CmaCh19G003250 (gene) Cucurbita maxima (Rimu) | Cucurbit Genomics Database (CuGenDB)

Overview


Name	CmaCh19G003250
Type	gene
Organism	Cucurbita maxima (Cucurbita maxima (Rimu))
Description	Retrovirus-related Pol polyprotein from transposon TNT 1-94
Location	Cma_Chr19 : 3104042 .. 3104791 (+)

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.

ATGTTACCCGAGACGCGGGTTGTGGAGAAGATCTTGAGGTCGTTAACAGACAACTTCAAGAATGTTGTATGTGCCATAAAAGAGTCGAAGGACCTAGTGACGTTCACGGACGATAAGCTTGTCAGTTCTCTCGTGGCACACGAGCAACGTAAGAAAAAGAAGAAGGAGACACTCGATCAAGCGCTTCAAACTAAGGCATCAATAAAAGATGAAAAGATACTCTACTCTCAAAATACTCAAGGTAGAGGTCGAGGAAGTCGCGGGAATGGTCGAGGTAGTCAAAGCAACAGTAAATTGGTGTGGAAGAGGATGCAGTCGAGGAAGAGGCGGCCGATCAAACATTCATTGCTATAAATGTCAAGAATATGGTACATGGGCTACCAAACATGGACTTTGAAGGAAAATTTTGTGAAGAATGTATGTTCAGCAAGCATGCGAGAACCTCAATTCAAAAGAAGGCTGAATTTTGGACTAAACAACCTTTCGAGTTGATCCATACATATATATGTGGATCAATTAACCCCTAGTCTAATTTAATAACTGTATATTTTTCTTCCCCATCGGAGTGCAAACTTATGTTGTAACAATGATGTGGTATATCTTCTGCAGGTTCATAAGCCGTTGAATCAAGTGCTTTTATCTATGGTTGATCAAGATGCTGGTCACGTTAATAATCATAACTTGAGTGCTGATGAACTGCAGCAAACTTACTCAGTGGACGAGTTTGAGATTCGGATTTTGGAACTGTAA

mRNA sequence

ATGTTACCCGAGACGCGGGTTGTGGAGAAGATCTTGAGGTCGTTAACAGACAACTTCAAGAATGTTGTATGTGCCATAAAAGAGTCGAAGGACCTAGTGACGTTCACGGACGATAAGCTTGTCAGTTCTCTCGTGGCACACGAGCAACGTAAGAAAAAGAAGAAGGAGACACTCGATCAAGCGCTTCAAACTAAGGCATCAATAAAAGATGAAAAGATACTCTACTCTCAAAATACTCAAGTCGAGGAAGAGGCGGCCGATCAAACATTCATTGCTATAAATGTCAAGAATATGGTTCATAAGCCGTTGAATCAAGTGCTTTTATCTATGGTTGATCAAGATGCTGGTCACGTTAATAATCATAACTTGAGTGCTGATGAACTGCAGCAAACTTACTCAGTGGACGAGTTTGAGATTCGGATTTTGGAACTGTAA

Coding sequence (CDS)

ATGTTACCCGAGACGCGGGTTGTGGAGAAGATCTTGAGGTCGTTAACAGACAACTTCAAGAATGTTGTATGTGCCATAAAAGAGTCGAAGGACCTAGTGACGTTCACGGACGATAAGCTTGTCAGTTCTCTCGTGGCACACGAGCAACGTAAGAAAAAGAAGAAGGAGACACTCGATCAAGCGCTTCAAACTAAGGCATCAATAAAAGATGAAAAGATACTCTACTCTCAAAATACTCAAGTCGAGGAAGAGGCGGCCGATCAAACATTCATTGCTATAAATGTCAAGAATATGGTTCATAAGCCGTTGAATCAAGTGCTTTTATCTATGGTTGATCAAGATGCTGGTCACGTTAATAATCATAACTTGAGTGCTGATGAACTGCAGCAAACTTACTCAGTGGACGAGTTTGAGATTCGGATTTTGGAACTGTAA

Protein sequence

MLPETRVVEKILRSLTDNFKNVVCAIKESKDLVTFTDDKLVSSLVAHEQRKKKKKETLDQALQTKASIKDEKILYSQNTQVEEEAADQTFIAINVKNMVHKPLNQVLLSMVDQDAGHVNNHNLSADELQQTYSVDEFEIRILEL

