CmoCh20G001250 (gene) Cucurbita moschata (Rifu) v1

Overview


Name	CmoCh20G001250
Type	gene
Organism	Cucurbita moschata (Cucurbita moschata (Rifu) v1)
Description	splicing factor 3B subunit 6-like protein
Location	Cmo_Chr20: 630842 .. 631066 (-)
RNA-Seq Expression	CmoCh20G001250
Synteny	CmoCh20G001250

Sequences

The following sequences are available for this feature:

Gene sequence (with intron)

Legend: exonCDSpolypeptide

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

ATGTATGATATCTTCGGCAAGTACGGGGCGATCCGGCAGATTCGGATTGGGACGAACAAGGATACGAGAGGTACCGCCTTTGTTGTTTACGAAGATATCTATGATGCTAAGACGGCAGTGGATCACCTCTCCGGTTTCAACGTTGCGAATCGGTATCTGATCGTGTTGTACTACCAGCAGGCCAAGATGAGCAAAAAGTTCGACCAAGAAGAAGAAAGAGGATGA

mRNA sequence

ATGTATGATATCTTCGGCAAGTACGGGGCGATCCGGCAGATTCGGATTGGGACGAACAAGGATACGAGAGGTACCGCCTTTGTTGTTTACGAAGATATCTATGATGCTAAGACGGCAGTGGATCACCTCTCCGGTTTCAACGTTGCGAATCGGTATCTGATCGTGTTGTACTACCAGCAGGCCAAGATGAGCAAAAAGTTCGACCAAGAAGAAGAAAGAGGATGA

Coding sequence (CDS)

ATGTATGATATCTTCGGCAAGTACGGGGCGATCCGGCAGATTCGGATTGGGACGAACAAGGATACGAGAGGTACCGCCTTTGTTGTTTACGAAGATATCTATGATGCTAAGACGGCAGTGGATCACCTCTCCGGTTTCAACGTTGCGAATCGGTATCTGATCGTGTTGTACTACCAGCAGGCCAAGATGAGCAAAAAGTTCGACCAAGAAGAAGAAAGAGGATGA

Protein sequence

MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQAKMSKKFDQEEERG

Homology

[Close]

BLAST of CmoCh20G001250 vs. ExPASy Swiss-Prot
Match: Q9FMP4 (Splicing factor 3B subunit 6-like protein OS=Arabidopsis thaliana OX=3702 GN=At5g12190 PE=1 SV=1)

HSP 1 Score: 131.7 bits (330), Expect = 3.4e-30
Identity = 63/71 (88.73%), Postives = 67/71 (94.37%), Query Frame = 0


Query: 1   MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ 60
           MYDIFGKYGAIRQIRIG +K T+GTAFVVYEDIYDAK AVDHLSGFNVANRYLIVLYYQ 
Sbjct: 35  MYDIFGKYGAIRQIRIGCDKATKGTAFVVYEDIYDAKNAVDHLSGFNVANRYLIVLYYQH 94

Query: 61  AKMSKKFDQEE 72
           AKMSKKFDQ++
Sbjct: 95  AKMSKKFDQKK 105

[Close]

BLAST of CmoCh20G001250 vs. ExPASy Swiss-Prot
Match: Q9VRV7 (Splicing factor 3B subunit 6 OS=Drosophila melanogaster OX=7227 GN=Sf3b6 PE=1 SV=1)

HSP 1 Score: 112.8 bits (281), Expect = 1.6e-24
Identity = 51/73 (69.86%), Postives = 61/73 (83.56%), Query Frame = 0


Query: 1   MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ 60
           MYDIFGK+GAIRQIR+G   +TRGTAFVVYEDI+DAK A DHLSGFNV NRYL+VLYYQ 
Sbjct: 31  MYDIFGKFGAIRQIRVGNTPETRGTAFVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYQS 90

