CmaCh16G002360 (gene) Cucurbita maxima (Rimu) | Cucurbit Genomics Database (CuGenDB)

Overview


Name	CmaCh16G002360
Type	gene
Organism	Cucurbita maxima (Cucurbita maxima (Rimu))
Description	DNA-directed RNA polymerase subunit beta
Location	Cma_Chr16 : 1086444 .. 1087230 (+)

Genome Viewer

Gene Expression

Sequences

The following sequences are available for this feature:

Gene sequence (with intron)

Legend: exonCDS

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

ATGTTTCGACGGGGTGCATTTGCTGCACGAGGGGTCCTCGGCCTCCCGCTTCTAAATGGAGAACAGCCGTTGTCTGCTTCGTCGTTTCGTGGTACTTTTCAACCCTTCCTTCCTCATTCTAGCTTGCATTTAGTTCATGGCTTGATGCTTGCTGCTTGCTGCAATAATATAAGATGAATTATATGAATGTAGATCTCGAAACACGTTTTCTCAAGATTGCAGGGTTATTCGAATTCTGCTCGGGTTCTTGATGGCTGACTGTTATGATATTGTTTGTGATTATATGATCTTATTTCTGCTTTGAAACAATTCCATGTTTTTGTTGTCATCTTTTTGGGCTCTTCTGCGGTTGTTAATTCATTATGAAAGTTGTGTTAGACTTCTTAATCCATGATCATTACAGTTGAAATGATTGATCTATTGTTCTTCGTGAATCCCTTTGGTCGAATTATTCCACGACTAAAAGAAAGCTCGATTCCTTATGTTCATCGGATAAATCAAGTTTGAGCCATGGCTTTTTTTCTGCAGGTTTACATTTGTGATAGCGTTTCTCCTGTTGATAACCGGTGCTGCACTGAACGGTGGAAGGAACGAACAAAGCAGCTATTTCGATTACTACTATTGCTATGTTCTGAAACCAGGAGTTTTTGCTGTTGCCACCGTTGTGGGTGCTGCAAGTTTAGCGCTGGGATTGTTCTACTACCTCATATTGAACTCTGCAAAGAATGACCCTGCTGTGTGGGGCAATCCTTCCATTCCTCCTCCAGCAAACATTGCAATGGCATAG

mRNA sequence

ATGTTTCGACGGGGTGCATTTGCTGCACGAGGGGTCCTCGGCCTCCCGCTTCTAAATGGAGAACAGCCGTTGTCTGCTTCGTCGTTTCGTGCGTTTCTCCTGTTGATAACCGGTGCTGCACTGAACGGTGGAAGGAACGAACAAAGCAGCTATTTCGATTACTACTATTGCTATGTTCTGAAACCAGGAGTTTTTGCTGTTGCCACCGTTGTGGGTGCTGCAAGTTTAGCGCTGGGATTGTTCTACTACCTCATATTGAACTCTGCAAAGAATGACCCTGCTGTGTGGGGCAATCCTTCCATTCCTCCTCCAGCAAACATTGCAATGGCATAG

Coding sequence (CDS)

ATGTTTCGACGGGGTGCATTTGCTGCACGAGGGGTCCTCGGCCTCCCGCTTCTAAATGGAGAACAGCCGTTGTCTGCTTCGTCGTTTCGTGCGTTTCTCCTGTTGATAACCGGTGCTGCACTGAACGGTGGAAGGAACGAACAAAGCAGCTATTTCGATTACTACTATTGCTATGTTCTGAAACCAGGAGTTTTTGCTGTTGCCACCGTTGTGGGTGCTGCAAGTTTAGCGCTGGGATTGTTCTACTACCTCATATTGAACTCTGCAAAGAATGACCCTGCTGTGTGGGGCAATCCTTCCATTCCTCCTCCAGCAAACATTGCAATGGCATAG

Protein sequence

MFRRGAFAARGVLGLPLLNGEQPLSASSFRAFLLLITGAALNGGRNEQSSYFDYYYCYVLKPGVFAVATVVGAASLALGLFYYLILNSAKNDPAVWGNPSIPPPANIAMA

Homology

[Close]

BLAST of CmaCh16G002360 vs. TrEMBL
Match: A0A0A0KU80_CUCSA (Uncharacterized protein OS=Cucumis sativus GN=Csa_4G025740 PE=4 SV=1)

