CmoCh11G011770 (gene) Cucurbita moschata (Rifu) | Cucurbit Genomics Database (CuGenDB)

Overview


Name	CmoCh11G011770
Type	gene
Organism	Cucurbita moschata (Cucurbita moschata (Rifu))
Description	Photosystem I assembly protein Ycf3
Location	Cmo_Chr11 : 6830983 .. 6832049 (-)

Genome Viewer

Gene Expression

Sequences

The following sequences are available for this feature:

Gene sequence (with intron)

Legend: CDSexon

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

ATGCGACTAGAAATCGATCCCTATGATCGAAGTTATATACTCTATAACATAGGTCTTATCCACACAAGGAACGGAGAACATACGAAAGCTTTGGAATATTATTTTCGGGCACTAGAACGAAACCCGTTCTTACCACAAGCTTTTAATAATATGGCTGTGATCTGTCATTACGTGCGACTATCTCCACTATAGAAAGAAAAAAAAAAGAGCAAATTCGATAATAAATACTAAAAAAAATAGGCTTTCTACATATGTATTGTCCAAACTAACGATTTGTATCAGCTGTAGCAAAGAAAGAAACTTCATAGAAGTAGAAATATGAAGAAATAGGTATGCCTAGATACTTTATTCTATGGATAAAGGATCTAATTGATAGAAGAAGCACCGTAAAGATCAATTAGTCAGGTTTTTGGCCGATACAATAAAAACTGCTTACTTATATCATGATATAAGATCAAAATGAAGGAATCCACTTATGTAATAGGGTGGATACCCTCCGATATTGAGCAGCGGTGTAGCATCAGATCCCAAAGACAGTAAGTCTTTTCTTTCTTATGAAAGAAAGTCTTTTTCAAGGATTCTATATCAATTTATAGATGAAACCGAGATAGTTATCTTTCAGAAAATTGTAACGATAGTGGAATGCCTATGCTTTATTCTTCTGAAGGTGGGAGAAAAGATAAAACTTATTTAATTATTCAGCAAAATTAAAGTTTGAAACTTATATAATTAACCTCTTTTGCTTAACTCGAGAAAAAAAATGGGCTAGATCTATGAGAAATTTGAATCCCAGCAGCCACAATTATTTTTTCACTCTTAAAAACATAAGCTTTACTTCCCCAAGTCTTTTTGAATCCCAGCAGCCACAATTATTTTTTCACTCTTAAAAACATAAGCTTTACTTCCCCAAGTCTTTCATGCTTCGTGCCTTCGATAACGTTGCCCTCTCGTCGTCTGCGAGATTTCGGGAGTTTGAAAACTGAACATATTTGTATGTTTAGGTACTCACAAGGACTTGGGACGTCGTGAGAGTGGAAGACACACTAGAATGGAGTCACAATAGATGA

mRNA sequence

ATGCGACTAGAAATCGATCCCTATGATCGAAGTTATATACTCTATAACATAGGTCTTATCCACACAAGGAACGGAGAACATACGAAAGCTTTGGAATATTATTTTCGGGCACTAGAACGAAACCCGTTCTTACCACAAGCTTTTAATAATATGGCTGTGATCTGTCATTACGTACTCACAAGGACTTGGGACGTCGTGAGAGTGGAAGACACACTAGAATGGAGTCACAATAGATGA

Coding sequence (CDS)

ATGCGACTAGAAATCGATCCCTATGATCGAAGTTATATACTCTATAACATAGGTCTTATCCACACAAGGAACGGAGAACATACGAAAGCTTTGGAATATTATTTTCGGGCACTAGAACGAAACCCGTTCTTACCACAAGCTTTTAATAATATGGCTGTGATCTGTCATTACGTACTCACAAGGACTTGGGACGTCGTGAGAGTGGAAGACACACTAGAATGGAGTCACAATAGATGA

Homology

[Close]

BLAST of CmoCh11G011770 vs. Swiss-Prot
Match: YCF3_CUCSA (Photosystem I assembly protein Ycf3 OS=Cucumis sativus GN=ycf3 PE=3 SV=1)