Query: 61  AKMSKKFDQEEER 74
            K  K+ D ++++
Sbjct: 91  NKAFKRVDMDKKQ 103

[Close]

BLAST of CmoCh20G001250 vs. ExPASy Swiss-Prot
Match: Q8ITY4 (Splicing factor 3B subunit 6-like protein OS=Caenorhabditis elegans OX=6239 GN=C50D2.5 PE=3 SV=2)

HSP 1 Score: 112.5 bits (280), Expect = 2.1e-24
Identity = 50/73 (68.49%), Postives = 62/73 (84.93%), Query Frame = 0


Query: 1   MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ 60
           MY+IFGK+GA+RQIR+G   +TRGTAFVVYEDI+DAKTA +HLSG+NV+NRYL+VLYYQ 
Sbjct: 35  MYEIFGKFGAVRQIRVGNTAETRGTAFVVYEDIFDAKTACEHLSGYNVSNRYLVVLYYQA 94

Query: 61  AKMSKKFDQEEER 74
            K  K+ D E+ R
Sbjct: 95  TKAWKRMDTEKAR 107

[Close]

BLAST of CmoCh20G001250 vs. ExPASy Swiss-Prot
Match: Q9Y3B4 (Splicing factor 3B subunit 6 OS=Homo sapiens OX=9606 GN=SF3B6 PE=1 SV=1)

HSP 1 Score: 107.1 bits (266), Expect = 8.8e-23
Identity = 48/72 (66.67%), Postives = 58/72 (80.56%), Query Frame = 0


Query: 1   MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ 60
           MYDIFGKYG IRQIR+G   +TRGTA+VVYEDI+DAK A DHLSGFNV NRYL+VLYY  
Sbjct: 35  MYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNA 94

Query: 61  AKMSKKFDQEEE 73
            +  +K D +++
Sbjct: 95  NRAFQKMDTKKK 106

[Close]

BLAST of CmoCh20G001250 vs. ExPASy Swiss-Prot
Match: P59708 (Splicing factor 3B subunit 6 OS=Mus musculus OX=10090 GN=Sf3b6 PE=1 SV=1)

HSP 1 Score: 107.1 bits (266), Expect = 8.8e-23
Identity = 48/72 (66.67%), Postives = 58/72 (80.56%), Query Frame = 0


Query: 1   MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ 60
           MYDIFGKYG IRQIR+G   +TRGTA+VVYEDI+DAK A DHLSGFNV NRYL+VLYY  
Sbjct: 35  MYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVLYYNA 94

Query: 61  AKMSKKFDQEEE 73
            +  +K D +++
Sbjct: 95  NRAFQKMDTKKK 106

[Close]

BLAST of CmoCh20G001250 vs. ExPASy TrEMBL
Match: B7FGI3 (Pre-mRNA branch site p14-like protein OS=Medicago truncatula OX=3880 GN=MTR_5g089300 PE=2 SV=1)

HSP 1 Score: 144.4 bits (363), Expect = 1.8e-31
Identity = 69/72 (95.83%), Postives = 72/72 (100.00%), Query Frame = 0


Query: 1   MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ 60
           MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ
Sbjct: 35  MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ 94

Query: 61  AKMSKKFDQEEE 73
           AKMSKKFDQ+++
Sbjct: 95  AKMSKKFDQKKK 106

[Close]

BLAST of CmoCh20G001250 vs. ExPASy TrEMBL
Match: A0A7J6H7N5 (RRM domain-containing protein OS=Cannabis sativa OX=3483 GN=F8388_008198 PE=4 SV=1)

HSP 1 Score: 144.4 bits (363), Expect = 1.8e-31
Identity = 69/72 (95.83%), Postives = 72/72 (100.00%), Query Frame = 0


Query: 1   MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ 60
           MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ
Sbjct: 35  MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ 94

Query: 61  AKMSKKFDQEEE 73
           AKMSKKFDQ+++
Sbjct: 95  AKMSKKFDQKKK 106

[Close]

