CmaCh12G011400 (gene) Cucurbita maxima (Rimu) | Cucurbit Genomics Database (CuGenDB)

Overview


Name	CmaCh12G011400
Type	gene
Organism	Cucurbita maxima (Cucurbita maxima (Rimu))
Description	Sigma factor binding protein 2, chloroplastic
Location	Cma_Chr12 : 8979314 .. 8979691 (+)

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.

ATGGAGAATCTTAGAAGCCTTCCTAATCATCTTCGTCACGAGAAACTCGAAGCTTCGAATTACCGAGCAACAATGGCGAACAAACCCATCAAAGTGAAGTACATTTCAAGTCCCATGATGGTGAAGGCCAACAACGAGTCTGAGTTTCGAGCCATAGTTCAGAAGCTCACCGGCCAGCACTCGGCCGATGATGCTTTTGATCGATCACCTCAAGAATTCAACCATGCCTTTTGTCCCTCGTCGTCTGCGACGACTTCTTTTGACTCAAAGGATTGTTATGGTTTGGTTTCTGGTGATGCTTACGATCTGATCGGGGTCGGTGAAATGAAAAATTCTTTATATGGGTTTCAAGCTTCTTATGTTGATGTATGGAGATAG

mRNA sequence

ATGGAGAATCTTAGAAGCCTTCCTAATCATCTTCGTCACGAGAAACTCGAAGCTTCGAATTACCGAGCAACAATGGCGAACAAACCCATCAAAGTGAAGTACATTTCAAGTCCCATGATGGTGAAGGCCAACAACGAGTCTGAGTTTCGAGCCATAGTTCAGAAGCTCACCGGCCAGCACTCGGCCGATGATGCTTTTGATCGATCACCTCAAGAATTCAACCATGCCTTTTGTCCCTCGTCGTCTGCGACGACTTCTTTTGACTCAAAGGATTGTTATGGTTTGGTTTCTGGTGATGCTTACGATCTGATCGGGGTCGGTGAAATGAAAAATTCTTTATATGGGTTTCAAGCTTCTTATGTTGATGTATGGAGATAG

Coding sequence (CDS)

ATGGAGAATCTTAGAAGCCTTCCTAATCATCTTCGTCACGAGAAACTCGAAGCTTCGAATTACCGAGCAACAATGGCGAACAAACCCATCAAAGTGAAGTACATTTCAAGTCCCATGATGGTGAAGGCCAACAACGAGTCTGAGTTTCGAGCCATAGTTCAGAAGCTCACCGGCCAGCACTCGGCCGATGATGCTTTTGATCGATCACCTCAAGAATTCAACCATGCCTTTTGTCCCTCGTCGTCTGCGACGACTTCTTTTGACTCAAAGGATTGTTATGGTTTGGTTTCTGGTGATGCTTACGATCTGATCGGGGTCGGTGAAATGAAAAATTCTTTATATGGGTTTCAAGCTTCTTATGTTGATGTATGGAGATAG

Protein sequence

MENLRSLPNHLRHEKLEASNYRATMANKPIKVKYISSPMMVKANNESEFRAIVQKLTGQHSADDAFDRSPQEFNHAFCPSSSATTSFDSKDCYGLVSGDAYDLIGVGEMKNSLYGFQASYVDVWR

Homology

[Close]

BLAST of CmaCh12G011400 vs. TrEMBL
Match: A0A0A0LFF9_CUCSA (Uncharacterized protein OS=Cucumis sativus GN=Csa_2G010160 PE=4 SV=1)

HSP 1 Score: 119.4 bits (298), Expect = 3.1e-24
Identity = 80/141 (56.74%), Postives = 94/141 (66.67%), Query Frame = 1


Query: 1   MENLRSLPNHLRHEKLEASNYRATM--ANKPIKVKYISSPMMVKANNESEFRAIVQKLTG 60
           MEN  +LP++  H+K+   + +AT+   NKPIKVKYISSPMMVKANNESEFRAIVQKLTG
Sbjct: 1   MENFTTLPSNFHHKKVSQVSNKATIDHQNKPIKVKYISSPMMVKANNESEFRAIVQKLTG 60

Query: 61  QHSADDAFDRSPQEFNHAFC---PSSSATTSFDSKDCYG-LVSGDA-YDLI--------G 120
           QHS D   D+S Q+FNH F    PSSS   SFD KDCYG   SGD  +D I         
Sbjct: 61  QHSPDHD-DQSVQDFNHVFYPPPPSSSPGVSFDPKDCYGNSASGDVLFDRIEDGDEGRYW 120

