CmoCh12G011610 (gene) Cucurbita moschata (Rifu) | Cucurbit Genomics Database (CuGenDB)

Overview


Name	CmoCh12G011610
Type	gene
Organism	Cucurbita moschata (Cucurbita moschata (Rifu))
Description	Sigma factor binding protein 1, chloroplastic
Location	Cmo_Chr12 : 10509784 .. 10510161 (+)

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.

ATGGAGAATCTTAAAAGCCTTCCTAATCATCTTCGTCACGAGAAACTCGAAGCTTCGAACTACCGAGCAACAATGGCGAACAAACCCATCAAAGTTAAGTACATTTCAAGTCCCATGATGGTGAAGGCCAACAACGAGTTTGAGTTTCGAGCCATAGTTCAGAAGCTCACCGGCCAACACTCGGCCGATGATGCTTTTGATCGATCACCTCAAGAATTCAACCATGCTTTTTGTCCCCCGTCGTCTACGGTGACTTCTTTTGACTCGAAGGATTGTTATGATTTGGTTTCTAGTGATGCTTACGATCCGATCGGGGTCGGTGAAATGAAAGATTCTTTATATGGGTTTCAAGCTTCTTATGTTGATGTATGGAGATGA

mRNA sequence

ATGGAGAATCTTAAAAGCCTTCCTAATCATCTTCGTCACGAGAAACTCGAAGCTTCGAACTACCGAGCAACAATGGCGAACAAACCCATCAAAGTTAAGTACATTTCAAGTCCCATGATGGTGAAGGCCAACAACGAGTTTGAGTTTCGAGCCATAGTTCAGAAGCTCACCGGCCAACACTCGGCCGATGATGCTTTTGATCGATCACCTCAAGAATTCAACCATGCTTTTTGTCCCCCGTCGTCTACGGTGACTTCTTTTGACTCGAAGGATTGTTATGATTTGGTTTCTAGTGATGCTTACGATCCGATCGGGGTCGGTGAAATGAAAGATTCTTTATATGGGTTTCAAGCTTCTTATGTTGATGTATGGAGATGA

Coding sequence (CDS)

ATGGAGAATCTTAAAAGCCTTCCTAATCATCTTCGTCACGAGAAACTCGAAGCTTCGAACTACCGAGCAACAATGGCGAACAAACCCATCAAAGTTAAGTACATTTCAAGTCCCATGATGGTGAAGGCCAACAACGAGTTTGAGTTTCGAGCCATAGTTCAGAAGCTCACCGGCCAACACTCGGCCGATGATGCTTTTGATCGATCACCTCAAGAATTCAACCATGCTTTTTGTCCCCCGTCGTCTACGGTGACTTCTTTTGACTCGAAGGATTGTTATGATTTGGTTTCTAGTGATGCTTACGATCCGATCGGGGTCGGTGAAATGAAAGATTCTTTATATGGGTTTCAAGCTTCTTATGTTGATGTATGGAGATGA

Homology

[Close]

BLAST of CmoCh12G011610 vs. TrEMBL
Match: A0A0A0LFF9_CUCSA (Uncharacterized protein OS=Cucumis sativus GN=Csa_2G010160 PE=4 SV=1)

HSP 1 Score: 114.8 bits (286), Expect = 7.7e-23
Identity = 74/141 (52.48%), Postives = 88/141 (62.41%), Query Frame = 1


Query: 1   MENLKSLPNHLRHEKLEASNYRATM--ANKPIKVKYISSPMMVKANNEFEFRAIVQKLTG 60
           MEN  +LP++  H+K+   + +AT+   NKPIKVKYISSPMMVKANNE EFRAIVQKLTG
Sbjct: 1   MENFTTLPSNFHHKKVSQVSNKATIDHQNKPIKVKYISSPMMVKANNESEFRAIVQKLTG 60

Query: 61  QHSADDAFDRSPQEFNHAFCPP---SSTVTSFDSKDCY----------DLVSSDAYDPIG 120
           QHS D   D+S Q+FNH F PP   SS   SFD KDCY          D +         
Sbjct: 61  QHSPDHD-DQSVQDFNHVFYPPPPSSSPGVSFDPKDCYGNSASGDVLFDRIEDGDEGRYW 120

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

[Close]

BLAST of CmoCh12G011610 vs. TrEMBL
Match: A0A0D2U3H7_GOSRA (Uncharacterized protein OS=Gossypium raimondii GN=B456_013G186400 PE=4 SV=1)