BLAST of CmoCh20G001250 vs. ExPASy TrEMBL
Match: A0A438DLJ3 (Splicing factor 3B subunit 6-like protein OS=Vitis vinifera OX=29760 GN=VvCHDh000810_0 PE=4 SV=1)

HSP 1 Score: 144.4 bits (363), Expect = 1.8e-31
Identity = 69/72 (95.83%), Postives = 72/72 (100.00%), Query Frame = 0


Query: 1   MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ 60
           MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ
Sbjct: 35  MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ 94

Query: 61  AKMSKKFDQEEE 73
           AKMSKKFDQ+++
Sbjct: 95  AKMSKKFDQKKK 106

[Close]

BLAST of CmoCh20G001250 vs. ExPASy TrEMBL
Match: A5AES3 (RRM domain-containing protein OS=Vitis vinifera OX=29760 GN=VIT_06s0009g02770 PE=4 SV=1)

HSP 1 Score: 144.4 bits (363), Expect = 1.8e-31
Identity = 69/72 (95.83%), Postives = 72/72 (100.00%), Query Frame = 0


Query: 1   MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ 60
           MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ
Sbjct: 35  MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ 94

Query: 61  AKMSKKFDQEEE 73
           AKMSKKFDQ+++
Sbjct: 95  AKMSKKFDQKKK 106

[Close]

BLAST of CmoCh20G001250 vs. ExPASy TrEMBL
Match: V7B6G4 (RRM domain-containing protein OS=Phaseolus vulgaris OX=3885 GN=PHAVU_008G202000g PE=4 SV=1)

HSP 1 Score: 144.4 bits (363), Expect = 1.8e-31
Identity = 69/72 (95.83%), Postives = 72/72 (100.00%), Query Frame = 0


Query: 1   MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ 60
           MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ
Sbjct: 35  MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ 94

Query: 61  AKMSKKFDQEEE 73
           AKMSKKFDQ+++
Sbjct: 95  AKMSKKFDQKKK 106

[Close]

BLAST of CmoCh20G001250 vs. NCBI nr
Match: VFQ65098.1 (unnamed protein product [Cuscuta campestris])

HSP 1 Score: 144.4 bits (363), Expect = 3.8e-31
Identity = 69/72 (95.83%), Postives = 72/72 (100.00%), Query Frame = 0


Query: 1   MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ 60
           MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ
Sbjct: 35  MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ 94

Query: 61  AKMSKKFDQEEE 73
           AKMSKKFDQ+++
Sbjct: 95  AKMSKKFDQKKK 106

[Close]

BLAST of CmoCh20G001250 vs. NCBI nr
Match: TMW81722.1 (hypothetical protein EJD97_008160, partial [Solanum chilense])

HSP 1 Score: 144.4 bits (363), Expect = 3.8e-31
Identity = 69/72 (95.83%), Postives = 72/72 (100.00%), Query Frame = 0


Query: 1  MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ 60
          MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ
Sbjct: 28 MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ 87

Query: 61 AKMSKKFDQEEE 73
          AKMSKKFDQ+++
Sbjct: 88 AKMSKKFDQKKK 99

[Close]

BLAST of CmoCh20G001250 vs. NCBI nr
Match: XP_024639474.1 (splicing factor 3B subunit 6-like protein [Medicago truncatula] >ACJ83862.1 unknown [Medicago truncatula] >AET00189.2 Pre-mRNA branch site p14-like protein [Medicago truncatula] >AFK49453.1 unknown [Medicago truncatula] >RHN57553.1 putative nucleotide-binding alpha-beta plait domain-containing protein [Medicago truncatula])

HSP 1 Score: 144.4 bits (363), Expect = 3.8e-31
Identity = 69/72 (95.83%), Postives = 72/72 (100.00%), Query Frame = 0


Query: 1   MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ 60
           MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ
Sbjct: 35  MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ 94