HSP 1 Score: 118.2 bits (295), Expect = 6.1e-24
Identity = 58/81 (71.60%), Postives = 67/81 (82.72%), Query Frame = 1


Query: 31  AFLLLITGAALNGGRNEQSSYFDYYYCYVLKPGVFAVATVVGAASLALGLFYYLILNSAK 90
           AFLL +TGAALN GR EQ +YF  Y CYVLKPGVF+ AT+VG ASL LG+ Y+LILNSAK
Sbjct: 107 AFLLFLTGAALNNGRGEQRNYFRDYDCYVLKPGVFSFATIVGMASLTLGMSYFLILNSAK 166

Query: 91  NDPA-VWGNPSIPPPANIAMA 111
           NDP+ VWG+PS+PP  NIAMA
Sbjct: 167 NDPSTVWGHPSVPPQPNIAMA 187

[Close]

BLAST of CmaCh16G002360 vs. TrEMBL
Match: A0A068U9S1_COFCA (Uncharacterized protein OS=Coffea canephora GN=GSCOC_T00019822001 PE=4 SV=1)

HSP 1 Score: 97.4 bits (241), Expect = 1.1e-17
Identity = 46/79 (58.23%), Postives = 56/79 (70.89%), Query Frame = 1


Query: 31  AFLLLITGAALNGGRNEQSSYFDYYYCYVLKPGVFAVATVVGAASLALGLFYYLILNSAK 90
           AFLLL+TGAALN    E++ YF+YYYCYV+KPGVFA A ++  AS+ LGL YY++L S K
Sbjct: 106 AFLLLLTGAALNDQHGEENMYFNYYYCYVVKPGVFAGAAILSLASVTLGLIYYVMLTSTK 165

Query: 91  NDPAVWGNPSIPPPANIAM 110
           N    WG  S P P  IAM
Sbjct: 166 NVIDAWGGSSAPVPGGIAM 184

[Close]

BLAST of CmaCh16G002360 vs. TrEMBL
Match: A0A067EBD4_CITSI (Uncharacterized protein OS=Citrus sinensis GN=CISIN_1g028344mg PE=4 SV=1)

HSP 1 Score: 94.7 bits (234), Expect = 7.3e-17
Identity = 47/79 (59.49%), Postives = 56/79 (70.89%), Query Frame = 1


Query: 31  AFLLLITGAALNGGRNEQSSYFDYYYCYVLKPGVFAVATVVGAASLALGLFYYLILNSAK 90
           AFLLL+TGAALN    E+S YF  YYCYV+KPGVFA   V+  AS+ LG+ YYL L+SAK
Sbjct: 106 AFLLLLTGAALNDQHGEESMYFGNYYCYVVKPGVFAGGAVLSLASVTLGILYYLTLHSAK 165

Query: 91  NDPAVWGNPSIPPPANIAM 110
           N   +WGN S+P    IAM
Sbjct: 166 NS-GLWGNSSVPQEGGIAM 183

[Close]

BLAST of CmaCh16G002360 vs. TrEMBL
Match: A0A067JD79_JATCU (Uncharacterized protein OS=Jatropha curcas GN=JCGZ_00583 PE=4 SV=1)

HSP 1 Score: 94.4 bits (233), Expect = 9.5e-17
Identity = 45/79 (56.96%), Postives = 55/79 (69.62%), Query Frame = 1


Query: 31  AFLLLITGAALNGGRNEQSSYFDYYYCYVLKPGVFAVATVVGAASLALGLFYYLILNSAK 90
           AFLLL+TGAALN    E+S YF  YYCYV+KPGVFA   V+  AS+ LG+ YYL LNS+K
Sbjct: 106 AFLLLLTGAALNDQHGEESMYFGNYYCYVVKPGVFAGGAVLSFASITLGILYYLTLNSSK 165

Query: 91  NDPAVWGNPSIPPPANIAM 110
           +  + WGNP +     IAM
Sbjct: 166 SINSTWGNPPVSSSTGIAM 184

[Close]

BLAST of CmaCh16G002360 vs. TrEMBL
Match: A0A061EZX5_THECC (Uncharacterized protein OS=Theobroma cacao GN=TCM_025365 PE=4 SV=1)