HSP 1 Score: 59.3 bits (142), Expect = 3.8e-06
Identity = 28/33 (84.85%), Postives = 31/33 (93.94%), Query Frame = 1


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

[Close]

BLAST of CmoCh12G011610 vs. TrEMBL
Match: W9RT96_9ROSA (Uncharacterized protein OS=Morus notabilis GN=L484_024544 PE=4 SV=1)

HSP 1 Score: 58.5 bits (140), Expect = 6.6e-06
Identity = 31/61 (50.82%), Postives = 40/61 (65.57%), Query Frame = 1


Query: 1  MENLKSLPNHLRHEKLEASNYRATMANKPIKVKYISSPMMVKANNEFEFRAIVQKLTGQH 60
          ME L     +  +  L +    +    KPIK+KYISSPMMV+ANN  EFRAIVQ+LTG++
Sbjct: 3  MEKLLGNSQYQNNPHLRSQKQPSKGKKKPIKIKYISSPMMVRANNASEFRAIVQELTGRN 62

Query: 61 S 62
          S
Sbjct: 63 S 63

[Close]

BLAST of CmoCh12G011610 vs. TrEMBL
Match: A0A0A0LIA7_CUCSA (Uncharacterized protein OS=Cucumis sativus GN=Csa_2G010150 PE=4 SV=1)

HSP 1 Score: 58.5 bits (140), Expect = 6.6e-06
Identity = 41/128 (32.03%), Postives = 63/128 (49.22%), Query Frame = 1


Query: 9   NHLRHEKLEASNYRAT-MANKPIKVKYISSPMMVKANNEFEFRAIVQKLTGQHSADDAFD 68
           NH  H + ++ N   T +  KPIKVKYISSPMM+KA+N  EFRAIVQ+LTG  S      
Sbjct: 11  NH-NHSQSQSQNQNPTKVQRKPIKVKYISSPMMIKASNALEFRAIVQQLTGFDSNTPTRR 70

Query: 69  RSPQEFNHAFCPPSS---------------------TVTSFDSKDCYDLVSSDAYDPIGV 115
           R+ +  +     PS+                     ++  FD + C++  +++   P  +
Sbjct: 71  RNQKLLSDCARTPSAMFHADRHEMEVLKFSDDHHMESLLQFDGQGCFETQNNNNILPNNI 130

[Close]

BLAST of CmoCh12G011610 vs. TAIR10
Match: AT3G56710.1 (AT3G56710.1 sigma factor binding protein 1)

HSP 1 Score: 49.7 bits (117), Expect = 1.5e-06
Identity = 32/91 (35.16%), Postives = 50/91 (54.95%), Query Frame = 1


Query: 22  RATMANKPIKVKYISSPMMVKANNEFEFRAIVQKLTGQHSADDAFD--RSPQEFNHAFCP 81
           + T  NKPIKV+YIS+PM V+     +FR +VQ+LTGQ + D   +   SP   +H   P
Sbjct: 32  KTTSTNKPIKVRYISNPMRVQTCAS-KFRELVQELTGQDAVDLQPEPIYSPSSDDHNLSP 91

Query: 82  PSSTVT-SFDSKDCYDLVSSDAYDPIGVGEM 110
           P+  +      ++ +    SD Y+P+   +M
Sbjct: 92  PAENLAPRVLHQEPFGERDSDCYEPLNAEDM 121

[Close]

BLAST of CmoCh12G011610 vs. NCBI nr
Match: gi|700205661|gb|KGN60780.1| (hypothetical protein Csa_2G010160 [Cucumis sativus])

HSP 1 Score: 114.8 bits (286), Expect = 1.1e-22
Identity = 74/141 (52.48%), Postives = 88/141 (62.41%), Query Frame = 1


Query: 1   MENLKSLPNHLRHEKLEASNYRATM--ANKPIKVKYISSPMMVKANNEFEFRAIVQKLTG 60
           MEN  +LP++  H+K+   + +AT+   NKPIKVKYISSPMMVKANNE EFRAIVQKLTG
Sbjct: 1   MENFTTLPSNFHHKKVSQVSNKATIDHQNKPIKVKYISSPMMVKANNESEFRAIVQKLTG 60

