRALVQELTGKDSDAARFMDVN- 65

Query: 61 SAASDRNLQSS 72
              D+NL SS
Sbjct: 66 --GGDQNLNSS 69

[Close]

BLAST of Cla009928 vs. NCBI nr
Match: gi|969999712|ref|XP_015084304.1| (PREDICTED: sigma factor binding protein 1, chloroplastic-like [Solanum pennellii])

HSP 1 Score: 75.1 bits (183), Expect = 1.1e-10
Identity = 39/65 (60.00%), Postives = 47/65 (72.31%), Query Frame = 1


Query: 6  KKQAKRSRKSAAADFKVVYISSPMKVKTSASKFRSLVQKLTGQDSDAKRFMELTASAASD 65
          K++ K   KS  A+FKVVYIS+PMKVKTSAS+FRSLVQ+LTGQDSD  R ME   S    
Sbjct: 7  KQKRKDGYKSKKANFKVVYISTPMKVKTSASRFRSLVQELTGQDSDIARIMETNGSITEY 66

Query: 66 RNLQS 71
           ++ S
Sbjct: 67 EDIHS 71

The following BLAST results are available for this feature:

BLAST of Cla009928 vs. Swiss-Prot


Match Name	E-value	Identity	Description
SIB1_ARATH	2.2e-06	32.28	Sigma factor binding protein 1, chloroplastic OS=Arabidopsis thaliana GN=SIB1 PE...	[more]

BLAST of Cla009928 vs. TrEMBL


Match Name	E-value	Identity	Description
D1MWZ4_CITLA	4.4e-70	95.89	Sigma factor binding protein 1 OS=Citrullus lanatus subsp. vulgaris GN=CitSIB PE...	[more]
A0A0A0KTR9_CUCSA	1.3e-42	66.44	Uncharacterized protein OS=Cucumis sativus GN=Csa_5G623915 PE=4 SV=1	[more]
A0A067L8W8_JATCU	1.9e-12	61.97	Uncharacterized protein OS=Jatropha curcas GN=JCGZ_24548 PE=4 SV=1	[more]
A0A061FST3_THECC	3.0e-10	44.26	Sigma factor binding protein 1, putative OS=Theobroma cacao GN=TCM_045032 PE=4 S...	[more]
M5XE50_PRUPE	3.9e-10	69.23	Uncharacterized protein OS=Prunus persica GN=PRUPE_ppa013276mg PE=4 SV=1	[more]

BLAST of Cla009928 vs. NCBI nr


Match Name	E-value	Identity	Description
gi\|270309002\|dbj\|BAI52954.1\|	6.3e-70	95.89	sigma factor binding protein 1 [Citrullus lanatus subsp. vulgaris]	[more]
gi\|659092245\|ref\|XP_008446972.1\|	8.3e-46	71.92	PREDICTED: sigma factor binding protein 1, chloroplastic-like [Cucumis melo]	[more]
gi\|449449264\|ref\|XP_004142385.1\|	1.9e-42	66.44	PREDICTED: uncharacterized protein LOC101217123 [Cucumis sativus]	[more]
gi\|802574171\|ref\|XP_012068696.1\|	2.7e-12	61.97	PREDICTED: uncharacterized protein LOC105631246 [Jatropha curcas]	[more]
gi\|969999712\|ref\|XP_015084304.1\|	1.1e-10	60.00	PREDICTED: sigma factor binding protein 1, chloroplastic-like [Solanum pennellii...	[more]

Annotated Terms

The following terms have been associated with this gene:

Vocabulary: **INTERPRO**
Term	Definition
IPR008889	VQ

GO Annotation

GO Assignments

This gene is annotated with the following GO terms.

Category	Term Accession	Term Name
biological_process	GO:0008150	biological_process
biological_process	GO:0071482	cellular response to light stimulus
biological_process	GO:0006952	defense response
biological_process	GO:0009816	defense response to bacterium, incompatible interaction
biological_process	GO:0051091	positive regulation of sequence-specific DNA binding transcription factor activity
cellular_component	GO:0005575	cellular_component
cellular_component	GO:0009507	chloroplast
cellular_component	GO:0005634	nucleus
cellular_component	GO:0009536	plastid
molecular_function	GO:0003674	molecular_function
molecular_function	GO:0005515	protein binding

Relationships

The following mRNA feature(s) are a part of this gene:


Feature Name	Unique Name	Type
Cla009928	Cla009928.1	mRNA

InterPro

Analysis Name: InterPro Annotations of watermelon (97103)
Date Performed: 2016-09-28


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
IPR008889	VQ	PFAM	PF05678	VQ	coord: 25..51 score: 1.0
None	No IPR available	PANTHER	PTHR33624	FAMILY NOT NAMED	coord: 6..75 score: 6.2
None	No IPR available	PANTHER	PTHR33624:SF5	SUBFAMILY NOT NAMED	coord: 6..75 score: 6.2

Synteny

The following gene(s) are orthologous to this gene:


Gene	Orthologue	Organism	Block
Cla009928	MELO3C012484	Melon (DHL92) v3.5.1	mewmB062
Cla009928	ClCG05G026910	Watermelon (Charleston Gray)	wcgwmB285
Cla009928	Cucsa.307850	Cucumber (Gy14) v1	cgywmB560
Cla009928	CmaCh18G008500	Cucurbita maxima (Rimu)	cmawmB376
Cla009928	CmaCh04G013220	Cucurbita maxima (Rimu)	cmawmB705
Cla009928	CmoCh04G013940	Cucurbita moschata (Rifu)	cmowmB701
Cla009928	Lsi04G000180	Bottle gourd (USVL1VR-Ls)	lsiwmB320
Cla009928	CsGy5G027140	Cucumber (Gy14) v2	cgybwmB371
Cla009928	MELO3C012484.2	Melon (DHL92) v3.6.1	medwmB062
Cla009928	Carg14413	Silver-seed gourd	carwmB0722
Cla009928	Carg02002	Silver-seed gourd	carwmB0840
Cla009928	CsaV3_5G036860	Cucumber (Chinese Long) v3	cucwmB422
Cla009928	Bhi07G001017	Wax gourd	wgowmB553

The following gene(s) are paralogous to this gene:

None

The following block(s) are covering this gene:


Gene	Organism	Block
Cla009928	Watermelon (97103) v2	wmwmbB207
Cla009928	Cucurbita moschata (Rifu)	cmowmB368
Cla009928	Cucumber (Chinese Long) v2	cuwmB396
Cla009928	Cucurbita pepo (Zucchini)	cpewmB029
Cla009928	Cucurbita pepo (Zucchini)	cpewmB435