CSPI01G16850 (gene) Wild cucumber (PI 183967) | Cucurbit Genomics Database (CuGenDB)

Overview


Name	CSPI01G16850
Type	gene
Organism	Cucumis sativus (Wild cucumber (PI 183967))
Description	Gypsy retrotransposon integrase-like protein 1
Location	Chr1 : 12598004 .. 12598174 (-)

Genome Viewer

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.

TGTCAAATTTATACGGATAAGATTCATGCAGCAGCAGCATCTCCATTGCATGTCTTGTCAGCACCATGGTCGTTTTCTTTATGGGGAATGGATGTTATTGGACCCATTGATCCTAAAGCCTCAAATGATCAACATTTTATTCTTGTGGCGATTGATTACTTCACTAAATGA

mRNA sequence

TGTCAAATTTATACGGATAAGATTCATGCAGCAGCAGCATCTCCATTGCATGTCTTGTCAGCACCATGGTCGTTTTCTTTATGGGGAATGGATGTTATTGGACCCATTGATCCTAAAGCCTCAAATGATCAACATTTTATTCTTGTGGCGATTGATTACTTCACTAAATGA

Coding sequence (CDS)

TGTCAAATTTATACGGATAAGATTCATGCAGCAGCAGCATCTCCATTGCATGTCTTGTCAGCACCATGGTCGTTTTCTTTATGGGGAATGGATGTTATTGGACCCATTGATCCTAAAGCCTCAAATGATCAACATTTTATTCTTGTGGCGATTGATTACTTCACTAAATGA

Homology

[Close]

BLAST of CSPI01G16850 vs. TrEMBL
Match: A0A061EKZ1_THECC (RNA-directed DNA polymerase (Reverse transcriptase), Ribonuclease H, putative OS=Theobroma cacao GN=TCM_020600 PE=4 SV=1)

HSP 1 Score: 92.4 bits (228), Expect = 1.9e-16
Identity = 42/56 (75.00%), Postives = 45/56 (80.36%), Query Frame = 1


Query: 1   CQIYTDKIHAAAASPLHVLSAPWSFSLWGMDVIGPIDPKASNDQHFILVAIDYFTK 57
           CQ+Y D+IHA  A PLHV SAPW FS+WGMDVIG I PKASN   FILVAIDYFTK
Sbjct: 665 CQVYADRIHAPPA-PLHVFSAPWPFSMWGMDVIGLITPKASNGHRFILVAIDYFTK 719

[Close]

BLAST of CSPI01G16850 vs. TrEMBL
Match: A0A061FF52_THECC (RNA-directed DNA polymerase, putative OS=Theobroma cacao GN=TCM_034880 PE=4 SV=1)

HSP 1 Score: 91.3 bits (225), Expect = 4.2e-16
Identity = 41/56 (73.21%), Postives = 45/56 (80.36%), Query Frame = 1


Query: 1    CQIYTDKIHAAAASPLHVLSAPWSFSLWGMDVIGPIDPKASNDQHFILVAIDYFTK 57
            CQ+Y D+IHA  A PLHV +APW FS+WGMDVIG I PKASN   FILVAIDYFTK
Sbjct: 1345 CQVYADRIHAPPA-PLHVFTAPWPFSMWGMDVIGLITPKASNGHRFILVAIDYFTK 1399

[Close]

BLAST of CSPI01G16850 vs. TrEMBL
Match: A0A061EGM3_THECC (RNA-directed DNA polymerase (Reverse transcriptase), Ribonuclease H OS=Theobroma cacao GN=TCM_018975 PE=4 SV=1)

HSP 1 Score: 91.3 bits (225), Expect = 4.2e-16
Identity = 41/56 (73.21%), Postives = 45/56 (80.36%), Query Frame = 1