Query: 61  QHSADDAFDRSPQEFNHAFCPP---SSTVTSFDSKDCY----------DLVSSDAYDPIG 120
           QHS D   D+S Q+FNH F PP   SS   SFD KDCY          D +         
Sbjct: 61  QHSPDHD-DQSVQDFNHVFYPPPPSSSPGVSFDPKDCYGNSASGDVLFDRIEDGDEGRYW 120

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

[Close]

BLAST of CmoCh12G011610 vs. NCBI nr
Match: gi|764619575|ref|XP_011468362.1| (PREDICTED: uncharacterized protein LOC105352572 [Fragaria vesca subsp. vesca])

HSP 1 Score: 59.7 bits (143), Expect = 4.2e-06
Identity = 39/122 (31.97%), Postives = 65/122 (53.28%), Query Frame = 1


Query: 4   LKSLPNHLRHEKLEASNYRATMANKPIKVKYISSPMMVKANNEFEFRAIVQKLTGQHSAD 63
           ++ L NH   ++      + + A  PI++KYISSPMMV+ANN  EFRAIVQ+LTGQ+S  
Sbjct: 1   MEQLRNHENRQQ-RTERRKRSKAETPIRIKYISSPMMVQANNASEFRAIVQELTGQNS-- 60

Query: 64  DAFDRSPQEFNHAFCPPSSTVTSFDSKDCYDLVSSDAYDPIGVGEMKDSLYGFQASYVDV 123
              D +  +    +C  ++ V+S  +    D+ + +  + +   +     +G Q   +  
Sbjct: 61  ---DATIPDHGTDYCEQANWVSSHRASQPADMKTQNGDELMKFSDDHVVAFG-QFDEIKF 115

Query: 124 WR 126
           WR
Sbjct: 121 WR 115

[Close]

BLAST of CmoCh12G011610 vs. NCBI nr
Match: gi|823261712|ref|XP_012463594.1| (PREDICTED: uncharacterized protein LOC105782992 [Gossypium raimondii])

HSP 1 Score: 59.3 bits (142), Expect = 5.5e-06
Identity = 28/33 (84.85%), Postives = 31/33 (93.94%), Query Frame = 1


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

[Close]

BLAST of CmoCh12G011610 vs. NCBI nr
Match: gi|700205660|gb|KGN60779.1| (hypothetical protein Csa_2G010150 [Cucumis sativus])

HSP 1 Score: 58.5 bits (140), Expect = 9.4e-06
Identity = 41/128 (32.03%), Postives = 63/128 (49.22%), Query Frame = 1


Query: 9   NHLRHEKLEASNYRAT-MANKPIKVKYISSPMMVKANNEFEFRAIVQKLTGQHSADDAFD 68
           NH  H + ++ N   T +  KPIKVKYISSPMM+KA+N  EFRAIVQ+LTG  S      
Sbjct: 11  NH-NHSQSQSQNQNPTKVQRKPIKVKYISSPMMIKASNALEFRAIVQQLTGFDSNTPTRR 70

Query: 69  RSPQEFNHAFCPPSS---------------------TVTSFDSKDCYDLVSSDAYDPIGV 115
           R+ +  +     PS+                     ++  FD + C++  +++   P  +
Sbjct: 71  RNQKLLSDCARTPSAMFHADRHEMEVLKFSDDHHMESLLQFDGQGCFETQNNNNILPNNI 130

[Close]

BLAST of CmoCh12G011610 vs. NCBI nr
Match: gi|703121161|ref|XP_010102262.1| (hypothetical protein L484_024544 [Morus notabilis])

HSP 1 Score: 58.5 bits (140), Expect = 9.4e-06
Identity = 31/61 (50.82%), Postives = 40/61 (65.57%), Query Frame = 1


Query: 1  MENLKSLPNHLRHEKLEASNYRATMANKPIKVKYISSPMMVKANNEFEFRAIVQKLTGQH 60
          ME L     +  +  L +    +    KPIK+KYISSPMMV+ANN  EFRAIVQ+LTG++
Sbjct: 3  MEKLLGNSQYQNNPHLRSQKQPSKGKKKPIKIKYISSPMMVRANNASEFRAIVQELTGRN 62

Query: 61 S 62
          S
Sbjct: 63 S 63

The following BLAST results are available for this feature:

