CU093546 (transcribed_cluster) Cucumber (Chinese Long) v2 | Cucurbit Genomics Database (CuGenDB)

Overview


Name	CU093546
Type	transcribed_cluster
Organism	Cucumis. sativus (Cucumber (Chinese Long) v2)
Description	U2 small nuclear ribonucleoprotein B
Location	Chr1 : 2964762 .. 2965363 (+)
Sequence length	297

Genome Viewer

Sequences

The following sequences are available for this feature:

transcribed_cluster sequence

ATCAATCTGCGATGCCCAATGGAACAACTACTGAGAATGGAGGTTCAAATGCCACATTCCGTCATGCAAATCCGAGTGCTACAGAAGCTACTCCAAACAACATACTATTTATTGAGAATTTGCCCCCATGAAACCTCTAGTATGATGTTGCAAGTCCTCTTCCAACAATATCCTGGATTCAGGGAAGTCCGGATGATTGAAGCAAAGCCGGGTATTGCTTTCGTTGAGTTTGAAGATGATGTTCAATCCTCTATGGCTATGCAGGCTCTTCAAGGTCTTTAAAATTCGACCCCCAAC

Library


Library category	ESTs
fruit (8DPP) library	2
hermaphrodite flower library	3

Homology

[Close]

BLAST of CU093546 vs. Swiss-Prot
Match: RU2B2_ARATH (U2 small nuclear ribonucleoprotein B'' 2 OS=Arabidopsis thaliana GN=At1g06960 PE=1 SV=1)

HSP 1 Score: 93.6 bits (231), Expect = 1.3e-18
Identity = 44/51 (86.27%), Postives = 48/51 (94.12%), Query Frame = 1


Query: 124 PHETSSMMLQVLFQQYPGFREVRMIEAKPGIAFVEFEDDVQSSMAMQALQG 183
           P ET+SMMLQ+LF+QYPGF+E+RMIEAKPGIAFVE+EDDVQSSMAMQALQG
Sbjct: 163 PIETNSMMLQLLFEQYPGFKEIRMIEAKPGIAFVEYEDDVQSSMAMQALQG 213

Query: 184  243
           
Sbjct: 223  213

Query: 244  277
           
Sbjct: 283  213

HSP 2 Score: 39.3 bits (90), Expect = 2.9e-02
Identity = 22/42 (52.38%), Postives = 24/42 (57.14%), Query Frame = 3


Query: 3   QSAMPNGTTTENGGSNATFRHANPSATEA-TPNNILFIENLP 62
           Q +MPNG TT+NG     F+   PS  +   PNNILFI NLP
Sbjct: 125 QPSMPNGATTQNGMPVPPFQ---PSGQDTMPPNNILFIHNLP 163

Query: 63   122
           
Sbjct: 185  163

Query: 123  126
           
Sbjct: 245  163

[Close]

BLAST of CU093546 vs. Swiss-Prot
Match: RU2B1_ARATH (U2 small nuclear ribonucleoprotein B'' OS=Arabidopsis thaliana GN=U2B'' PE=1 SV=1)

HSP 1 Score: 92.0 bits (227), Expect = 3.8e-18
Identity = 41/51 (80.39%), Postives = 48/51 (94.12%), Query Frame = 1


Query: 124 PHETSSMMLQVLFQQYPGFREVRMIEAKPGIAFVEFEDDVQSSMAMQALQG 183
           PHET+SMMLQ+LF+QYPGF+E+RMI+AKPGIAFVE+EDDVQ+S+AMQ LQG
Sbjct: 166 PHETTSMMLQLLFEQYPGFKEIRMIDAKPGIAFVEYEDDVQASIAMQPLQG 216

Query: 184  243
           
Sbjct: 226  216

Query: 244  277
           
Sbjct: 286  216

HSP 2 Score: 31.2 bits (69), Expect = 7.9e+00
Identity = 18/37 (48.65%), Postives = 20/37 (54.05%), Query Frame = 3


Query: 18  NGTTTENGGSNATFRHANPSATEAT-PNNILFIENLP 77
           NG +  NG    +F+   PS  E   PNNILFI+NLP
Sbjct: 133 NGPSANNGVPAPSFQ---PSGQETMPPNNILFIQNLP 166