Query: 1   CQIYTDKIHAAAASPLHVLSAPWSFSLWGMDVIGPIDPKASNDQHFILVAIDYFTK 57
           CQ+Y D+IHA  A PLHV +APW FS+WGMDVIG I PKASN   FILVAIDYFTK
Sbjct: 46  CQVYADRIHALPA-PLHVFTAPWPFSMWGMDVIGLITPKASNGHRFILVAIDYFTK 100

[Close]

BLAST of CSPI01G16850 vs. TrEMBL
Match: A0A061EXZ3_THECC (RNA-directed DNA polymerase (Reverse transcriptase), Ribonuclease H, putative OS=Theobroma cacao GN=TCM_024700 PE=4 SV=1)

HSP 1 Score: 91.3 bits (225), Expect = 4.2e-16
Identity = 41/56 (73.21%), Postives = 45/56 (80.36%), Query Frame = 1


Query: 1    CQIYTDKIHAAAASPLHVLSAPWSFSLWGMDVIGPIDPKASNDQHFILVAIDYFTK 57
            CQ+Y D+IHA  A PLHV +APW FS+WGMDVIG I PKASN   FILVAIDYFTK
Sbjct: 1250 CQVYADRIHAPPA-PLHVFTAPWPFSMWGMDVIGLITPKASNGHRFILVAIDYFTK 1304

[Close]

BLAST of CSPI01G16850 vs. TrEMBL
Match: A0A061GA98_THECC (RNA-directed DNA polymerase (Reverse transcriptase), Ribonuclease H OS=Theobroma cacao GN=TCM_028282 PE=4 SV=1)

HSP 1 Score: 90.1 bits (222), Expect = 9.3e-16
Identity = 42/56 (75.00%), Postives = 45/56 (80.36%), Query Frame = 1


Query: 1   CQIYTDKIHAAAASPLHVLSAPWSFSLWGMDVIGPIDPKASNDQHFILVAIDYFTK 57
           CQIY DKIH  A S LHVL++PW FS+WGMDVIG I PKASN   FILVAIDYFTK
Sbjct: 77  CQIYADKIHTPANS-LHVLTSPWPFSMWGMDVIGLITPKASNGHRFILVAIDYFTK 131

[Close]

BLAST of CSPI01G16850 vs. NCBI nr
Match: gi|659134004|ref|XP_008466990.1| (PREDICTED: uncharacterized protein LOC103504389 [Cucumis melo])

HSP 1 Score: 98.2 bits (243), Expect = 4.9e-18
Identity = 44/56 (78.57%), Postives = 48/56 (85.71%), Query Frame = 1


Query: 1   CQIYTDKIHAAAASPLHVLSAPWSFSLWGMDVIGPIDPKASNDQHFILVAIDYFTK 57
           CQIY DK HA A SPLHVL+APW FS+WG+DVIGPI+PKASN   FILVAIDYFTK
Sbjct: 244 CQIYADKTHAPA-SPLHVLTAPWPFSMWGLDVIGPIEPKASNGHRFILVAIDYFTK 298

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BLAST of CSPI01G16850 vs. NCBI nr
Match: gi|778708460|ref|XP_011656202.1| (PREDICTED: LOW QUALITY PROTEIN: uncharacterized protein K02A2.6-like [Cucumis sativus])

HSP 1 Score: 97.4 bits (241), Expect = 8.3e-18
Identity = 46/56 (82.14%), Postives = 48/56 (85.71%), Query Frame = 1


Query: 1   CQIYTDKIHAAAASPLHVLSAPWSFSLWGMDVIGPIDPKASNDQHFILVAIDYFTK 57
           CQIY D+IHAAA SPLHVLS P  FSLWG+DVIGPIDPKASN   FILVAIDYFTK
Sbjct: 151 CQIYMDRIHAAA-SPLHVLSTPXPFSLWGIDVIGPIDPKASNGHRFILVAIDYFTK 205

[Close]

BLAST of CSPI01G16850 vs. NCBI nr
Match: gi|823145327|ref|XP_012472556.1| (PREDICTED: uncharacterized protein LOC105789739 [Gossypium raimondii])

