CU089451 (transcribed_cluster) Cucumber (Chinese Long) v2 | Cucurbit Genomics Database (CuGenDB)

Overview


Name	CU089451
Type	transcribed_cluster
Organism	Cucumis. sativus (Cucumber (Chinese Long) v2)
Description	Exosome complex component Rrp42
Location	Chr4 : 8537821 .. 8544039 (+)
Sequence length	316

Genome Viewer

Sequences

The following sequences are available for this feature:

transcribed_cluster sequence

TTGGACCAGTATCTTCTGCAAACGGGTCAGCCCTGGCTAAGATTGGTTCGACGACAATGTTGGCTGCTATCAAAATGGAAGTAATGACACCTTCTGTTGAGTCACCGGATGAGGGTTACATAGCTCTTGATTTCCACATGCCTCCAGTATGCTCTCCAATTGTTAGGCCTGGGAGACCAGCGGAAGCAGCACCTGTGATTTCAAAGCAGTTATCTGACACTATTTCGAGTTCTGGGATGATTGATCTGAGAGAACTATCTCTTGTTAAAAGGAAAAACTGCTTGGATGGCTTACTTGGATATTTACTGTTTGGACG

Library


Library category	ESTs
gynoecious flower library	2

Homology

[Close]

BLAST of CU089451 vs. Swiss-Prot
Match: EXOS8_HUMAN (Exosome complex component RRP43 OS=Homo sapiens GN=EXOSC8 PE=1 SV=1)

HSP 1 Score: 78.2 bits (191), Expect = 6.0e-14
Identity = 35/87 (40.23%), Postives = 56/87 (64.37%), Query Frame = 3


Query: 3   GPVSSANGSALAKIGSTTMLAAIKMEVMTPSVESPDEGYIALDFHMPPVCSPIVRPGRPA 62
           G +S+A+GSAL K+G+TT++  +K E   PS ++PD+GY+  +  +PP+CS   R G P 
Sbjct: 40  GSISTADGSALVKLGNTTVICGVKAEFAAPSTDAPDKGYVVPNVDLPPLCSSRFRSGPPG 99

Query: 63  EAAPVISKQLSDTISSSGMIDLRELSL 122
           E A V S+ ++D I +S +I   +L +
Sbjct: 100 EEAQVASQFIADVIENSQIIQKEDLCI 126

Query: 123  182
           
Sbjct: 160  126

Query: 183  242
           
Sbjct: 220  126

Query: 243  264
           
Sbjct: 280  126

[Close]

BLAST of CU089451 vs. Swiss-Prot
Match: EXOS8_MOUSE (Exosome complex component RRP43 OS=Mus musculus GN=Exosc8 PE=1 SV=1)

HSP 1 Score: 76.6 bits (187), Expect = 1.7e-13
Identity = 34/87 (39.08%), Postives = 54/87 (62.07%), Query Frame = 3


Query: 3   GPVSSANGSALAKIGSTTMLAAIKMEVMTPSVESPDEGYIALDFHMPPVCSPIVRPGRPA 62
           G +S+A+GSAL K+G+TT++  +K E   P V++PD GY+  +  +PP+CS   R G P 
Sbjct: 40  GSISTADGSALVKLGNTTVICGVKAEFAAPPVDAPDRGYVVPNVDLPPLCSSRFRTGPPG 99

Query: 63  EAAPVISKQLSDTISSSGMIDLRELSL 122
           E A V S+ ++D + +S +I   +L +
Sbjct: 100 EEAQVTSQFIADVVDNSQVIKKEDLCI 126

Query: 123  182
           
Sbjct: 160  126

Query: 183  242
           
Sbjct: 220  126

Query: 243  264
           
Sbjct: 280  126

[Close]

BLAST of CU089451 vs. Swiss-Prot
Match: RRP43_SCHPO (Exosome complex component rrp43 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rrp43 PE=3 SV=1)

HSP 1 Score: 73.6 bits (179), Expect = 1.5e-12
Identity = 32/89 (35.96%), Postives = 54/89 (60.67%), Query Frame = 3