Query: 78   126
           
Sbjct: 193  166

[Close]

BLAST of CU093546 vs. Swiss-Prot
Match: RU2B_ORYSJ (U2 small nuclear ribonucleoprotein B'' OS=Oryza sativa subsp. japonica GN=Os03g0298800 PE=2 SV=1)

HSP 1 Score: 91.7 bits (226), Expect = 5.0e-18
Identity = 44/51 (86.27%), Postives = 46/51 (90.20%), Query Frame = 1


Query: 124 PHETSSMMLQVLFQQYPGFREVRMIEAKPGIAFVEFEDDVQSSMAMQALQG 183
           P ET+SMMLQ+LFQQYPGFREVRMIEAKPGIAFVE+EDD QS +AMQALQG
Sbjct: 166 PAETTSMMLQILFQQYPGFREVRMIEAKPGIAFVEYEDDSQSMVAMQALQG 216

Query: 184  243
           
Sbjct: 226  216

Query: 244  277
           
Sbjct: 286  216

HSP 2 Score: 32.0 bits (71), Expect = 4.6e+00
Identity = 18/42 (42.86%), Postives = 19/42 (45.24%), Query Frame = 3


Query: 3   QSAMPNGTTTENG-GSNATFRHANPSATEATPNNILFIENLP 62
           Q + PN     NG G  A+          A PNNILFI+NLP
Sbjct: 125 QQSGPNAAAQSNGTGYQASRLGKTSQEPPAPPNNILFIQNLP 166

Query: 63   122
           
Sbjct: 185  166

Query: 123  126
           
Sbjct: 245  166

[Close]

BLAST of CU093546 vs. Swiss-Prot
Match: RU2B_ORYSI (U2 small nuclear ribonucleoprotein B'' OS=Oryza sativa subsp. indica GN=OsI_11177 PE=3 SV=1)

HSP 1 Score: 91.7 bits (226), Expect = 5.0e-18
Identity = 44/51 (86.27%), Postives = 46/51 (90.20%), Query Frame = 1


Query: 124 PHETSSMMLQVLFQQYPGFREVRMIEAKPGIAFVEFEDDVQSSMAMQALQG 183
           P ET+SMMLQ+LFQQYPGFREVRMIEAKPGIAFVE+EDD QS +AMQALQG
Sbjct: 166 PAETTSMMLQILFQQYPGFREVRMIEAKPGIAFVEYEDDSQSMVAMQALQG 216

Query: 184  243
           
Sbjct: 226  216

Query: 244  277
           
Sbjct: 286  216

HSP 2 Score: 32.0 bits (71), Expect = 4.6e+00
Identity = 18/42 (42.86%), Postives = 19/42 (45.24%), Query Frame = 3


Query: 3   QSAMPNGTTTENG-GSNATFRHANPSATEATPNNILFIENLP 62
           Q + PN     NG G  A+          A PNNILFI+NLP
Sbjct: 125 QQSGPNAAAQSNGTGYQASRLGKTSQEPPAPPNNILFIQNLP 166

Query: 63   122
           
Sbjct: 185  166

Query: 123  126
           
Sbjct: 245  166

[Close]

BLAST of CU093546 vs. Swiss-Prot
Match: RU1A_ARATH (U1 small nuclear ribonucleoprotein A OS=Arabidopsis thaliana GN=U1A PE=1 SV=1)

HSP 1 Score: 81.6 bits (200), Expect = 5.2e-15
Identity = 38/51 (74.51%), Postives = 44/51 (86.27%), Query Frame = 1


Query: 124 PHETSSMMLQVLFQQYPGFREVRMIEAKPGIAFVEFEDDVQSSMAMQALQG 183
           PHET+ M+LQ+LF QY GF+EVRMIEAKPGIAFVEF D++QS++AMQ LQG
Sbjct: 185 PHETTPMVLQMLFCQYQGFKEVRMIEAKPGIAFVEFADEMQSTVAMQGLQG 235

Query: 184  243
           
Sbjct: 245  235

Query: 244  277
           
Sbjct: 305  235

[Close]

BLAST of CU093546 vs. TrEMBL
Match: A0A0A0LPT7_CUCSA (Uncharacterized protein OS=Cucumis sativus GN=Csa_1G025950 PE=4 SV=1)