HSP 1 Score: 125.9 bits (315), Expect = 1.9e-28
Identity = 57/57 (100.00%), Postives = 57/57 (100.00%), Query Frame = 1


Query: 1   MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHY 58
           MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHY
Sbjct: 63  MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHY 119

[Close]

BLAST of CmoCh11G011770 vs. Swiss-Prot
Match: YCF3_MORIN (Photosystem I assembly protein Ycf3 OS=Morus indica GN=ycf3 PE=3 SV=1)

HSP 1 Score: 125.9 bits (315), Expect = 1.9e-28
Identity = 57/57 (100.00%), Postives = 57/57 (100.00%), Query Frame = 1


Query: 1   MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHY 58
           MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHY
Sbjct: 62  MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHY 118

[Close]

BLAST of CmoCh11G011770 vs. Swiss-Prot
Match: YCF3_GOSBA (Photosystem I assembly protein Ycf3 OS=Gossypium barbadense GN=ycf3 PE=3 SV=1)

HSP 1 Score: 123.6 bits (309), Expect = 9.3e-28
Identity = 56/57 (98.25%), Postives = 56/57 (98.25%), Query Frame = 1


Query: 1   MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHY 58
           MRLEIDPYDRSYILYNIGLIHT NGEHTKALEYYFRALERNPFLPQAFNNMAVICHY
Sbjct: 62  MRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFRALERNPFLPQAFNNMAVICHY 118

[Close]

BLAST of CmoCh11G011770 vs. Swiss-Prot
Match: YCF3_SOLBU (Photosystem I assembly protein Ycf3 OS=Solanum bulbocastanum GN=ycf3 PE=3 SV=1)

HSP 1 Score: 123.6 bits (309), Expect = 9.3e-28
Identity = 56/57 (98.25%), Postives = 56/57 (98.25%), Query Frame = 1


Query: 1   MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHY 58
           MRLEIDPYDRSYILYNIGLIHT NGEHTKALEYYFRALERNPFLPQAFNNMAVICHY
Sbjct: 62  MRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFRALERNPFLPQAFNNMAVICHY 118

[Close]

BLAST of CmoCh11G011770 vs. Swiss-Prot
Match: YCF3_GOSHI (Photosystem I assembly protein Ycf3 OS=Gossypium hirsutum GN=ycf3 PE=3 SV=1)

HSP 1 Score: 123.6 bits (309), Expect = 9.3e-28
Identity = 56/57 (98.25%), Postives = 56/57 (98.25%), Query Frame = 1


Query: 1   MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHY 58
           MRLEIDPYDRSYILYNIGLIHT NGEHTKALEYYFRALERNPFLPQAFNNMAVICHY
Sbjct: 62  MRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFRALERNPFLPQAFNNMAVICHY 118

[Close]

BLAST of CmoCh11G011770 vs. TrEMBL
Match: X2F3U2_LAGSI (Hypothetical chloroplast RF34 OS=Lagenaria siceraria GN=ycf3 PE=4 SV=1)

HSP 1 Score: 127.5 bits (319), Expect = 7.2e-27
Identity = 58/58 (100.00%), Postives = 58/58 (100.00%), Query Frame = 1


Query: 1   MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHYV 59
           MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHYV
Sbjct: 63  MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHYV 120

[Close]

BLAST of CmoCh11G011770 vs. TrEMBL
Match: D3WE36_9ROSA (Photosystem I assembly protein Ycf3 OS=Ficus sp. Moore 315 GN=ycf3 PE=3 SV=1)

HSP 1 Score: 126.7 bits (317), Expect = 1.2e-26
Identity = 61/71 (85.92%), Postives = 63/71 (88.73%), Query Frame = 1


Query: 1   MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHYVLT 60
           MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHY   
Sbjct: 62  MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHY--- 121

Query: 61  RTWDVVRVEDT 72
           R   V+R  D+
Sbjct: 122 RGEQVIRQGDS 129

[Close]