Homology

[Close]

BLAST of CmaCh19G003250 vs. Swiss-Prot
Match: CPSF1_ARATH (Cleavage and polyadenylation specificity factor subunit 1 OS=Arabidopsis thaliana GN=CPSF160 PE=1 SV=2)

HSP 1 Score: 65.1 bits (157), Expect = 7.3e-10
Identity = 33/59 (55.93%), Postives = 47/59 (79.66%), Query Frame = 1


Query: 86   ADQTFIAINVKNMVHKPLNQVLLSMVDQDAGH-VNNHNLSADELQQTYSVDEFEIRILE 144
            A++    + V   V KPLNQVL S+VDQ+AG  ++NHN+S+D+LQ+TY+V+EFEI+ILE
Sbjct: 1031 AEKNLYPLIVSYPVSKPLNQVLSSLVDQEAGQQLDNHNMSSDDLQRTYTVEEFEIQILE 1089

[Close]

BLAST of CmaCh19G003250 vs. Swiss-Prot
Match: CPSF1_ORYSJ (Probable cleavage and polyadenylation specificity factor subunit 1 OS=Oryza sativa subsp. japonica GN=Os04g0252200 PE=3 SV=2)

HSP 1 Score: 55.5 bits (132), Expect = 5.7e-07
Identity = 31/60 (51.67%), Postives = 42/60 (70.00%), Query Frame = 1


Query: 86   ADQTFIAINVKNMVHKPLNQVLLSMVDQDA-GHVNNHNLSADELQQTYSVDEFEIRILEL 145
            A+Q+   + V   V +PLNQVL SM DQ++  H++N   S D L +TY+VDEFE+RILEL
Sbjct: 1029 AEQSLYPLIVSVPVVRPLNQVLSSMADQESVHHMDNDVTSTDALHKTYTVDEFEVRILEL 1088

[Close]

BLAST of CmaCh19G003250 vs. TrEMBL
Match: A0A059QBK0_PHAVU (Polyprotein OS=Phaseolus vulgaris PE=4 SV=1)

HSP 1 Score: 110.5 bits (275), Expect = 1.7e-21
Identity = 60/80 (75.00%), Postives = 70/80 (87.50%), Query Frame = 1


Query: 2   LPETRVVEKILRSLTDNFKNVVCAIKESKDLVTFTDDKLVSSLVAHEQRKKKKK-ETLDQ 61
           L + RVVEKILR+LTDNF+++VCAI+ESKDL T T D+L  SL AHEQRKKKKK ETL+Q
Sbjct: 153 LTDARVVEKILRTLTDNFESIVCAIEESKDLATLTVDELAGSLEAHEQRKKKKKEETLEQ 212

Query: 62  ALQTKASIKDEKILYSQNTQ 81
           ALQTKASIKDEK+LY QN+Q
Sbjct: 213 ALQTKASIKDEKVLYHQNSQ 232

[Close]

BLAST of CmaCh19G003250 vs. TrEMBL
Match: A0A151RCL3_CAJCA (Uncharacterized protein OS=Cajanus cajan GN=KK1_038469 PE=4 SV=1)

HSP 1 Score: 101.7 bits (252), Expect = 7.8e-19
Identity = 57/78 (73.08%), Postives = 65/78 (83.33%), Query Frame = 1


Query: 2   LPETRVVEKILRSLTDNFKNVVCAIKESKDLVTFTDDKLVSSLVAHEQRKKKK-KETLDQ 61
           L + RVVEKILRSLTD+F+NV+CAI+ESKDL   T D+L  SL AHEQRKKKK +E L+Q
Sbjct: 153 LTDVRVVEKILRSLTDSFENVICAIEESKDLTMITVDELAESLEAHEQRKKKKEEEILEQ 212

Query: 62  ALQTKASIKDEKILYSQN 79
           ALQ KASIKDEK LYSQN
Sbjct: 213 ALQIKASIKDEKALYSQN 230

[Close]

BLAST of CmaCh19G003250 vs. TrEMBL
Match: A0A151T3L7_CAJCA (Gag-Pol polyprotein OS=Cajanus cajan GN=KK1_016136 PE=4 SV=1)

HSP 1 Score: 101.3 bits (251), Expect = 1.0e-18
Identity = 55/82 (67.07%), Postives = 69/82 (84.15%), Query Frame = 1