HSP 1 Score: 92.8 bits (229), Expect = 2.1e-16
Identity = 41/56 (73.21%), Postives = 45/56 (80.36%), Query Frame = 1


Query: 1    CQIYTDKIHAAAASPLHVLSAPWSFSLWGMDVIGPIDPKASNDQHFILVAIDYFTK 57
            CQIY DKIHA   SPLHV+++PW FS+WGMDVIGPI PKASN   FI V IDYFTK
Sbjct: 1062 CQIYGDKIHAPP-SPLHVMTSPWPFSMWGMDVIGPISPKASNGHRFIFVVIDYFTK 1116

[Close]

BLAST of CSPI01G16850 vs. NCBI nr
Match: gi|590658014|ref|XP_007034729.1| (RNA-directed DNA polymerase (Reverse transcriptase), Ribonuclease H, putative [Theobroma cacao])

HSP 1 Score: 92.4 bits (228), Expect = 2.7e-16
Identity = 42/56 (75.00%), Postives = 45/56 (80.36%), Query Frame = 1


Query: 1   CQIYTDKIHAAAASPLHVLSAPWSFSLWGMDVIGPIDPKASNDQHFILVAIDYFTK 57
           CQ+Y D+IHA  A PLHV SAPW FS+WGMDVIG I PKASN   FILVAIDYFTK
Sbjct: 665 CQVYADRIHAPPA-PLHVFSAPWPFSMWGMDVIGLITPKASNGHRFILVAIDYFTK 719

[Close]

BLAST of CSPI01G16850 vs. NCBI nr
Match: gi|823232073|ref|XP_012448745.1| (PREDICTED: uncharacterized protein LOC105771914 [Gossypium raimondii])

HSP 1 Score: 91.3 bits (225), Expect = 6.0e-16
Identity = 40/56 (71.43%), Postives = 43/56 (76.79%), Query Frame = 1


Query: 1   CQIYTDKIHAAAASPLHVLSAPWSFSLWGMDVIGPIDPKASNDQHFILVAIDYFTK 57
           CQIY DKIH    SPLH ++APW FS+WGMDVIGPI PKASN   FI V IDYFTK
Sbjct: 52  CQIYGDKIHVPP-SPLHAMTAPWQFSMWGMDVIGPISPKASNGHRFIFVVIDYFTK 106

The following BLAST results are available for this feature:

BLAST of CSPI01G16850 vs. Swiss-Prot


Match Name	E-value	Identity	Description

BLAST of CSPI01G16850 vs. TrEMBL


Match Name	E-value	Identity	Description
A0A061EKZ1_THECC	1.9e-16	75.00	RNA-directed DNA polymerase (Reverse transcriptase), Ribonuclease H, putative OS...	[more]
A0A061FF52_THECC	4.2e-16	73.21	RNA-directed DNA polymerase, putative OS=Theobroma cacao GN=TCM_034880 PE=4 SV=1	[more]
A0A061EGM3_THECC	4.2e-16	73.21	RNA-directed DNA polymerase (Reverse transcriptase), Ribonuclease H OS=Theobroma...	[more]
A0A061EXZ3_THECC	4.2e-16	73.21	RNA-directed DNA polymerase (Reverse transcriptase), Ribonuclease H, putative OS...	[more]
A0A061GA98_THECC	9.3e-16	75.00	RNA-directed DNA polymerase (Reverse transcriptase), Ribonuclease H OS=Theobroma...	[more]