BLAST of CmoCh11G011770 vs. TrEMBL
Match: A0A0F7BI44_9SOLA (Photosystem I assembly protein Ycf3 OS=Dunalia solanacea GN=ycf3 PE=3 SV=1)

HSP 1 Score: 126.3 bits (316), Expect = 1.6e-26
Identity = 58/64 (90.62%), Postives = 59/64 (92.19%), Query Frame = 1


Query: 1   MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHYVLT 60
           MRLEIDPYDRSYILYNIGLIHT NGEHTKALEYYFRALERNPFLPQAFNNMAVICHYV  
Sbjct: 63  MRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFRALERNPFLPQAFNNMAVICHYVAE 122

Query: 61  RTWD 65
             +D
Sbjct: 123 AWFD 126

[Close]

BLAST of CmoCh11G011770 vs. TrEMBL
Match: A0A0A0YN86_9ROSA (Photosystem I assembly protein Ycf3 OS=Morus mongolica GN=ycf3 PE=3 SV=1)

HSP 1 Score: 125.9 bits (315), Expect = 2.1e-26
Identity = 57/57 (100.00%), Postives = 57/57 (100.00%), Query Frame = 1


Query: 1   MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHY 58
           MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHY
Sbjct: 62  MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHY 118

[Close]

BLAST of CmoCh11G011770 vs. TrEMBL
Match: A0A159YMP6_MORAL (Hypothetical chloroplast RF34 OS=Morus alba var. multicaulis GN=ycf3 PE=4 SV=1)

HSP 1 Score: 125.9 bits (315), Expect = 2.1e-26
Identity = 57/57 (100.00%), Postives = 57/57 (100.00%), Query Frame = 1


Query: 1   MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHY 58
           MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHY
Sbjct: 62  MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHY 118

[Close]

BLAST of CmoCh11G011770 vs. TAIR10
Match: ATCG00360.1 (ATCG00360.1 Tetratricopeptide repeat (TPR)-like superfamily protein)

HSP 1 Score: 123.6 bits (309), Expect = 5.2e-29
Identity = 56/57 (98.25%), Postives = 56/57 (98.25%), Query Frame = 1


Query: 1  MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHY 58
          MRLEIDPYDRSYILYNIGLIHT NGEHTKALEYYFRALERNPFLPQAFNNMAVICHY
Sbjct: 20 MRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFRALERNPFLPQAFNNMAVICHY 76

[Close]

BLAST of CmoCh11G011770 vs. NCBI nr
Match: gi|595645221|gb|AHM88684.1| (hypothetical chloroplast RF34 (chloroplast) [Lagenaria siceraria])

HSP 1 Score: 127.5 bits (319), Expect = 1.0e-26
Identity = 58/58 (100.00%), Postives = 58/58 (100.00%), Query Frame = 1


Query: 1   MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHYV 59
           MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHYV
Sbjct: 63  MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHYV 120

[Close]

BLAST of CmoCh11G011770 vs. NCBI nr
Match: gi|290488972|gb|ADD30870.1| (putative RF3 protein (chloroplast) [Ficus sp. Moore 315])

HSP 1 Score: 126.7 bits (317), Expect = 1.8e-26
Identity = 61/71 (85.92%), Postives = 63/71 (88.73%), Query Frame = 1


Query: 1   MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHYVLT 60
           MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHY   
Sbjct: 62  MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHY--- 121

Query: 61  RTWDVVRVEDT 72
           R   V+R  D+
Sbjct: 122 RGEQVIRQGDS 129

[Close]

BLAST of CmoCh11G011770 vs. NCBI nr
Match: gi|821318335|ref|YP_009139469.1| (hypothetical chloroplast RF34 (chloroplast) [Dunalia solanacea])

HSP 1 Score: 126.3 bits (316), Expect = 2.3e-26
Identity = 58/64 (90.62%), Postives = 59/64 (92.19%), Query Frame = 1


Query: 1   MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHYVLT 60
           MRLEIDPYDRSYILYNIGLIHT NGEHTKALEYYFRALERNPFLPQAFNNMAVICHYV  
Sbjct: 63  MRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFRALERNPFLPQAFNNMAVICHYVAE 122