HSP 1 Score: 93.2 bits (230), Expect = 2.1e-16
Identity = 44/79 (55.70%), Postives = 54/79 (68.35%), Query Frame = 1


Query: 31  AFLLLITGAALNGGRNEQSSYFDYYYCYVLKPGVFAVATVVGAASLALGLFYYLILNSAK 90
           AFLLL+TG+ALN    E+S YF  YYCYV+KPGVFA   V+  AS+ LG+FYYL +N AK
Sbjct: 106 AFLLLLTGSALNDQHGEESVYFGNYYCYVVKPGVFAGGAVLALASVTLGIFYYLTVNMAK 165

Query: 91  NDPAVWGNPSIPPPANIAM 110
           +    WGN  +P    IAM
Sbjct: 166 DSTGPWGNAPVPNQGGIAM 184

[Close]

BLAST of CmaCh16G002360 vs. TAIR10
Match: AT5G17210.1 (AT5G17210.1 Protein of unknown function (DUF1218))

HSP 1 Score: 64.7 bits (156), Expect = 4.1e-11
Identity = 34/81 (41.98%), Postives = 46/81 (56.79%), Query Frame = 1


Query: 31  AFLLLITGAALNGGRNEQSSYFDYYYCYVLKPGVFAVATVVGAASLALGLFYYLILNSAK 90
           AFL+L++GAALN    E+S     Y+CY++KPGVF+   V+   ++ALG+ YYL L S K
Sbjct: 109 AFLVLLSGAALNDEHTEESMNAGTYFCYIVKPGVFSTGAVLSLVTIALGIVYYLCLTSNK 168

Query: 91  NDPA---------VWGNPSIP 103
              A           G P IP
Sbjct: 169 QIVAATTTQGTGIAMGQPQIP 189

[Close]

BLAST of CmaCh16G002360 vs. NCBI nr
Match: gi|449458299|ref|XP_004146885.1| (PREDICTED: uncharacterized protein LOC101221478 [Cucumis sativus])

HSP 1 Score: 118.2 bits (295), Expect = 8.8e-24
Identity = 58/81 (71.60%), Postives = 67/81 (82.72%), Query Frame = 1


Query: 31  AFLLLITGAALNGGRNEQSSYFDYYYCYVLKPGVFAVATVVGAASLALGLFYYLILNSAK 90
           AFLL +TGAALN GR EQ +YF  Y CYVLKPGVF+ AT+VG ASL LG+ Y+LILNSAK
Sbjct: 107 AFLLFLTGAALNNGRGEQRNYFRDYDCYVLKPGVFSFATIVGMASLTLGMSYFLILNSAK 166

Query: 91  NDPA-VWGNPSIPPPANIAMA 111
           NDP+ VWG+PS+PP  NIAMA
Sbjct: 167 NDPSTVWGHPSVPPQPNIAMA 187

[Close]

BLAST of CmaCh16G002360 vs. NCBI nr
Match: gi|659107725|ref|XP_008453825.1| (PREDICTED: uncharacterized protein LOC103494435 [Cucumis melo])

HSP 1 Score: 116.7 bits (291), Expect = 2.6e-23
Identity = 56/81 (69.14%), Postives = 67/81 (82.72%), Query Frame = 1


Query: 31  AFLLLITGAALNGGRNEQSSYFDYYYCYVLKPGVFAVATVVGAASLALGLFYYLILNSAK 90
           AFLL +TGAALN GR++Q +Y   Y CYVLKPGVF+ AT+VG ASL LG+ Y+LILNSAK
Sbjct: 105 AFLLFLTGAALNNGRDQQRNYLGNYECYVLKPGVFSFATIVGVASLTLGMSYFLILNSAK 164

Query: 91  NDPA-VWGNPSIPPPANIAMA 111
           NDP+ VWG+PS+PP  NIAMA
Sbjct: 165 NDPSTVWGHPSVPPQPNIAMA 185

[Close]

BLAST of CmaCh16G002360 vs. NCBI nr
Match: gi|661891067|emb|CDP04949.1| (unnamed protein product [Coffea canephora])

HSP 1 Score: 97.4 bits (241), Expect = 1.6e-17
Identity = 46/79 (58.23%), Postives = 56/79 (70.89%), Query Frame = 1