Query: 121 VGEMK-NSLYGFQA-SYVDVW 125
            GEM+  S  GFQA S V++W
Sbjct: 121 RGEMELGSFSGFQASSCVNIW 140

[Close]

BLAST of CmaCh12G011400 vs. TrEMBL
Match: W9RT96_9ROSA (Uncharacterized protein OS=Morus notabilis GN=L484_024544 PE=4 SV=1)

HSP 1 Score: 60.1 bits (144), Expect = 2.3e-06
Identity = 32/61 (52.46%), Postives = 41/61 (67.21%), Query Frame = 1


Query: 1  MENLRSLPNHLRHEKLEASNYRATMANKPIKVKYISSPMMVKANNESEFRAIVQKLTGQH 60
          ME L     +  +  L +    +    KPIK+KYISSPMMV+ANN SEFRAIVQ+LTG++
Sbjct: 3  MEKLLGNSQYQNNPHLRSQKQPSKGKKKPIKIKYISSPMMVRANNASEFRAIVQELTGRN 62

Query: 61 S 62
          S
Sbjct: 63 S 63

[Close]

BLAST of CmaCh12G011400 vs. TrEMBL
Match: A0A0D2U3H7_GOSRA (Uncharacterized protein OS=Gossypium raimondii GN=B456_013G186400 PE=4 SV=1)

HSP 1 Score: 60.1 bits (144), Expect = 2.3e-06
Identity = 28/33 (84.85%), Postives = 31/33 (93.94%), Query Frame = 1


Query: 29 PIKVKYISSPMMVKANNESEFRAIVQKLTGQHS 62
          P+KVKYISSPMMVKA+N  EFRAIVQ+LTGQHS
Sbjct: 19 PVKVKYISSPMMVKASNAEEFRAIVQELTGQHS 51

[Close]

BLAST of CmaCh12G011400 vs. TrEMBL
Match: M5WL38_PRUPE (Uncharacterized protein OS=Prunus persica GN=PRUPE_ppa017028mg PE=4 SV=1)

HSP 1 Score: 58.9 bits (141), Expect = 5.0e-06
Identity = 35/67 (52.24%), Postives = 45/67 (67.16%), Query Frame = 1


Query: 1  MENLRSLPNHLRHEKLEASNYRATMANKPIKVKYISSPMMVKANNESEFRAIVQKLTGQH 60
          ME LR+L +H  H+     + + T A  P  +KYISSPMMV+A+N SEFRAIVQ+LTGQ 
Sbjct: 1  MEQLRNLHSH--HQPQSDQSKKPTKAKAPT-IKYISSPMMVQASNASEFRAIVQQLTGQD 60

Query: 61 SADDAFD 68
          S  +  D
Sbjct: 61 SNIEVLD 64

[Close]

BLAST of CmaCh12G011400 vs. TAIR10
Match: AT2G41180.1 (AT2G41180.1 VQ motif-containing protein)

HSP 1 Score: 47.4 bits (111), Expect = 7.7e-06
Identity = 39/107 (36.45%), Postives = 54/107 (50.47%), Query Frame = 1


Query: 22  RATMANKPIKVKYISSPMMVKANNESEFRAIVQKLTGQHSADDAFDRSPQEFN----HAF 81
           ++T  +KPIKV+YIS+PM V+    S+FR +VQ+LTGQ +AD     SP  F     H  
Sbjct: 29  KSTTTHKPIKVRYISNPMRVE-TCPSKFRELVQELTGQDAAD--LPPSPTTFTAVDLHRP 88

Query: 82  CPSSSATTSFDSKDCYGLVSGDAY-----DLIGVGEMKNSLYGFQAS 120
           C S       D     G V G+ Y     ++    +M   L GF +S
Sbjct: 89  CESEMNLEPLD-----GEVRGEYYSPLDEEVFNAPQMSAGLSGFFSS 127

[Close]

BLAST of CmaCh12G011400 vs. NCBI nr
Match: gi|700205661|gb|KGN60780.1| (hypothetical protein Csa_2G010160 [Cucumis sativus])

HSP 1 Score: 119.4 bits (298), Expect = 4.5e-24
Identity = 80/141 (56.74%), Postives = 94/141 (66.67%), Query Frame = 1