Query: 61  RTWD 65
             +D
Sbjct: 123 AWFD 126

[Close]

BLAST of CmoCh11G011770 vs. NCBI nr
Match: gi|984914576|gb|AMC32716.1| (photosystem I assembly protein Ycf3 (chloroplast) [Ceanothus herbaceus])

HSP 1 Score: 125.9 bits (315), Expect = 3.0e-26
Identity = 57/57 (100.00%), Postives = 57/57 (100.00%), Query Frame = 1


Query: 1   MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHY 58
           MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHY
Sbjct: 62  MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHY 118

[Close]

BLAST of CmoCh11G011770 vs. NCBI nr
Match: gi|511265858|gb|AGN71965.1| (photosystem I assembly protein ycf3 [Dasiphora fruticosa subsp. floribunda])

HSP 1 Score: 125.9 bits (315), Expect = 3.0e-26
Identity = 57/57 (100.00%), Postives = 57/57 (100.00%), Query Frame = 1


Query: 1   MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHY 58
           MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHY
Sbjct: 62  MRLEIDPYDRSYILYNIGLIHTRNGEHTKALEYYFRALERNPFLPQAFNNMAVICHY 118

The following BLAST results are available for this feature:

BLAST of CmoCh11G011770 vs. Swiss-Prot


Match Name	E-value	Identity	Description
YCF3_CUCSA	1.9e-28	100.00	Photosystem I assembly protein Ycf3 OS=Cucumis sativus GN=ycf3 PE=3 SV=1	[more]
YCF3_MORIN	1.9e-28	100.00	Photosystem I assembly protein Ycf3 OS=Morus indica GN=ycf3 PE=3 SV=1	[more]
YCF3_GOSBA	9.3e-28	98.25	Photosystem I assembly protein Ycf3 OS=Gossypium barbadense GN=ycf3 PE=3 SV=1	[more]
YCF3_SOLBU	9.3e-28	98.25	Photosystem I assembly protein Ycf3 OS=Solanum bulbocastanum GN=ycf3 PE=3 SV=1	[more]
YCF3_GOSHI	9.3e-28	98.25	Photosystem I assembly protein Ycf3 OS=Gossypium hirsutum GN=ycf3 PE=3 SV=1	[more]

BLAST of CmoCh11G011770 vs. TrEMBL


Match Name	E-value	Identity	Description
X2F3U2_LAGSI	7.2e-27	100.00	Hypothetical chloroplast RF34 OS=Lagenaria siceraria GN=ycf3 PE=4 SV=1	[more]
D3WE36_9ROSA	1.2e-26	85.92	Photosystem I assembly protein Ycf3 OS=Ficus sp. Moore 315 GN=ycf3 PE=3 SV=1	[more]
A0A0F7BI44_9SOLA	1.6e-26	90.63	Photosystem I assembly protein Ycf3 OS=Dunalia solanacea GN=ycf3 PE=3 SV=1	[more]
A0A0A0YN86_9ROSA	2.1e-26	100.00	Photosystem I assembly protein Ycf3 OS=Morus mongolica GN=ycf3 PE=3 SV=1	[more]
A0A159YMP6_MORAL	2.1e-26	100.00	Hypothetical chloroplast RF34 OS=Morus alba var. multicaulis GN=ycf3 PE=4 SV=1	[more]

BLAST of CmoCh11G011770 vs. TAIR10


Match Name	E-value	Identity	Description
ATCG00360.1	5.2e-29	98.25	ATCG00360.1 Tetratricopeptide repeat (TPR)-like superfamily protein	[more]