Query: 61  AKMSKKFDQEEE 73
           AKMSKKFDQ+++
Sbjct: 95  AKMSKKFDQKKK 106

[Close]

BLAST of CmoCh20G001250 vs. NCBI nr
Match: XP_021888985.1 (splicing factor 3B subunit 6-like protein [Carica papaya])

HSP 1 Score: 144.4 bits (363), Expect = 3.8e-31
Identity = 69/72 (95.83%), Postives = 72/72 (100.00%), Query Frame = 0


Query: 1   MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ 60
           MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ
Sbjct: 35  MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ 94

Query: 61  AKMSKKFDQEEE 73
           AKMSKKFDQ+++
Sbjct: 95  AKMSKKFDQKKK 106

[Close]

BLAST of CmoCh20G001250 vs. NCBI nr
Match: MCH99409.1 (pre-mRNA branch site p14-like [Trifolium medium])

HSP 1 Score: 144.4 bits (363), Expect = 3.8e-31
Identity = 69/72 (95.83%), Postives = 72/72 (100.00%), Query Frame = 0


Query: 1   MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ 60
           MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ
Sbjct: 35  MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ 94

Query: 61  AKMSKKFDQEEE 73
           AKMSKKFDQ+++
Sbjct: 95  AKMSKKFDQKKK 106

[Close]

BLAST of CmoCh20G001250 vs. TAIR 10
Match: AT5G12190.1 (RNA-binding (RRM/RBD/RNP motifs) family protein )

HSP 1 Score: 131.7 bits (330), Expect = 2.4e-31
Identity = 63/71 (88.73%), Postives = 67/71 (94.37%), Query Frame = 0


Query: 1   MYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQ 60
           MYDIFGKYGAIRQIRIG +K T+GTAFVVYEDIYDAK AVDHLSGFNVANRYLIVLYYQ 
Sbjct: 35  MYDIFGKYGAIRQIRIGCDKATKGTAFVVYEDIYDAKNAVDHLSGFNVANRYLIVLYYQH 94

Query: 61  AKMSKKFDQEE 72
           AKMSKKFDQ++
Sbjct: 95  AKMSKKFDQKK 105

[Close]

BLAST of CmoCh20G001250 vs. TAIR 10
Match: AT2G14870.1 (RNA-binding (RRM/RBD/RNP motifs) family protein )

HSP 1 Score: 73.6 bits (179), Expect = 7.7e-14
Identity = 32/42 (76.19%), Postives = 36/42 (85.71%), Query Frame = 0


Query: 2  YDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHL 44
          YD+FG+Y  IRQ+RIG  K T+GTAFVVYEDIYDAK AVDHL
Sbjct: 37 YDLFGRYSTIRQVRIGCEKGTKGTAFVVYEDIYDAKKAVDHL 78

The following BLAST results are available for this feature:

BLAST of CmoCh20G001250 vs. ExPASy Swiss-Prot


Match Name	E-value	Identity	Description
Q9FMP4	3.4e-30	88.73	Splicing factor 3B subunit 6-like protein OS=Arabidopsis thaliana OX=3702 GN=At5...	[more]
Q9VRV7	1.6e-24	69.86	Splicing factor 3B subunit 6 OS=Drosophila melanogaster OX=7227 GN=Sf3b6 PE=1 SV...	[more]
Q8ITY4	2.1e-24	68.49	Splicing factor 3B subunit 6-like protein OS=Caenorhabditis elegans OX=6239 GN=C...	[more]
Q9Y3B4	8.8e-23	66.67	Splicing factor 3B subunit 6 OS=Homo sapiens OX=9606 GN=SF3B6 PE=1 SV=1	[more]
P59708	8.8e-23	66.67	Splicing factor 3B subunit 6 OS=Mus musculus OX=10090 GN=Sf3b6 PE=1 SV=1	[more]