HSP 1 Score: 104.0 bits (258), Expect = 1.1e-19
Identity = 51/51 (100.00%), Postives = 51/51 (100.00%), Query Frame = 1


Query: 124 PHETSSMMLQVLFQQYPGFREVRMIEAKPGIAFVEFEDDVQSSMAMQALQG 183
           PHETSSMMLQVLFQQYPGFREVRMIEAKPGIAFVEFEDDVQSSMAMQALQG
Sbjct: 165 PHETSSMMLQVLFQQYPGFREVRMIEAKPGIAFVEFEDDVQSSMAMQALQG 215

Query: 184  243
           
Sbjct: 225  215

Query: 244  277
           
Sbjct: 285  215

[Close]

BLAST of CU093546 vs. TrEMBL
Match: A0A0A0LPT7_CUCSA (Uncharacterized protein OS=Cucumis sativus GN=Csa_1G025950 PE=4 SV=1)

HSP 1 Score: 87.8 bits (216), Expect = 7.9e-15
Identity = 41/41 (100.00%), Postives = 41/41 (100.00%), Query Frame = 3


Query: 3   QSAMPNGTTTENGGSNATFRHANPSATEATPNNILFIENLP 62
           QSAMPNGTTTENGGSNATFRHANPSATEATPNNILFIENLP
Sbjct: 125 QSAMPNGTTTENGGSNATFRHANPSATEATPNNILFIENLP 165

Query: 63   122
           
Sbjct: 185  165

Query: 123  126
           
Sbjct: 245  165

HSP 2 Score: 102.8 bits (255), Expect = 2.4e-19
Identity = 50/51 (98.04%), Postives = 51/51 (100.00%), Query Frame = 1


Query: 124 PHETSSMMLQVLFQQYPGFREVRMIEAKPGIAFVEFEDDVQSSMAMQALQG 183
           PHET+SMMLQVLFQQYPGFREVRMIEAKPGIAFVEFEDDVQSSMAMQALQG
Sbjct: 167 PHETTSMMLQVLFQQYPGFREVRMIEAKPGIAFVEFEDDVQSSMAMQALQG 217

Query: 184  243
           
Sbjct: 227  217

Query: 244  277
           
Sbjct: 287  217

[Close]

BLAST of CU093546 vs. TrEMBL
Match: U5FWN4_POPTR (Small nuclear ribonucleoprotein U2B OS=Populus trichocarpa GN=POPTR_0013s14980g PE=4 SV=1)

HSP 1 Score: 47.0 bits (110), Expect = 1.5e-02
Identity = 24/42 (57.14%), Postives = 27/42 (64.29%), Query Frame = 3


Query: 3   QSAMPNGTTTENGGSNATFRHANPSATE-ATPNNILFIENLP 62
           QSA  NG   E+ G   +FRH N  A E A PNNILFI+NLP
Sbjct: 126 QSAPANGKPAESNGGPTSFRHGNQGAQETAPPNNILFIQNLP 167

Query: 63   122
           
Sbjct: 186  167

Query: 123  126
           
Sbjct: 246  167

HSP 2 Score: 102.8 bits (255), Expect = 2.4e-19
Identity = 50/51 (98.04%), Postives = 51/51 (100.00%), Query Frame = 1


Query: 124 PHETSSMMLQVLFQQYPGFREVRMIEAKPGIAFVEFEDDVQSSMAMQALQG 183
           PHET+SMMLQVLFQQYPGFREVRMIEAKPGIAFVEFEDDVQSSMAMQALQG
Sbjct: 160 PHETTSMMLQVLFQQYPGFREVRMIEAKPGIAFVEFEDDVQSSMAMQALQG 210

Query: 184  243
           
Sbjct: 220  210

Query: 244  277
           
Sbjct: 280  210

[Close]

BLAST of CU093546 vs. TrEMBL
Match: U5FTH6_POPTR (Uncharacterized protein OS=Populus trichocarpa GN=POPTR_0013s14980g PE=4 SV=1)

HSP 1 Score: 47.0 bits (110), Expect = 1.5e-02
Identity = 24/42 (57.14%), Postives = 27/42 (64.29%), Query Frame = 3