Query: 31  AFLLLITGAALNGGRNEQSSYFDYYYCYVLKPGVFAVATVVGAASLALGLFYYLILNSAK 90
           AFLLL+TGAALN    E++ YF+YYYCYV+KPGVFA A ++  AS+ LGL YY++L S K
Sbjct: 106 AFLLLLTGAALNDQHGEENMYFNYYYCYVVKPGVFAGAAILSLASVTLGLIYYVMLTSTK 165

Query: 91  NDPAVWGNPSIPPPANIAM 110
           N    WG  S P P  IAM
Sbjct: 166 NVIDAWGGSSAPVPGGIAM 184

[Close]

BLAST of CmaCh16G002360 vs. NCBI nr
Match: gi|641833512|gb|KDO52524.1| (hypothetical protein CISIN_1g028344mg [Citrus sinensis])

HSP 1 Score: 94.7 bits (234), Expect = 1.0e-16
Identity = 47/79 (59.49%), Postives = 56/79 (70.89%), Query Frame = 1


Query: 31  AFLLLITGAALNGGRNEQSSYFDYYYCYVLKPGVFAVATVVGAASLALGLFYYLILNSAK 90
           AFLLL+TGAALN    E+S YF  YYCYV+KPGVFA   V+  AS+ LG+ YYL L+SAK
Sbjct: 106 AFLLLLTGAALNDQHGEESMYFGNYYCYVVKPGVFAGGAVLSLASVTLGILYYLTLHSAK 165

Query: 91  NDPAVWGNPSIPPPANIAM 110
           N   +WGN S+P    IAM
Sbjct: 166 NS-GLWGNSSVPQEGGIAM 183

[Close]

BLAST of CmaCh16G002360 vs. NCBI nr
Match: gi|568877605|ref|XP_006491818.1| (PREDICTED: uncharacterized protein LOC102608001 [Citrus sinensis])

HSP 1 Score: 94.7 bits (234), Expect = 1.0e-16
Identity = 47/79 (59.49%), Postives = 56/79 (70.89%), Query Frame = 1


Query: 31  AFLLLITGAALNGGRNEQSSYFDYYYCYVLKPGVFAVATVVGAASLALGLFYYLILNSAK 90
           AFLLL+TGAALN    E+S YF  YYCYV+KPGVFA   V+  AS+ LG+ YYL L+SAK
Sbjct: 106 AFLLLLTGAALNDQHGEESMYFGNYYCYVVKPGVFAGGAVLSLASVTLGILYYLTLHSAK 165

Query: 91  NDPAVWGNPSIPPPANIAM 110
           N   +WGN S+P    IAM
Sbjct: 166 NS-GLWGNSSVPQEGGIAM 183

The following BLAST results are available for this feature:

BLAST of CmaCh16G002360 vs. Swiss-Prot


Match Name	E-value	Identity	Description

BLAST of CmaCh16G002360 vs. TrEMBL


Match Name	E-value	Identity	Description
A0A0A0KU80_CUCSA	6.1e-24	71.60	Uncharacterized protein OS=Cucumis sativus GN=Csa_4G025740 PE=4 SV=1	[more]
A0A068U9S1_COFCA	1.1e-17	58.23	Uncharacterized protein OS=Coffea canephora GN=GSCOC_T00019822001 PE=4 SV=1	[more]
A0A067EBD4_CITSI	7.3e-17	59.49	Uncharacterized protein OS=Citrus sinensis GN=CISIN_1g028344mg PE=4 SV=1	[more]
A0A067JD79_JATCU	9.5e-17	56.96	Uncharacterized protein OS=Jatropha curcas GN=JCGZ_00583 PE=4 SV=1	[more]
A0A061EZX5_THECC	2.1e-16	55.70	Uncharacterized protein OS=Theobroma cacao GN=TCM_025365 PE=4 SV=1	[more]

BLAST of CmaCh16G002360 vs. TAIR10


Match Name	E-value	Identity	Description
AT5G17210.1	4.1e-11	41.98	Protein of unknown function (DUF1218)	[more]