Query: 1   MENLRSLPNHLRHEKLEASNYRATM--ANKPIKVKYISSPMMVKANNESEFRAIVQKLTG 60
           MEN  +LP++  H+K+   + +AT+   NKPIKVKYISSPMMVKANNESEFRAIVQKLTG
Sbjct: 1   MENFTTLPSNFHHKKVSQVSNKATIDHQNKPIKVKYISSPMMVKANNESEFRAIVQKLTG 60

Query: 61  QHSADDAFDRSPQEFNHAFC---PSSSATTSFDSKDCYG-LVSGDA-YDLI--------G 120
           QHS D   D+S Q+FNH F    PSSS   SFD KDCYG   SGD  +D I         
Sbjct: 61  QHSPDHD-DQSVQDFNHVFYPPPPSSSPGVSFDPKDCYGNSASGDVLFDRIEDGDEGRYW 120

Query: 121 VGEMK-NSLYGFQA-SYVDVW 125
            GEM+  S  GFQA S V++W
Sbjct: 121 RGEMELGSFSGFQASSCVNIW 140

[Close]

BLAST of CmaCh12G011400 vs. NCBI nr
Match: gi|764619575|ref|XP_011468362.1| (PREDICTED: uncharacterized protein LOC105352572 [Fragaria vesca subsp. vesca])

HSP 1 Score: 60.8 bits (146), Expect = 1.9e-06
Identity = 35/61 (57.38%), Postives = 45/61 (73.77%), Query Frame = 1


Query: 1  MENLRSLPNHLRHEKLEASNYRATMANKPIKVKYISSPMMVKANNESEFRAIVQKLTGQH 60
          ME LR+  N  R ++ E    + + A  PI++KYISSPMMV+ANN SEFRAIVQ+LTGQ+
Sbjct: 1  MEQLRNHEN--RQQRTERR--KRSKAETPIRIKYISSPMMVQANNASEFRAIVQELTGQN 57

Query: 61 S 62
          S
Sbjct: 61 S 57

[Close]

BLAST of CmaCh12G011400 vs. NCBI nr
Match: gi|703121161|ref|XP_010102262.1| (hypothetical protein L484_024544 [Morus notabilis])

HSP 1 Score: 60.1 bits (144), Expect = 3.2e-06
Identity = 32/61 (52.46%), Postives = 41/61 (67.21%), Query Frame = 1


Query: 1  MENLRSLPNHLRHEKLEASNYRATMANKPIKVKYISSPMMVKANNESEFRAIVQKLTGQH 60
          ME L     +  +  L +    +    KPIK+KYISSPMMV+ANN SEFRAIVQ+LTG++
Sbjct: 3  MEKLLGNSQYQNNPHLRSQKQPSKGKKKPIKIKYISSPMMVRANNASEFRAIVQELTGRN 62

Query: 61 S 62
          S
Sbjct: 63 S 63

[Close]

BLAST of CmaCh12G011400 vs. NCBI nr
Match: gi|823261712|ref|XP_012463594.1| (PREDICTED: uncharacterized protein LOC105782992 [Gossypium raimondii])

HSP 1 Score: 60.1 bits (144), Expect = 3.2e-06
Identity = 28/33 (84.85%), Postives = 31/33 (93.94%), Query Frame = 1


Query: 29 PIKVKYISSPMMVKANNESEFRAIVQKLTGQHS 62
          P+KVKYISSPMMVKA+N  EFRAIVQ+LTGQHS
Sbjct: 19 PVKVKYISSPMMVKASNAEEFRAIVQELTGQHS 51

[Close]

BLAST of CmaCh12G011400 vs. NCBI nr
Match: gi|595831738|ref|XP_007206331.1| (hypothetical protein PRUPE_ppa017028mg [Prunus persica])

HSP 1 Score: 58.9 bits (141), Expect = 7.2e-06
Identity = 35/67 (52.24%), Postives = 45/67 (67.16%), Query Frame = 1


Query: 1  MENLRSLPNHLRHEKLEASNYRATMANKPIKVKYISSPMMVKANNESEFRAIVQKLTGQH 60
          ME LR+L +H  H+     + + T A  P  +KYISSPMMV+A+N SEFRAIVQ+LTGQ 
Sbjct: 1  MEQLRNLHSH--HQPQSDQSKKPTKAKAPT-IKYISSPMMVQASNASEFRAIVQQLTGQD 60

Query: 61 SADDAFD 68
          S  +  D
Sbjct: 61 SNIEVLD 64

The following BLAST results are available for this feature:

BLAST of CmaCh12G011400 vs. Swiss-Prot


Match Name	E-value	Identity	Description

BLAST of CmaCh12G011400 vs. TrEMBL


Match Name	E-value	Identity	Description
A0A0A0LFF9_CUCSA	3.1e-24	56.74	Uncharacterized protein OS=Cucumis sativus GN=Csa_2G010160 PE=4 SV=1	[more]
W9RT96_9ROSA	2.3e-06	52.46	Uncharacterized protein OS=Morus notabilis GN=L484_024544 PE=4 SV=1	[more]
A0A0D2U3H7_GOSRA	2.3e-06	84.85	Uncharacterized protein OS=Gossypium raimondii GN=B456_013G186400 PE=4 SV=1	[more]
M5WL38_PRUPE	5.0e-06	52.24	Uncharacterized protein OS=Prunus persica GN=PRUPE_ppa017028mg PE=4 SV=1	[more]

BLAST of CmaCh12G011400 vs. TAIR10


Match Name	E-value	Identity	Description
AT2G41180.1	7.7e-06	36.45	VQ motif-containing protein	[more]

BLAST of CmaCh12G011400 vs. NCBI nr


Match Name	E-value	Identity	Description
gi\|700205661\|gb\|KGN60780.1\|	4.5e-24	56.74	hypothetical protein Csa_2G010160 [Cucumis sativus]	[more]
gi\|764619575\|ref\|XP_011468362.1\|	1.9e-06	57.38	PREDICTED: uncharacterized protein LOC105352572 [Fragaria vesca subsp. vesca]	[more]
gi\|703121161\|ref\|XP_010102262.1\|	3.2e-06	52.46	hypothetical protein L484_024544 [Morus notabilis]	[more]
gi\|823261712\|ref\|XP_012463594.1\|	3.2e-06	84.85	PREDICTED: uncharacterized protein LOC105782992 [Gossypium raimondii]	[more]
gi\|595831738\|ref\|XP_007206331.1\|	7.2e-06	52.24	hypothetical protein PRUPE_ppa017028mg [Prunus persica]	[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
cellular_component	GO:0005575	cellular_component
molecular_function	GO:0003674	molecular_function

Relationships

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


Feature Name	Unique Name	Type
CmaCh12G011400.1	CmaCh12G011400.1	mRNA

InterPro

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


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
IPR008889	VQ	PFAM	PF05678	VQ	coord: 35..63 score: 1.
None	No IPR available	PANTHER	PTHR33624	FAMILY NOT NAMED	coord: 27..61 score: 5.1

Synteny

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


Gene	Orthologue	Organism	Block
CmaCh12G011400	Cla013632	Watermelon (97103) v1	cmawmB170
CmaCh12G011400	Csa2G010160	Cucumber (Chinese Long) v2	cmacuB173
CmaCh12G011400	MELO3C004408	Melon (DHL92) v3.5.1	cmameB172
CmaCh12G011400	ClCG02G016900	Watermelon (Charleston Gray)	cmawcgB156
CmaCh12G011400	CSPI02G02700	Wild cucumber (PI 183967)	cmacpiB174
CmaCh12G011400	CmoCh12G011610	Cucurbita moschata (Rifu)	cmacmoB177
CmaCh12G011400	Lsi11G004180	Bottle gourd (USVL1VR-Ls)	cmalsiB159
CmaCh12G011400	Cp4.1LG07g09800	Cucurbita pepo (Zucchini)	cmacpeB203
CmaCh12G011400	MELO3C004408.2	Melon (DHL92) v3.6.1	cmamedB187
CmaCh12G011400	CsaV3_2G003860	Cucumber (Chinese Long) v3	cmacucB0202
CmaCh12G011400	Cla97C02G042630	Watermelon (97103) v2	cmawmbB175
CmaCh12G011400	CsGy2G002800	Cucumber (Gy14) v2	cgybcmaB178

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

None

The following block(s) are covering this gene:


Gene	Organism	Block
CmaCh12G011400	Wax gourd	cmawgoB0177
CmaCh12G011400	Cucurbita maxima (Rimu)	cmacmaB190
CmaCh12G011400	Cucumber (Gy14) v1	cgycmaB0364
CmaCh12G011400	Cucurbita moschata (Rifu)	cmacmoB190
CmaCh12G011400	Cucurbita pepo (Zucchini)	cmacpeB171
CmaCh12G011400	Silver-seed gourd	carcmaB0355
CmaCh12G011400	Silver-seed gourd	carcmaB1074
CmaCh12G011400	Silver-seed gourd	carcmaB1483