Query: 2   LPETRVVEKILRSLTDNFKNVVCAIKESKDLVTFTDDKLVSSLVAHEQRKKKKK---ETL 61
           LP +RVVEKILRSLTD+F+N+VCAI+ESKDL T T ++L  SL A+EQRKK KK   E+L
Sbjct: 128 LPSSRVVEKILRSLTDDFENIVCAIEESKDLSTLTVEELTGSLEAYEQRKKNKKEKGESL 187

Query: 62  DQALQTKASIKDEKILYSQNTQ 81
           +QALQ KA+IKDEK+LY+QN +
Sbjct: 188 EQALQAKATIKDEKVLYAQNNR 209

[Close]

BLAST of CmaCh19G003250 vs. TrEMBL
Match: A0A151QZS0_CAJCA (Retrovirus-related Pol polyprotein from transposon TNT 1-94 OS=Cajanus cajan GN=KK1_043206 PE=4 SV=1)

HSP 1 Score: 99.8 bits (247), Expect = 3.0e-18
Identity = 54/82 (65.85%), Postives = 69/82 (84.15%), Query Frame = 1


Query: 2   LPETRVVEKILRSLTDNFKNVVCAIKESKDLVTFTDDKLVSSLVAHEQRKKKKK---ETL 61
           LP +RVVEKILRSLTD+F+N+VCAI+ESKDL T T ++L  SL A+EQRKK KK   E+L
Sbjct: 153 LPSSRVVEKILRSLTDDFENIVCAIEESKDLSTLTVEELTGSLEAYEQRKKNKKEKGESL 212

Query: 62  DQALQTKASIKDEKILYSQNTQ 81
           +QALQ KA+IK+EK+LY+QN +
Sbjct: 213 EQALQAKATIKEEKVLYAQNNR 234

[Close]

BLAST of CmaCh19G003250 vs. TrEMBL
Match: A0A151TA96_CAJCA (Gag polyprotein OS=Cajanus cajan GN=KK1_018540 PE=4 SV=1)

HSP 1 Score: 99.8 bits (247), Expect = 3.0e-18
Identity = 54/82 (65.85%), Postives = 69/82 (84.15%), Query Frame = 1


Query: 2   LPETRVVEKILRSLTDNFKNVVCAIKESKDLVTFTDDKLVSSLVAHEQRKKKKK---ETL 61
           LP +RVVEKILRSLTD+F+N+VCAI+ESKDL T T ++L  SL A+EQRKK KK   E+L
Sbjct: 153 LPSSRVVEKILRSLTDDFENIVCAIEESKDLSTLTVEELTGSLEAYEQRKKNKKEKGESL 212

Query: 62  DQALQTKASIKDEKILYSQNTQ 81
           +QALQ KA+IK+EK+LY+QN +
Sbjct: 213 EQALQAKATIKEEKVLYAQNNR 234

[Close]

BLAST of CmaCh19G003250 vs. TAIR10
Match: AT5G51660.1 (AT5G51660.1 cleavage and polyadenylation specificity factor 160)

HSP 1 Score: 65.1 bits (157), Expect = 4.1e-11
Identity = 33/59 (55.93%), Postives = 47/59 (79.66%), Query Frame = 1


Query: 86   ADQTFIAINVKNMVHKPLNQVLLSMVDQDAGH-VNNHNLSADELQQTYSVDEFEIRILE 144
            A++    + V   V KPLNQVL S+VDQ+AG  ++NHN+S+D+LQ+TY+V+EFEI+ILE
Sbjct: 1031 AEKNLYPLIVSYPVSKPLNQVLSSLVDQEAGQQLDNHNMSSDDLQRTYTVEEFEIQILE 1089

[Close]

BLAST of CmaCh19G003250 vs. NCBI nr
Match: gi|545693870|gb|AGW47867.1| (polyprotein [Phaseolus vulgaris])

HSP 1 Score: 110.5 bits (275), Expect = 2.4e-21
Identity = 60/80 (75.00%), Postives = 70/80 (87.50%), Query Frame = 1


Query: 2   LPETRVVEKILRSLTDNFKNVVCAIKESKDLVTFTDDKLVSSLVAHEQRKKKKK-ETLDQ 61
           L + RVVEKILR+LTDNF+++VCAI+ESKDL T T D+L  SL AHEQRKKKKK ETL+Q
Sbjct: 153 LTDARVVEKILRTLTDNFESIVCAIEESKDLATLTVDELAGSLEAHEQRKKKKKEETLEQ 212