Query: 3   QSAMPNGTTTENGGSNATFRHANPSATE-ATPNNILFIENLP 62
           QSA  NG   E+ G   +FRH N  A E A PNNILFI+NLP
Sbjct: 119 QSAPANGKPAESNGGPTSFRHGNQGAQETAPPNNILFIQNLP 160

Query: 63   122
           
Sbjct: 179  160

Query: 123  126
           
Sbjct: 239  160

HSP 2 Score: 102.8 bits (255), Expect = 2.4e-19
Identity = 50/51 (98.04%), Postives = 51/51 (100.00%), Query Frame = 1


Query: 124 PHETSSMMLQVLFQQYPGFREVRMIEAKPGIAFVEFEDDVQSSMAMQALQG 183
           PHET+SMMLQVLFQQYPGFREVRMIEAKPGIAFVEFEDDVQSSMAMQALQG
Sbjct: 209 PHETTSMMLQVLFQQYPGFREVRMIEAKPGIAFVEFEDDVQSSMAMQALQG 259

Query: 184  243
           
Sbjct: 269  259

Query: 244  277
           
Sbjct: 329  259

[Close]

BLAST of CU093546 vs. TrEMBL
Match: B9INS5_POPTR (Uncharacterized protein OS=Populus trichocarpa GN=POPTR_0019s14440g PE=4 SV=2)

HSP 1 Score: 44.3 bits (103), Expect = 1.0e-01
Identity = 23/42 (54.76%), Postives = 26/42 (61.90%), Query Frame = 3


Query: 3   QSAMPNGTTTENGGSNATFRHANPSATEAT-PNNILFIENLP 62
           QSA  NG   E+ G   +FR  N SA E   PNNILFI+NLP
Sbjct: 168 QSAPANGKPAESNGGPTSFRQGNQSAQETVPPNNILFIQNLP 209

Query: 63   122
           
Sbjct: 228  209

Query: 123  126
           
Sbjct: 288  209

HSP 2 Score: 100.5 bits (249), Expect = 1.2e-18
Identity = 49/50 (98.00%), Postives = 50/50 (100.00%), Query Frame = 1


Query: 124 PHETSSMMLQVLFQQYPGFREVRMIEAKPGIAFVEFEDDVQSSMAMQALQ 183
           PHET+SMMLQVLFQQYPGFREVRMIEAKPGIAFVEFEDDVQSSMAMQALQ
Sbjct: 167 PHETTSMMLQVLFQQYPGFREVRMIEAKPGIAFVEFEDDVQSSMAMQALQ 216

Query: 184  243
           
Sbjct: 227  216

Query: 244  274
           
Sbjct: 287  216

[Close]

BLAST of CU093546 vs. NCBI nr
Match: gi|449439191|ref|XP_004137370.1| (PREDICTED: U2 small nuclear ribonucleoprotein B'' 2-like [Cucumis sativus])

HSP 1 Score: 105.1 bits (261), Expect = 6.9e-20
Identity = 51/51 (100.00%), Postives = 51/51 (100.00%), Query Frame = 1


Query: 124 PHETSSMMLQVLFQQYPGFREVRMIEAKPGIAFVEFEDDVQSSMAMQALQG 183
           PHETSSMMLQVLFQQYPGFREVRMIEAKPGIAFVEFEDDVQSSMAMQALQG
Sbjct: 165 PHETSSMMLQVLFQQYPGFREVRMIEAKPGIAFVEFEDDVQSSMAMQALQG 215

Query: 184  243
           
Sbjct: 225  215

Query: 244  277
           
Sbjct: 285  215

[Close]

BLAST of CU093546 vs. NCBI nr
Match: gi|659114937|ref|XP_008457301.1| (PREDICTED: U2 small nuclear ribonucleoprotein B'' 2-like [Cucumis melo])

HSP 1 Score: 105.1 bits (261), Expect = 6.9e-20
Identity = 51/51 (100.00%), Postives = 51/51 (100.00%), Query Frame = 1


Query: 124 PHETSSMMLQVLFQQYPGFREVRMIEAKPGIAFVEFEDDVQSSMAMQALQG 183
           PHETSSMMLQVLFQQYPGFREVRMIEAKPGIAFVEFEDDVQSSMAMQALQG
Sbjct: 165 PHETSSMMLQVLFQQYPGFREVRMIEAKPGIAFVEFEDDVQSSMAMQALQG 215