Query: 9   VSSANGSALAKIGSTTMLAAIKMEVMTPSVESPDEGYIALDFHMPPVCSPIVRPGRPAEA 68
           +S+ANGSA+ + G    +  IK E+  P   SP+EG+I  +  + P+CS   +PG P++ 
Sbjct: 54  ISTANGSAIIRAGENVFVCGIKAEIAEPFENSPNEGWIVPNLELSPLCSSKFKPGPPSDL 113

Query: 69  APVISKQLSDTISSSGMIDLRELSLVKRK 128
           A V+S++L  T+  S +I+L+ L + ++K
Sbjct: 114 AQVVSQELHQTLQQSNLINLQSLCIFEKK 142

Query: 129  188
           
Sbjct: 174  142

Query: 189  248
           
Sbjct: 234  142

Query: 249  276
           
Sbjct: 294  142

[Close]

BLAST of CU089451 vs. Swiss-Prot
Match: RRP42_METKA (Exosome complex component Rrp42 OS=Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938) GN=rrp42 PE=3 SV=1)

HSP 1 Score: 73.6 bits (179), Expect = 1.5e-12
Identity = 36/93 (38.71%), Postives = 56/93 (60.22%), Query Frame = 3


Query: 3   GPVSSANGSALAKIGSTTMLAAIKMEVMTPSVESPDEGYIALDFHMPPVCSPIVRPGRPA 62
           G +S ANGSAL ++G+T ++  +K+EV  P  +SP+EG +A++  + P+  P   PG P 
Sbjct: 40  GVISKANGSALVRLGNTQLVVGVKLEVGRPYPDSPNEGALAVNAELVPLADPSFEPGPPD 99

Query: 63  EAAPVISKQLSDTISSSGMIDLRELSLVKRKNC 122
           E A  +S+ +   I  S MIDL EL + + ++C
Sbjct: 100 ENAIELSRVVDRGIRESEMIDLEELCIEEGEHC 132

Query: 123  182
           
Sbjct: 160  132

Query: 183  242
           
Sbjct: 220  132

Query: 243  282
           
Sbjct: 280  132

[Close]

BLAST of CU089451 vs. Swiss-Prot
Match: EXOS8_BOVIN (Exosome complex component RRP43 OS=Bos taurus GN=EXOSC8 PE=2 SV=1)

HSP 1 Score: 71.6 bits (174), Expect = 5.6e-12
Identity = 34/91 (37.36%), Postives = 53/91 (58.24%), Query Frame = 3


Query: 3   GPVSSANGSALAKIGSTTMLAAIKMEVMTPSVESPDEGYIALDFHMPPVCSPIVRPGRPA 62
           G + +A+GSAL K+G+TT++  IK E   P  ++PD+GY+  +  + P+CS   R G P 
Sbjct: 40  GSIGTADGSALVKLGNTTVICGIKAEFGAPPTDAPDKGYVVPNVDLSPLCSSRFRSGPPG 99

Query: 63  EAAPVISKQLSDTISSSGMIDLRELSLVKRK 122
           E A V S+ ++D I +S +I   +L +   K
Sbjct: 100 EEAQVASQFIADVIENSQIIQKEDLCISSGK 130

Query: 123  182
           
Sbjct: 160  130

Query: 183  242
           
Sbjct: 220  130

Query: 243  276
           
Sbjct: 280  130

[Close]

BLAST of CU089451 vs. TrEMBL
Match: U5G927_POPTR (Uncharacterized protein OS=Populus trichocarpa GN=POPTR_0006s04970g PE=4 SV=1)

HSP 1 Score: 156.8 bits (395), Expect = 1.5e-35
Identity = 79/91 (86.81%), Postives = 86/91 (94.51%), Query Frame = 3


Query: 3   GPVSSANGSALAKIGSTTMLAAIKMEVMTPSVESPDEGYIALDFHMPPVCSPIVRPGRPA 62
           G V+SA+GSALAKIGSTTMLAAIKMEVMTPS ESP+EG IA+DFHMPP+CSPIVRPGRPA
Sbjct: 54  GAVASAHGSALAKIGSTTMLAAIKMEVMTPSTESPEEGSIAIDFHMPPICSPIVRPGRPA 113