Query: 62  ALQTKASIKDEKILYSQNTQ 81
           ALQTKASIKDEK+LY QN+Q
Sbjct: 213 ALQTKASIKDEKVLYHQNSQ 232

[Close]

BLAST of CmaCh19G003250 vs. NCBI nr
Match: gi|1012328580|gb|KYP40213.1| (hypothetical protein KK1_038469 [Cajanus cajan])

HSP 1 Score: 101.7 bits (252), Expect = 1.1e-18
Identity = 57/78 (73.08%), Postives = 65/78 (83.33%), Query Frame = 1


Query: 2   LPETRVVEKILRSLTDNFKNVVCAIKESKDLVTFTDDKLVSSLVAHEQRKKKK-KETLDQ 61
           L + RVVEKILRSLTD+F+NV+CAI+ESKDL   T D+L  SL AHEQRKKKK +E L+Q
Sbjct: 153 LTDVRVVEKILRSLTDSFENVICAIEESKDLTMITVDELAESLEAHEQRKKKKEEEILEQ 212

Query: 62  ALQTKASIKDEKILYSQN 79
           ALQ KASIKDEK LYSQN
Sbjct: 213 ALQIKASIKDEKALYSQN 230

[Close]

BLAST of CmaCh19G003250 vs. NCBI nr
Match: gi|1012350441|gb|KYP61630.1| (Gag-Pol polyprotein [Cajanus cajan])

HSP 1 Score: 101.3 bits (251), Expect = 1.5e-18
Identity = 55/82 (67.07%), Postives = 69/82 (84.15%), Query Frame = 1


Query: 2   LPETRVVEKILRSLTDNFKNVVCAIKESKDLVTFTDDKLVSSLVAHEQRKKKKK---ETL 61
           LP +RVVEKILRSLTD+F+N+VCAI+ESKDL T T ++L  SL A+EQRKK KK   E+L
Sbjct: 128 LPSSRVVEKILRSLTDDFENIVCAIEESKDLSTLTVEELTGSLEAYEQRKKNKKEKGESL 187

Query: 62  DQALQTKASIKDEKILYSQNTQ 81
           +QALQ KA+IKDEK+LY+QN +
Sbjct: 188 EQALQAKATIKDEKVLYAQNNR 209

[Close]

BLAST of CmaCh19G003250 vs. NCBI nr
Match: gi|1012352765|gb|KYP63953.1| (Gag polyprotein [Cajanus cajan])

HSP 1 Score: 99.8 bits (247), Expect = 4.2e-18
Identity = 54/82 (65.85%), Postives = 69/82 (84.15%), Query Frame = 1


Query: 2   LPETRVVEKILRSLTDNFKNVVCAIKESKDLVTFTDDKLVSSLVAHEQRKKKKK---ETL 61
           LP +RVVEKILRSLTD+F+N+VCAI+ESKDL T T ++L  SL A+EQRKK KK   E+L
Sbjct: 153 LPSSRVVEKILRSLTDDFENIVCAIEESKDLSTLTVEELTGSLEAYEQRKKNKKEKGESL 212

Query: 62  DQALQTKASIKDEKILYSQNTQ 81
           +QALQ KA+IK+EK+LY+QN +
Sbjct: 213 EQALQAKATIKEEKVLYAQNNR 234

[Close]

BLAST of CmaCh19G003250 vs. NCBI nr
Match: gi|1012323647|gb|KYP35753.1| (Retrovirus-related Pol polyprotein from transposon TNT 1-94 [Cajanus cajan])

HSP 1 Score: 99.8 bits (247), Expect = 4.2e-18
Identity = 54/82 (65.85%), Postives = 69/82 (84.15%), Query Frame = 1


Query: 2   LPETRVVEKILRSLTDNFKNVVCAIKESKDLVTFTDDKLVSSLVAHEQRKKKKK---ETL 61
           LP +RVVEKILRSLTD+F+N+VCAI+ESKDL T T ++L  SL A+EQRKK KK   E+L
Sbjct: 153 LPSSRVVEKILRSLTDDFENIVCAIEESKDLSTLTVEELTGSLEAYEQRKKNKKEKGESL 212