Query: 184  243
           
Sbjct: 225  215

Query: 244  277
           
Sbjct: 285  215

[Close]

BLAST of CU093546 vs. NCBI nr
Match: gi|743897119|ref|XP_011041843.1| (PREDICTED: U2 small nuclear ribonucleoprotein B'' 2-like [Populus euphratica])

HSP 1 Score: 104.0 bits (258), Expect = 1.5e-19
Identity = 50/51 (98.04%), Postives = 51/51 (100.00%), Query Frame = 1


Query: 124 PHETSSMMLQVLFQQYPGFREVRMIEAKPGIAFVEFEDDVQSSMAMQALQG 183
           PHET+SMMLQVLFQQYPGFREVRMIEAKPGIAFVEFEDDVQSSMAMQALQG
Sbjct: 167 PHETTSMMLQVLFQQYPGFREVRMIEAKPGIAFVEFEDDVQSSMAMQALQG 217

Query: 184  243
           
Sbjct: 227  217

Query: 244  277
           
Sbjct: 287  217

[Close]

BLAST of CU093546 vs. NCBI nr
Match: gi|566201401|ref|XP_006376548.1| (hypothetical protein POPTR_0013s14980g [Populus trichocarpa])

HSP 1 Score: 104.0 bits (258), Expect = 1.5e-19
Identity = 50/51 (98.04%), Postives = 51/51 (100.00%), Query Frame = 1


Query: 124 PHETSSMMLQVLFQQYPGFREVRMIEAKPGIAFVEFEDDVQSSMAMQALQG 183
           PHET+SMMLQVLFQQYPGFREVRMIEAKPGIAFVEFEDDVQSSMAMQALQG
Sbjct: 160 PHETTSMMLQVLFQQYPGFREVRMIEAKPGIAFVEFEDDVQSSMAMQALQG 210

Query: 184  243
           
Sbjct: 220  210

Query: 244  277
           
Sbjct: 280  210

[Close]

BLAST of CU093546 vs. NCBI nr
Match: gi|743819938|ref|XP_011021009.1| (PREDICTED: U2 small nuclear ribonucleoprotein B'' 2-like [Populus euphratica])

HSP 1 Score: 104.0 bits (258), Expect = 1.5e-19
Identity = 50/51 (98.04%), Postives = 51/51 (100.00%), Query Frame = 1


Query: 124 PHETSSMMLQVLFQQYPGFREVRMIEAKPGIAFVEFEDDVQSSMAMQALQG 183
           PHET+SMMLQVLFQQYPGFREVRMIEAKPGIAFVEFEDDVQSSMAMQALQG
Sbjct: 167 PHETTSMMLQVLFQQYPGFREVRMIEAKPGIAFVEFEDDVQSSMAMQALQG 217

Query: 184  243
           
Sbjct: 227  217

Query: 244  277
           
Sbjct: 287  217

The following BLAST results are available for this feature:

BLAST of CU093546 vs. Swiss-Prot


Match Name	E-value	Identity	Description
RU2B2_ARATH	1.3e-18	86.27	U2 small nuclear ribonucleoprotein B'' 2 OS=Arabidopsis thaliana GN=At1g06960 PE...	[more]
RU2B1_ARATH	3.8e-18	80.39	U2 small nuclear ribonucleoprotein B'' OS=Arabidopsis thaliana GN=U2B'' PE=1 SV=...	[more]
RU2B_ORYSJ	5.0e-18	86.27	U2 small nuclear ribonucleoprotein B'' OS=Oryza sativa subsp. japonica GN=Os03g0...	[more]
RU2B_ORYSI	5.0e-18	86.27	U2 small nuclear ribonucleoprotein B'' OS=Oryza sativa subsp. indica GN=OsI_1117...	[more]
RU1A_ARATH	5.2e-15	74.51	U1 small nuclear ribonucleoprotein A OS=Arabidopsis thaliana GN=U1A PE=1 SV=1	[more]