Query: 63  EAAPVISKQLSDTISSSGMIDLRELSLVKRK 122
           EAAPVISKQLSDTISSSGMI+L+ELSLV  K
Sbjct: 114 EAAPVISKQLSDTISSSGMINLKELSLVSGK 144

Query: 123  182
           
Sbjct: 174  144

Query: 183  242
           
Sbjct: 234  144

Query: 243  276
           
Sbjct: 294  144

[Close]

BLAST of CU089451 vs. TrEMBL
Match: A0A0D2Q4I8_GOSRA (Uncharacterized protein OS=Gossypium raimondii GN=B456_002G116000 PE=4 SV=1)

HSP 1 Score: 155.6 bits (392), Expect = 3.3e-35
Identity = 77/91 (84.62%), Postives = 86/91 (94.51%), Query Frame = 3


Query: 3   GPVSSANGSALAKIGSTTMLAAIKMEVMTPSVESPDEGYIALDFHMPPVCSPIVRPGRPA 62
           G V+SANGSALAKIGSTTMLAAIKMEVMTPS+E+PDEG IA+DFHMPP+CSPIVRPGRPA
Sbjct: 54  GAVASANGSALAKIGSTTMLAAIKMEVMTPSLETPDEGCIAIDFHMPPICSPIVRPGRPA 113

Query: 63  EAAPVISKQLSDTISSSGMIDLRELSLVKRK 122
           EAAPV++KQLSDTI SSGMI+L+ELSLV  K
Sbjct: 114 EAAPVVAKQLSDTILSSGMINLKELSLVSGK 144

Query: 123  182
           
Sbjct: 174  144

Query: 183  242
           
Sbjct: 234  144

Query: 243  276
           
Sbjct: 294  144

[Close]

BLAST of CU089451 vs. TrEMBL
Match: A0A0D2QBI8_GOSRA (Uncharacterized protein OS=Gossypium raimondii GN=B456_002G116000 PE=4 SV=1)

HSP 1 Score: 155.6 bits (392), Expect = 3.3e-35
Identity = 77/91 (84.62%), Postives = 86/91 (94.51%), Query Frame = 3


Query: 3   GPVSSANGSALAKIGSTTMLAAIKMEVMTPSVESPDEGYIALDFHMPPVCSPIVRPGRPA 62
           G V+SANGSALAKIGSTTMLAAIKMEVMTPS+E+PDEG IA+DFHMPP+CSPIVRPGRPA
Sbjct: 54  GAVASANGSALAKIGSTTMLAAIKMEVMTPSLETPDEGCIAIDFHMPPICSPIVRPGRPA 113

Query: 63  EAAPVISKQLSDTISSSGMIDLRELSLVKRK 122
           EAAPV++KQLSDTI SSGMI+L+ELSLV  K
Sbjct: 114 EAAPVVAKQLSDTILSSGMINLKELSLVSGK 144

Query: 123  182
           
Sbjct: 174  144

Query: 183  242
           
Sbjct: 234  144

Query: 243  276
           
Sbjct: 294  144

[Close]

BLAST of CU089451 vs. TrEMBL
Match: V4U5Z9_9ROSI (Uncharacterized protein OS=Citrus clementina GN=CICLE_v10005512mg PE=4 SV=1)

HSP 1 Score: 154.1 bits (388), Expect = 9.5e-35
Identity = 75/91 (82.42%), Postives = 87/91 (95.60%), Query Frame = 3


Query: 3   GPVSSANGSALAKIGSTTMLAAIKMEVMTPSVESPDEGYIALDFHMPPVCSPIVRPGRPA 62
           G V+SA+GSALAKIGSTTMLAAIKMEVMTPS+ESPDEG +++DFHMPP+CSP+VRPGRPA
Sbjct: 54  GAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPA 113

Query: 63  EAAPVISKQLSDTISSSGMIDLRELSLVKRK 122
           EAAPV++KQLSDTISSSGMI+L+ELSLV  K
Sbjct: 114 EAAPVVAKQLSDTISSSGMINLKELSLVGGK 144