Query: 62  DQALQTKASIKDEKILYSQNTQ 81
           +QALQ KA+IK+EK+LY+QN +
Sbjct: 213 EQALQAKATIKEEKVLYAQNNR 234

The following BLAST results are available for this feature:

BLAST of CmaCh19G003250 vs. Swiss-Prot


Match Name	E-value	Identity	Description
CPSF1_ARATH	7.3e-10	55.93	Cleavage and polyadenylation specificity factor subunit 1 OS=Arabidopsis thalian...	[more]
CPSF1_ORYSJ	5.7e-07	51.67	Probable cleavage and polyadenylation specificity factor subunit 1 OS=Oryza sati...	[more]

BLAST of CmaCh19G003250 vs. TrEMBL


Match Name	E-value	Identity	Description
A0A059QBK0_PHAVU	1.7e-21	75.00	Polyprotein OS=Phaseolus vulgaris PE=4 SV=1	[more]
A0A151RCL3_CAJCA	7.8e-19	73.08	Uncharacterized protein OS=Cajanus cajan GN=KK1_038469 PE=4 SV=1	[more]
A0A151T3L7_CAJCA	1.0e-18	67.07	Gag-Pol polyprotein OS=Cajanus cajan GN=KK1_016136 PE=4 SV=1	[more]
A0A151QZS0_CAJCA	3.0e-18	65.85	Retrovirus-related Pol polyprotein from transposon TNT 1-94 OS=Cajanus cajan GN=...	[more]
A0A151TA96_CAJCA	3.0e-18	65.85	Gag polyprotein OS=Cajanus cajan GN=KK1_018540 PE=4 SV=1	[more]

BLAST of CmaCh19G003250 vs. TAIR10


Match Name	E-value	Identity	Description
AT5G51660.1	4.1e-11	55.93	cleavage and polyadenylation specificity factor 160	[more]

BLAST of CmaCh19G003250 vs. NCBI nr


Match Name	E-value	Identity	Description
gi\|545693870\|gb\|AGW47867.1\|	2.4e-21	75.00	polyprotein [Phaseolus vulgaris]	[more]
gi\|1012328580\|gb\|KYP40213.1\|	1.1e-18	73.08	hypothetical protein KK1_038469 [Cajanus cajan]	[more]
gi\|1012350441\|gb\|KYP61630.1\|	1.5e-18	67.07	Gag-Pol polyprotein [Cajanus cajan]	[more]
gi\|1012352765\|gb\|KYP63953.1\|	4.2e-18	65.85	Gag polyprotein [Cajanus cajan]	[more]
gi\|1012323647\|gb\|KYP35753.1\|	4.2e-18	65.85	Retrovirus-related Pol polyprotein from transposon TNT 1-94 [Cajanus cajan]	[more]

Annotated Terms

The following terms have been associated with this gene:

Vocabulary: **INTERPRO**
Term	Definition

GO Annotation

GO Assignments

This gene is annotated with the following GO terms.

Category	Term Accession	Term Name
biological_process	GO:0015074	DNA integration
cellular_component	GO:0005634	nucleus
molecular_function	GO:0003676	nucleic acid binding
molecular_function	GO:0008270	zinc ion binding

Relationships

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


Feature Name	Unique Name	Type
CmaCh19G003250.1	CmaCh19G003250.1	mRNA

InterPro

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


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
None	No IPR available	unknown	Coil	Coil	coord: 44..71 scor
None	No IPR available	PFAM	PF14223	Retrotran_gag_2	coord: 2..54 score: 6.

Synteny

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


Gene	Orthologue	Organism	Block
CmaCh19G003250	Bhi05G000501	Wax gourd	cmawgoB0649

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

None

The following block(s) are covering this gene:


Gene	Organism	Block
CmaCh19G003250	Watermelon (97103) v2	cmawmbB551
CmaCh19G003250	Watermelon (97103) v2	cmawmbB560
CmaCh19G003250	Cucurbita moschata (Rifu)	cmacmoB508
CmaCh19G003250	Cucurbita moschata (Rifu)	cmacmoB509
CmaCh19G003250	Cucurbita moschata (Rifu)	cmacmoB511
CmaCh19G003250	Cucurbita pepo (Zucchini)	cmacpeB522
CmaCh19G003250	Bottle gourd (USVL1VR-Ls)	cmalsiB482