BLAST of CU093546 vs. TrEMBL


Match Name	E-value	Identity	Description
A0A0A0LPT7_CUCSA	1.1e-19	100.00	Uncharacterized protein OS=Cucumis sativus GN=Csa_1G025950 PE=4 SV=1	[more]
A0A0A0LPT7_CUCSA	7.9e-15	100.00	Uncharacterized protein OS=Cucumis sativus GN=Csa_1G025950 PE=4 SV=1	[more]
U5FWN4_POPTR	1.5e-02	57.14	Small nuclear ribonucleoprotein U2B OS=Populus trichocarpa GN=POPTR_0013s14980g ...	[more]
U5FTH6_POPTR	1.5e-02	57.14	Uncharacterized protein OS=Populus trichocarpa GN=POPTR_0013s14980g PE=4 SV=1	[more]
B9INS5_POPTR	1.0e-01	54.76	Uncharacterized protein OS=Populus trichocarpa GN=POPTR_0019s14440g PE=4 SV=2	[more]

BLAST of CU093546 vs. NCBI nr


Match Name	E-value	Identity	Description
gi\|449439191\|ref\|XP_004137370.1\|	6.9e-20	100.00	PREDICTED: U2 small nuclear ribonucleoprotein B'' 2-like [Cucumis sativus]	[more]
gi\|659114937\|ref\|XP_008457301.1\|	6.9e-20	100.00	PREDICTED: U2 small nuclear ribonucleoprotein B'' 2-like [Cucumis melo]	[more]
gi\|743897119\|ref\|XP_011041843.1\|	1.5e-19	98.04	PREDICTED: U2 small nuclear ribonucleoprotein B'' 2-like [Populus euphratica]	[more]
gi\|566201401\|ref\|XP_006376548.1\|	1.5e-19	98.04	hypothetical protein POPTR_0013s14980g [Populus trichocarpa]	[more]
gi\|743819938\|ref\|XP_011021009.1\|	1.5e-19	98.04	PREDICTED: U2 small nuclear ribonucleoprotein B'' 2-like [Populus euphratica]	[more]

Annotated Terms

The following terms have been associated with this transcribed_cluster:

Vocabulary: **INTERPRO**
Term	Definition
IPR000504	RRM_dom
IPR012677	Nucleotide-bd_a/b_plait_sf
IPR024888	U1 small nuclear ribonucleoprotein A/U2 small nuclear ribonucleoprotein B''

Vocabulary: **Molecular Function**
Term	Definition
GO:0003676	nucleic acid binding
GO:0000166	nucleotide binding
GO:0017069	snRNA binding

Vocabulary: **Biological Process**
Term	Definition
GO:0000398	mRNA splicing, via spliceosome

GO Annotation

GO Assignments

This transcribed_cluster is annotated with the following GO terms.

Category	Term Accession	Term Name
biological_process	GO:0000398	mRNA splicing, via spliceosome
molecular_function	GO:0003676	nucleic acid binding
molecular_function	GO:0000166	nucleotide binding
molecular_function	GO:0017069	snRNA binding

Relationships

This transcribed_cluster is associated with the following gene feature(s):


Feature Name	Unique Name	Type
Csa1G025950	Csa1G025950	gene

The following EST feature(s) are a part of this transcribed_cluster:


Feature Name	Unique Name	Type
FKNP3UI02K199Q	FKNP3UI02K199Q	EST
FKNP3UI02KILG4	FKNP3UI02KILG4	EST
H0127966	H0127966	EST
H0144629	H0144629	EST
H0183243	H0183243	EST

InterPro

Analysis Name: InterPro Annotations of cucumber unigene v3
Date Performed: 2016-11-16


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
IPR000504	RNA recognition motif domain	PFAM	PF00076	RRM_1	coord: 36..92 score: 2.3
IPR000504	RNA recognition motif domain	PROFILE	PS50102	RRM	coord: 34..93 score: 11
IPR012677	Nucleotide-binding alpha-beta plait domain	GENE3D	G3DSA:3.30.70.330		coord: 24..92 score: 2.0
IPR012677	Nucleotide-binding alpha-beta plait domain	unknown	SSF54928	RNA-binding domain, RBD	coord: 27..92 score: 4.57
IPR024888	U1 small nuclear ribonucleoprotein A/U2 small nuclear ribonucleoprotein B''	PANTHER	PTHR10501	U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A/U2 SMALL NUCLEAR RIBONUCLEOPROTEIN B	coord: 29..92 score: 4.8