BLAST of CmaCh16G002360 vs. NCBI nr


Match Name	E-value	Identity	Description
gi\|449458299\|ref\|XP_004146885.1\|	8.8e-24	71.60	PREDICTED: uncharacterized protein LOC101221478 [Cucumis sativus]	[more]
gi\|659107725\|ref\|XP_008453825.1\|	2.6e-23	69.14	PREDICTED: uncharacterized protein LOC103494435 [Cucumis melo]	[more]
gi\|661891067\|emb\|CDP04949.1\|	1.6e-17	58.23	unnamed protein product [Coffea canephora]	[more]
gi\|641833512\|gb\|KDO52524.1\|	1.0e-16	59.49	hypothetical protein CISIN_1g028344mg [Citrus sinensis]	[more]
gi\|568877605\|ref\|XP_006491818.1\|	1.0e-16	59.49	PREDICTED: uncharacterized protein LOC102608001 [Citrus sinensis]	[more]

Annotated Terms

The following terms have been associated with this gene:

Vocabulary: **INTERPRO**
Term	Definition
IPR009606	DUF1218

GO Annotation

GO Assignments

This gene is annotated with the following GO terms.

Category	Term Accession	Term Name
biological_process	GO:0008150	biological_process
cellular_component	GO:0005575	cellular_component
cellular_component	GO:0016021	integral component of membrane
molecular_function	GO:0003674	molecular_function

Relationships

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


Feature Name	Unique Name	Type
CmaCh16G002360.1	CmaCh16G002360.1	mRNA

InterPro

Analysis Name: InterPro Annotations of Cucurbita maxima
Date Performed: 2017-05-20


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
IPR009606	Protein of unknown function DUF1218	PFAM	PF06749	DUF1218	coord: 29..75 score: 1.
None	No IPR available	PANTHER	PTHR31769	FAMILY NOT NAMED	coord: 31..110 score: 3.5
None	No IPR available	PANTHER	PTHR31769:SF8	SUBFAMILY NOT NAMED	coord: 31..110 score: 3.5

Synteny

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


Gene	Orthologue	Organism	Block
CmaCh16G002360	Cucsa.093840	Cucumber (Gy14) v1	cgycmaB0196
CmaCh16G002360	Cla010685	Watermelon (97103) v1	cmawmB313
CmaCh16G002360	Csa4G025740	Cucumber (Chinese Long) v2	cmacuB332
CmaCh16G002360	MELO3C017618	Melon (DHL92) v3.5.1	cmameB304
CmaCh16G002360	ClCG07G017290	Watermelon (Charleston Gray)	cmawcgB302
CmaCh16G002360	CSPI04G04390	Wild cucumber (PI 183967)	cmacpiB337
CmaCh16G002360	CmoCh16G002540	Cucurbita moschata (Rifu)	cmacmoB322
CmaCh16G002360	CmoCh04G004000	Cucurbita moschata (Rifu)	cmacmoB338
CmaCh16G002360	Lsi07G001450	Bottle gourd (USVL1VR-Ls)	cmalsiB323
CmaCh16G002360	Cp4.1LG01g03260	Cucurbita pepo (Zucchini)	cmacpeB351
CmaCh16G002360	Cp4.1LG14g05200	Cucurbita pepo (Zucchini)	cmacpeB344
CmaCh16G002360	MELO3C017618.2	Melon (DHL92) v3.6.1	cmamedB355
CmaCh16G002360	CsaV3_4G004490	Cucumber (Chinese Long) v3	cmacucB0387
CmaCh16G002360	CsaV3_5G005270	Cucumber (Chinese Long) v3	cmacucB0405
CmaCh16G002360	Cla97C07G144300	Watermelon (97103) v2	cmawmbB352
CmaCh16G002360	Bhi01G001973	Wax gourd	cmawgoB0440
CmaCh16G002360	CsGy4G004300	Cucumber (Gy14) v2	cgybcmaB493
CmaCh16G002360	Carg16777	Silver-seed gourd	carcmaB1206
CmaCh16G002360	Carg08475	Silver-seed gourd	carcmaB0995
CmaCh16G002360	Carg08052	Silver-seed gourd	carcmaB0526

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


Gene	Paralogue	Organism	Block
CmaCh16G002360	CmaCh04G003790	Cucurbita maxima (Rimu)	cmacmaB351

The following block(s) are covering this gene:


Gene	Organism	Block
CmaCh16G002360	Wax gourd	cmawgoB0410
CmaCh16G002360	Melon (DHL92) v3.6.1	cmamedB359