BLAST of CmoCh12G011610 vs. Swiss-Prot


Match Name	E-value	Identity	Description

BLAST of CmoCh12G011610 vs. TrEMBL


Match Name	E-value	Identity	Description
A0A0A0LFF9_CUCSA	7.7e-23	52.48	Uncharacterized protein OS=Cucumis sativus GN=Csa_2G010160 PE=4 SV=1	[more]
A0A0D2U3H7_GOSRA	3.8e-06	84.85	Uncharacterized protein OS=Gossypium raimondii GN=B456_013G186400 PE=4 SV=1	[more]
W9RT96_9ROSA	6.6e-06	50.82	Uncharacterized protein OS=Morus notabilis GN=L484_024544 PE=4 SV=1	[more]
A0A0A0LIA7_CUCSA	6.6e-06	32.03	Uncharacterized protein OS=Cucumis sativus GN=Csa_2G010150 PE=4 SV=1	[more]

BLAST of CmoCh12G011610 vs. TAIR10


Match Name	E-value	Identity	Description
AT3G56710.1	1.5e-06	35.16	sigma factor binding protein 1	[more]

BLAST of CmoCh12G011610 vs. NCBI nr


Match Name	E-value	Identity	Description
gi\|700205661\|gb\|KGN60780.1\|	1.1e-22	52.48	hypothetical protein Csa_2G010160 [Cucumis sativus]	[more]
gi\|764619575\|ref\|XP_011468362.1\|	4.2e-06	31.97	PREDICTED: uncharacterized protein LOC105352572 [Fragaria vesca subsp. vesca]	[more]
gi\|823261712\|ref\|XP_012463594.1\|	5.5e-06	84.85	PREDICTED: uncharacterized protein LOC105782992 [Gossypium raimondii]	[more]
gi\|700205660\|gb\|KGN60779.1\|	9.4e-06	32.03	hypothetical protein Csa_2G010150 [Cucumis sativus]	[more]
gi\|703121161\|ref\|XP_010102262.1\|	9.4e-06	50.82	hypothetical protein L484_024544 [Morus notabilis]	[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
CmoCh12G011610.1	CmoCh12G011610.1	mRNA

InterPro

Analysis Name: InterPro Annotations of Cucurbita moschata
Date Performed: 2017-05-19


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
IPR008889	VQ	PFAM	PF05678	VQ	coord: 35..63 score: 2.
None	No IPR available	PANTHER	PTHR33624	FAMILY NOT NAMED	coord: 27..61 score: 2.8

Synteny

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


Gene	Orthologue	Organism	Block
CmoCh12G011610	CmaCh12G011400	Cucurbita maxima (Rimu)	cmacmoB177
CmoCh12G011610	Cla013632	Watermelon (97103) v1	cmowmB156
CmoCh12G011610	Csa2G010160	Cucumber (Chinese Long) v2	cmocuB157
CmoCh12G011610	MELO3C004408	Melon (DHL92) v3.5.1	cmomeB161
CmoCh12G011610	ClCG02G016900	Watermelon (Charleston Gray)	cmowcgB144
CmoCh12G011610	CSPI02G02700	Wild cucumber (PI 183967)	cmocpiB159
CmoCh12G011610	Lsi11G004180	Bottle gourd (USVL1VR-Ls)	cmolsiB148
CmoCh12G011610	Cp4.1LG07g09800	Cucurbita pepo (Zucchini)	cmocpeB175
CmoCh12G011610	MELO3C004408.2	Melon (DHL92) v3.6.1	cmomedB177
CmoCh12G011610	CsaV3_2G003860	Cucumber (Chinese Long) v3	cmocucB0185
CmoCh12G011610	Cla97C02G042630	Watermelon (97103) v2	cmowmbB161
CmoCh12G011610	CsGy2G002800	Cucumber (Gy14) v2	cgybcmoB170

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

None

The following block(s) are covering this gene:


Gene	Organism	Block
CmoCh12G011610	Cucurbita pepo (Zucchini)	cmocpeB147
CmoCh12G011610	Bottle gourd (USVL1VR-Ls)	cmolsiB142
CmoCh12G011610	Silver-seed gourd	carcmoB0356
CmoCh12G011610	Silver-seed gourd	carcmoB1441
CmoCh12G011610	Wax gourd	cmowgoB0171
CmoCh12G011610	Cucurbita moschata (Rifu)	cmocmoB086
CmoCh12G011610	Cucurbita moschata (Rifu)	cmocmoB148
CmoCh12G011610	Cucumber (Gy14) v1	cgycmoB0359
CmoCh12G011610	Cucurbita maxima (Rimu)	cmacmoB763