Query: 123  182
           
Sbjct: 174  144

Query: 183  242
           
Sbjct: 234  144

Query: 243  276
           
Sbjct: 294  144

[Close]

BLAST of CU089451 vs. TrEMBL
Match: A0A067DQC7_CITSI (Uncharacterized protein OS=Citrus sinensis GN=CISIN_1g022140mg PE=4 SV=1)

HSP 1 Score: 154.1 bits (388), Expect = 9.5e-35
Identity = 75/91 (82.42%), Postives = 87/91 (95.60%), Query Frame = 3


Query: 3   GPVSSANGSALAKIGSTTMLAAIKMEVMTPSVESPDEGYIALDFHMPPVCSPIVRPGRPA 62
           G V+SA+GSALAKIGSTTMLAAIKMEVMTPS+ESPDEG +++DFHMPP+CSP+VRPGRPA
Sbjct: 54  GAVASADGSALAKIGSTTMLAAIKMEVMTPSLESPDEGCVSIDFHMPPICSPLVRPGRPA 113

Query: 63  EAAPVISKQLSDTISSSGMIDLRELSLVKRK 122
           EAAPV++KQLSDTISSSGMI+L+ELSLV  K
Sbjct: 114 EAAPVVAKQLSDTISSSGMINLKELSLVGGK 144

Query: 123  182
           
Sbjct: 174  144

Query: 183  242
           
Sbjct: 234  144

Query: 243  276
           
Sbjct: 294  144

[Close]

BLAST of CU089451 vs. NCBI nr
Match: gi|449463354|ref|XP_004149399.1| (PREDICTED: exosome complex component RRP43 [Cucumis sativus])

HSP 1 Score: 169.5 bits (428), Expect = 3.2e-39
Identity = 89/91 (97.80%), Postives = 89/91 (97.80%), Query Frame = 3


Query: 3   GPVSSANGSALAKIGSTTMLAAIKMEVMTPSVESPDEGYIALDFHMPPVCSPIVRPGRPA 62
           GPVSSANGSALAKIGSTTMLAAIKMEVMTPSVESPDEG IALDFHMPPVCSPIVRPGRPA
Sbjct: 55  GPVSSANGSALAKIGSTTMLAAIKMEVMTPSVESPDEGCIALDFHMPPVCSPIVRPGRPA 114

Query: 63  EAAPVISKQLSDTISSSGMIDLRELSLVKRK 122
           EAAPVISKQLSDTISSSGMIDLRELSLVK K
Sbjct: 115 EAAPVISKQLSDTISSSGMIDLRELSLVKGK 145

Query: 123  182
           
Sbjct: 175  145

Query: 183  242
           
Sbjct: 235  145

Query: 243  276
           
Sbjct: 295  145

[Close]

BLAST of CU089451 vs. NCBI nr
Match: gi|659121681|ref|XP_008460772.1| (PREDICTED: exosome complex component RRP43 isoform X1 [Cucumis melo])

HSP 1 Score: 169.5 bits (428), Expect = 3.2e-39
Identity = 89/91 (97.80%), Postives = 89/91 (97.80%), Query Frame = 3


Query: 3   GPVSSANGSALAKIGSTTMLAAIKMEVMTPSVESPDEGYIALDFHMPPVCSPIVRPGRPA 62
           GPVSSANGSALAKIGSTTMLAAIKMEVMTPSVESPDEG IALDFHMPPVCSPIVRPGRPA
Sbjct: 67  GPVSSANGSALAKIGSTTMLAAIKMEVMTPSVESPDEGCIALDFHMPPVCSPIVRPGRPA 126

Query: 63  EAAPVISKQLSDTISSSGMIDLRELSLVKRK 122
           EAAPVISKQLSDTISSSGMIDLRELSLVK K
Sbjct: 127 EAAPVISKQLSDTISSSGMIDLRELSLVKGK 157

Query: 123  182
           
Sbjct: 187  157

Query: 183  242
           
Sbjct: 247  157

Query: 243  276
           
Sbjct: 307  157

[Close]

BLAST of CU089451 vs. NCBI nr
Match: gi|659121683|ref|XP_008460773.1| (PREDICTED: exosome complex component RRP43 isoform X2 [Cucumis melo])