BLAST of CmoCh11G011770 vs. NCBI nr


Match Name	E-value	Identity	Description
gi\|595645221\|gb\|AHM88684.1\|	1.0e-26	100.00	hypothetical chloroplast RF34 (chloroplast) [Lagenaria siceraria]	[more]
gi\|290488972\|gb\|ADD30870.1\|	1.8e-26	85.92	putative RF3 protein (chloroplast) [Ficus sp. Moore 315]	[more]
gi\|821318335\|ref\|YP_009139469.1\|	2.3e-26	90.63	hypothetical chloroplast RF34 (chloroplast) [Dunalia solanacea]	[more]
gi\|984914576\|gb\|AMC32716.1\|	3.0e-26	100.00	photosystem I assembly protein Ycf3 (chloroplast) [Ceanothus herbaceus]	[more]
gi\|511265858\|gb\|AGN71965.1\|	3.0e-26	100.00	photosystem I assembly protein ycf3 [Dasiphora fruticosa subsp. floribunda]	[more]

Annotated Terms

The following terms have been associated with this gene:

Vocabulary: **INTERPRO**
Term	Definition
IPR001440	TPR_1
IPR011990	TPR-like_helical_dom_sf
IPR013026	TPR-contain_dom
IPR019734	TPR_repeat

Vocabulary: **Molecular Function**
Term	Definition
GO:0005515	protein binding

GO Annotation

GO Assignments

This gene is annotated with the following GO terms.

Category	Term Accession	Term Name
biological_process	GO:0015979	photosynthesis
cellular_component	GO:0009535	chloroplast thylakoid membrane
molecular_function	GO:0005515	protein binding

Relationships

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


Feature Name	Unique Name	Type
CmoCh11G011770.1	CmoCh11G011770.1	mRNA

InterPro

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


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
IPR001440	Tetratricopeptide repeat 1	PFAM	PF00515	TPR_1	coord: 12..42 score: 1.
IPR011990	Tetratricopeptide-like helical domain	GENE3D	G3DSA:1.25.40.10		coord: 3..56 score: 1.5
IPR011990	Tetratricopeptide-like helical domain	unknown	SSF48452	TPR-like	coord: 3..56 score: 6.33
IPR013026	Tetratricopeptide repeat-containing domain	PROFILE	PS50293	TPR_REGION	coord: 1..44 score: 12
IPR019734	Tetratricopeptide repeat	SMART	SM00028	tpr_5	coord: 11..44 score: 3.
IPR019734	Tetratricopeptide repeat	PROFILE	PS50005	TPR	coord: 11..44 score: 10
None	No IPR available	PANTHER	PTHR26312	FAMILY NOT NAMED	coord: 1..57 score: 4.4
None	No IPR available	PANTHER	PTHR26312:SF81	PHOTOSYSTEM I ASSEMBLY PROTEIN YCF3	coord: 1..57 score: 4.4

Synteny

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

None

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

None

The following block(s) are covering this gene:


Gene	Organism	Block
CmoCh11G011770	Cucumber (Gy14) v1	cgycmoB0519
CmoCh11G011770	Cucurbita maxima (Rimu)	cmacmoB070
CmoCh11G011770	Cucurbita maxima (Rimu)	cmacmoB112
CmoCh11G011770	Wild cucumber (PI 183967)	cmocpiB092
CmoCh11G011770	Cucumber (Chinese Long) v2	cmocuB087
CmoCh11G011770	Melon (DHL92) v3.5.1	cmomeB110
CmoCh11G011770	Watermelon (Charleston Gray)	cmowcgB097
CmoCh11G011770	Watermelon (97103) v1	cmowmB083
CmoCh11G011770	Cucurbita pepo (Zucchini)	cmocpeB110
CmoCh11G011770	Cucurbita pepo (Zucchini)	cmocpeB127
CmoCh11G011770	Bottle gourd (USVL1VR-Ls)	cmolsiB130
CmoCh11G011770	Cucumber (Gy14) v2	cgybcmoB039
CmoCh11G011770	Melon (DHL92) v3.6.1	cmomedB118
CmoCh11G011770	Silver-seed gourd	carcmoB0346
CmoCh11G011770	Cucumber (Chinese Long) v3	cmocucB0102
CmoCh11G011770	Watermelon (97103) v2	cmowmbB096
CmoCh11G011770	Wax gourd	cmowgoB0153
CmoCh11G011770	Wax gourd	cmowgoB0167
CmoCh11G011770	Cucurbita moschata (Rifu)	cmocmoB040