BLAST of CSPI01G16850 vs. TAIR10


Match Name	E-value	Identity	Description

BLAST of CSPI01G16850 vs. NCBI nr


Match Name	E-value	Identity	Description
gi\|659134004\|ref\|XP_008466990.1\|	4.9e-18	78.57	PREDICTED: uncharacterized protein LOC103504389 [Cucumis melo]	[more]
gi\|778708460\|ref\|XP_011656202.1\|	8.3e-18	82.14	PREDICTED: LOW QUALITY PROTEIN: uncharacterized protein K02A2.6-like [Cucumis sa...	[more]
gi\|823145327\|ref\|XP_012472556.1\|	2.1e-16	73.21	PREDICTED: uncharacterized protein LOC105789739 [Gossypium raimondii]	[more]
gi\|590658014\|ref\|XP_007034729.1\|	2.7e-16	75.00	RNA-directed DNA polymerase (Reverse transcriptase), Ribonuclease H, putative [T...	[more]
gi\|823232073\|ref\|XP_012448745.1\|	6.0e-16	71.43	PREDICTED: uncharacterized protein LOC105771914 [Gossypium raimondii]	[more]

Annotated Terms

The following terms have been associated with this gene:

Vocabulary: **INTERPRO**
Term	Definition
IPR012337	RNaseH-like_sf

Vocabulary: **Molecular Function**
Term	Definition
GO:0003676	nucleic acid binding

GO Annotation

GO Assignments

This gene is annotated with the following GO terms.

Category	Term Accession	Term Name
biological_process	GO:0015074	DNA integration
biological_process	GO:0051252	regulation of RNA metabolic process
biological_process	GO:0006278	RNA-dependent DNA biosynthetic process
biological_process	GO:0090502	RNA phosphodiester bond hydrolysis, endonucleolytic
cellular_component	GO:0005575	cellular_component
molecular_function	GO:0003676	nucleic acid binding
molecular_function	GO:0003964	RNA-directed DNA polymerase activity
molecular_function	GO:0004523	RNA-DNA hybrid ribonuclease activity

Relationships

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


Feature Name	Unique Name	Type
CSPI01G16850.1	CSPI01G16850.1	mRNA

InterPro

Analysis Name: InterPro Annotations of cucumber (PI183967)
Date Performed: 2017-01-17


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
IPR012337	Ribonuclease H-like domain	GENE3D	G3DSA:3.30.420.10		coord: 20..56 score: 2.
IPR012337	Ribonuclease H-like domain	unknown	SSF53098	Ribonuclease H-like	coord: 20..56 score: 9.

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
CSPI01G16850	Melon (DHL92) v3.6.1	cpimedB044
CSPI01G16850	Cucumber (Gy14) v2	cgybcpiB006
CSPI01G16850	Silver-seed gourd	carcpiB0040
CSPI01G16850	Silver-seed gourd	carcpiB0138
CSPI01G16850	Silver-seed gourd	carcpiB0142
CSPI01G16850	Cucumber (Chinese Long) v3	cpicucB005
CSPI01G16850	Watermelon (97103) v2	cpiwmbB074
CSPI01G16850	Wax gourd	cpiwgoB089
CSPI01G16850	Cucurbita maxima (Rimu)	cmacpiB056
CSPI01G16850	Cucurbita maxima (Rimu)	cmacpiB094
CSPI01G16850	Cucurbita moschata (Rifu)	cmocpiB047
CSPI01G16850	Cucurbita moschata (Rifu)	cmocpiB085
CSPI01G16850	Cucumber (Chinese Long) v2	cpicuB000
CSPI01G16850	Melon (DHL92) v3.5.1	cpimeB050
CSPI01G16850	Watermelon (Charleston Gray)	cpiwcgB079
CSPI01G16850	Watermelon (97103) v1	cpiwmB092
CSPI01G16850	Cucurbita pepo (Zucchini)	cpecpiB351
CSPI01G16850	Cucurbita pepo (Zucchini)	cpecpiB368
CSPI01G16850	Cucurbita pepo (Zucchini)	cpecpiB640
CSPI01G16850	Cucurbita pepo (Zucchini)	cpecpiB663
CSPI01G16850	Bottle gourd (USVL1VR-Ls)	cpilsiB078