HSP 1 Score: 169.5 bits (428), Expect = 3.2e-39
Identity = 89/91 (97.80%), Postives = 89/91 (97.80%), Query Frame = 3


Query: 3   GPVSSANGSALAKIGSTTMLAAIKMEVMTPSVESPDEGYIALDFHMPPVCSPIVRPGRPA 62
           GPVSSANGSALAKIGSTTMLAAIKMEVMTPSVESPDEG IALDFHMPPVCSPIVRPGRPA
Sbjct: 55  GPVSSANGSALAKIGSTTMLAAIKMEVMTPSVESPDEGCIALDFHMPPVCSPIVRPGRPA 114

Query: 63  EAAPVISKQLSDTISSSGMIDLRELSLVKRK 122
           EAAPVISKQLSDTISSSGMIDLRELSLVK K
Sbjct: 115 EAAPVISKQLSDTISSSGMIDLRELSLVKGK 145

Query: 123  182
           
Sbjct: 175  145

Query: 183  242
           
Sbjct: 235  145

Query: 243  276
           
Sbjct: 295  145

[Close]

BLAST of CU089451 vs. NCBI nr
Match: gi|743909151|ref|XP_011048048.1| (PREDICTED: exosome complex component RRP43-like [Populus euphratica])

HSP 1 Score: 154.5 bits (389), Expect = 1.0e-34
Identity = 79/91 (86.81%), Postives = 86/91 (94.51%), Query Frame = 3


Query: 3   GPVSSANGSALAKIGSTTMLAAIKMEVMTPSVESPDEGYIALDFHMPPVCSPIVRPGRPA 62
           G V+SA+GSALAKIGSTTMLAAIK+EVMTPS ESPDEG IA+DFHMPP+CSPIVRPGRPA
Sbjct: 54  GAVASAHGSALAKIGSTTMLAAIKLEVMTPSTESPDEGSIAIDFHMPPICSPIVRPGRPA 113

Query: 63  EAAPVISKQLSDTISSSGMIDLRELSLVKRK 122
           EAAPVISKQLSDTISSSGMI+L+ELSLV  K
Sbjct: 114 EAAPVISKQLSDTISSSGMINLKELSLVSGK 144

Query: 123  182
           
Sbjct: 174  144

Query: 183  242
           
Sbjct: 234  144

Query: 243  276
           
Sbjct: 294  144

[Close]

BLAST of CU089451 vs. NCBI nr
Match: gi|566174533|ref|XP_006381009.1| (hypothetical protein POPTR_0006s04970g [Populus trichocarpa])

HSP 1 Score: 154.1 bits (388), Expect = 1.4e-34
Identity = 79/91 (86.81%), Postives = 86/91 (94.51%), Query Frame = 3


Query: 3   GPVSSANGSALAKIGSTTMLAAIKMEVMTPSVESPDEGYIALDFHMPPVCSPIVRPGRPA 62
           G V+SA+GSALAKIGSTTMLAAIKMEVMTPS ESP+EG IA+DFHMPP+CSPIVRPGRPA
Sbjct: 54  GAVASAHGSALAKIGSTTMLAAIKMEVMTPSTESPEEGSIAIDFHMPPICSPIVRPGRPA 113

Query: 63  EAAPVISKQLSDTISSSGMIDLRELSLVKRK 122
           EAAPVISKQLSDTISSSGMI+L+ELSLV  K
Sbjct: 114 EAAPVISKQLSDTISSSGMINLKELSLVSGK 144

Query: 123  182
           
Sbjct: 174  144

Query: 183  242
           
Sbjct: 234  144

Query: 243  276
           
Sbjct: 294  144

The following BLAST results are available for this feature:

BLAST of CU089451 vs. Swiss-Prot


Match Name	E-value	Identity	Description
EXOS8_HUMAN	6.0e-14	40.23	Exosome complex component RRP43 OS=Homo sapiens GN=EXOSC8 PE=1 SV=1	[more]
EXOS8_MOUSE	1.7e-13	39.08	Exosome complex component RRP43 OS=Mus musculus GN=Exosc8 PE=1 SV=1	[more]
RRP43_SCHPO	1.5e-12	35.96	Exosome complex component rrp43 OS=Schizosaccharomyces pombe (strain 972 / ATCC ...	[more]
RRP42_METKA	1.5e-12	38.71	Exosome complex component Rrp42 OS=Methanopyrus kandleri (strain AV19 / DSM 6324...	[more]
EXOS8_BOVIN	5.6e-12	37.36	Exosome complex component RRP43 OS=Bos taurus GN=EXOSC8 PE=2 SV=1	[more]

BLAST of CU089451 vs. TrEMBL


Match Name	E-value	Identity	Description
U5G927_POPTR	1.5e-35	86.81	Uncharacterized protein OS=Populus trichocarpa GN=POPTR_0006s04970g PE=4 SV=1	[more]
A0A0D2Q4I8_GOSRA	3.3e-35	84.62	Uncharacterized protein OS=Gossypium raimondii GN=B456_002G116000 PE=4 SV=1	[more]
A0A0D2QBI8_GOSRA	3.3e-35	84.62	Uncharacterized protein OS=Gossypium raimondii GN=B456_002G116000 PE=4 SV=1	[more]
V4U5Z9_9ROSI	9.5e-35	82.42	Uncharacterized protein OS=Citrus clementina GN=CICLE_v10005512mg PE=4 SV=1	[more]
A0A067DQC7_CITSI	9.5e-35	82.42	Uncharacterized protein OS=Citrus sinensis GN=CISIN_1g022140mg PE=4 SV=1	[more]

BLAST of CU089451 vs. NCBI nr


Match Name	E-value	Identity	Description
gi\|449463354\|ref\|XP_004149399.1\|	3.2e-39	97.80	PREDICTED: exosome complex component RRP43 [Cucumis sativus]	[more]
gi\|659121681\|ref\|XP_008460772.1\|	3.2e-39	97.80	PREDICTED: exosome complex component RRP43 isoform X1 [Cucumis melo]	[more]
gi\|659121683\|ref\|XP_008460773.1\|	3.2e-39	97.80	PREDICTED: exosome complex component RRP43 isoform X2 [Cucumis melo]	[more]
gi\|743909151\|ref\|XP_011048048.1\|	1.0e-34	86.81	PREDICTED: exosome complex component RRP43-like [Populus euphratica]	[more]
gi\|566174533\|ref\|XP_006381009.1\|	1.4e-34	86.81	hypothetical protein POPTR_0006s04970g [Populus trichocarpa]	[more]

Annotated Terms

The following terms have been associated with this transcribed_cluster:

Vocabulary: **INTERPRO**
Term	Definition
IPR001247	ExoRNase_PH_dom1
IPR020568	Ribosomal_S5_D2-typ_fold

Vocabulary: **Cellular Component**
Term	Definition
GO:0000178	exosome (RNase complex)

Vocabulary: **Biological Process**
Term	Definition
GO:0006396	RNA processing
GO:0006401	RNA catabolic process

GO Annotation

GO Assignments

This transcribed_cluster is annotated with the following GO terms.

Category	Term Accession	Term Name
biological_process	GO:0006401	RNA catabolic process
biological_process	GO:0006396	RNA processing
cellular_component	GO:0000178	exosome (RNase complex)

Relationships

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


Feature Name	Unique Name	Type
Csa4G165870	Csa4G165870	gene
Csa4G165880	Csa4G165880	gene

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


Feature Name	Unique Name	Type
G0069099	G0069099	EST
G0196620	G0196620	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
IPR001247	Exoribonuclease, phosphorolytic domain 1	PFAM	PF01138	RNase_PH	coord: 2..85 score: 1.8
IPR020568	Ribosomal protein S5 domain 2-type fold	unknown	SSF54211	Ribosomal protein S5 domain 2-like	coord: 6..93 score: 3.85
None	No IPR available	PANTHER	PTHR11097	EXOSOME COMPLEX EXONUCLEASE RIBOSOMAL RNA PROCESSING PROTEIN	coord: 2..92 score: 3.5