BLAST of CmoCh20G001250 vs. ExPASy TrEMBL


Match Name	E-value	Identity	Description
B7FGI3	1.8e-31	95.83	Pre-mRNA branch site p14-like protein OS=Medicago truncatula OX=3880 GN=MTR_5g08...	[more]
A0A7J6H7N5	1.8e-31	95.83	RRM domain-containing protein OS=Cannabis sativa OX=3483 GN=F8388_008198 PE=4 SV...	[more]
A0A438DLJ3	1.8e-31	95.83	Splicing factor 3B subunit 6-like protein OS=Vitis vinifera OX=29760 GN=VvCHDh00...	[more]
A5AES3	1.8e-31	95.83	RRM domain-containing protein OS=Vitis vinifera OX=29760 GN=VIT_06s0009g02770 PE...	[more]
V7B6G4	1.8e-31	95.83	RRM domain-containing protein OS=Phaseolus vulgaris OX=3885 GN=PHAVU_008G202000g...	[more]

BLAST of CmoCh20G001250 vs. NCBI nr


Match Name	E-value	Identity	Description
VFQ65098.1	3.8e-31	95.83	unnamed protein product [Cuscuta campestris]	[more]
TMW81722.1	3.8e-31	95.83	hypothetical protein EJD97_008160, partial [Solanum chilense]	[more]
XP_024639474.1	3.8e-31	95.83	splicing factor 3B subunit 6-like protein [Medicago truncatula] >ACJ83862.1 unkn...	[more]
XP_021888985.1	3.8e-31	95.83	splicing factor 3B subunit 6-like protein [Carica papaya]	[more]
MCH99409.1	3.8e-31	95.83	pre-mRNA branch site p14-like [Trifolium medium]	[more]

BLAST of CmoCh20G001250 vs. TAIR 10


Match Name	E-value	Identity	Description
AT5G12190.1	2.4e-31	88.73	RNA-binding (RRM/RBD/RNP motifs) family protein	[more]
AT2G14870.1	7.7e-14	76.19	RNA-binding (RRM/RBD/RNP motifs) family protein	[more]

InterPro

Analysis Name: InterPro Annotations of Cucurbita moschata (Rifu) v1
Date Performed: 2021-10-25


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
IPR012677	Nucleotide-binding alpha-beta plait domain superfamily	GENE3D	3.30.70.330		coord: 1..74 e-value: 2.9E-13 score: 52.0
IPR000504	RNA recognition motif domain	PFAM	PF00076	RRM_1	coord: 2..53 e-value: 8.3E-11 score: 41.6
IPR000504	RNA recognition motif domain	PROSITE	PS50102	RRM	coord: 1..60 score: 12.014563
None	No IPR available	PANTHER	PTHR12785	SPLICING FACTOR 3B	coord: 1..71
None	No IPR available	PANTHER	PTHR12785:SF7	SPLICING FACTOR 3B SUBUNIT 6	coord: 1..71
IPR034150	SF3B6, RNA recognition motif	CDD	cd12241	RRM_SF3B14	coord: 1..59 e-value: 2.10973E-38 score: 120.029
IPR035979	RNA-binding domain superfamily	SUPERFAMILY	54928	RNA-binding domain, RBD	coord: 2..70

Relationships

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


Feature Name	Unique Name	Type
CmoCh20G001250.1	CmoCh20G001250.1	mRNA

GO Annotation

GO Assignments

This gene is annotated with the following GO terms.

Category	Term Accession	Term Name
biological_process	GO:0000398	mRNA splicing, via spliceosome
cellular_component	GO:0071013	catalytic step 2 spliceosome
cellular_component	GO:0016021	integral component of membrane
cellular_component	GO:0071011	precatalytic spliceosome
cellular_component	GO:0005689	U12-type spliceosomal complex
cellular_component	GO:0005686	U2 snRNP
cellular_component	GO:0005684	U2-type spliceosomal complex
molecular_function	GO:0003723	RNA binding
molecular_function	GO:0003676	nucleic acid binding