Cucsa.374740 (gene) Cucumber (Gy14) v1 | Cucurbit Genomics Database (CuGenDB)

Overview


Name	Cucsa.374740
Type	gene
Organism	Cucumis sativus (Cucumber (Gy14) v1)
Description	Exosome complex exonuclease rrp43, putative
Location	scaffold03735 : 206823 .. 207636 (+)

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.

ATGCCAATGATCAATGGTTATTTTATTATTTGAAAATTTTAATAATTTCTCTTTATAAGCTGAAAAATGTTAATGAGATTTTTTTTCCATCTTGTTTGGTAATTTGGTAGGTTGAACTACTTTAAAACGATTAGTACCCTTTTTCTTTGTTGAGCCGTATTTTAAACTCCTTCCTGGTTTATATTTTTAGTGCAAATCCCTGTTGTTGCTCTAAATGATGATGGAAAAGTAGTATTTGTCTGTGAGGAAGAAGGGGGAGAAAACTTTGAGAAGGAACCTGTCAATAAAGAGAACAGGAAACTGAAATTGAACTCTATTCCTTTCTCATTAACGTGCCTACTCCACAAGAAGTACATCTTGGCCGATCCTACTGCAGAGGAGGAGTCCGTCATGGAAACTATTGTAACTGTGGTTTTGGATTCATCAGGTCAACTTGTTTCCTTCTACAAGCCGGGTGGATCCGTTCTTGCTTATACATCAGCTGTTCAGGTTGGTCTTTCCTTTCTCCCACAACTTTATTGATGGATTGGTTCCGGATTTTGTCATTCTTCACACTTTCCCCGTCTCTTAAGTTTGGATTTTCATGAACAATCATTTAGGGCTCGTTTAGTAATTAATTGGTTTTGAAAATTAAACCTATTTTGTATCAATTTCTTACCATGGTTTCATATTTCTTGAGTAAAAGAGTGAATTTTGAACCAAATTTAAAAAGCAAGTACAAATTTTTAAATATTTTTTATTAGTTTTTAAAACTTAATTTGGCTTTTGGAAACATTGGCAGAAAGTAGATAAAAAAGCAACCGGTAGAAAGTAG

mRNA sequence

ATGCCAATGATCAATGTGCAAATCCCTGTTGTTGCTCTAAATGATGATGGAAAAGTAGTATTTGTCTGTGAGGAAGAAGGGGGAGAAAACTTTGAGAAGGAACCTGTCAATAAAGAGAACAGGAAACTGAAATTGAACTCTATTCCTTTCTCATTAACGTGCCTACTCCACAAGAAGTACATCTTGGCCGATCCTACTGCAGAGGAGGAGTCCGTCATGGAAACTATTGTAACTGTGGTTTTGGATTCATCAGGTCAACTTGTTTCCTTCTACAAGCCGGGTGGATCCGTTCTTGCTTATACATCAGCTGTTCAGaaagtagataaaaaagcaaccggtagaaagtag

Coding sequence (CDS)

ATGCCAATGATCAATGTGCAAATCCCTGTTGTTGCTCTAAATGATGATGGAAAAGTAGTATTTGTCTGTGAGGAAGAAGGGGGAGAAAACTTTGAGAAGGAACCTGTCAATAAAGAGAACAGGAAACTGAAATTGAACTCTATTCCTTTCTCATTAACGTGCCTACTCCACAAGAAGTACATCTTGGCCGATCCTACTGCAGAGGAGGAGTCCGTCATGGAAACTATTGTAACTGTGGTTTTGGATTCATCAGGTCAACTTGTTTCCTTCTACAAGCCGGGTGGATCCGTTCTTGCTTATACATCAGCTGTTCAGAAAGTAGATAAAAAAGCAACCGGTAGAAAGTAG

Protein sequence

MPMINVQIPVVALNDDGKVVFVCEEEGGENFEKEPVNKENRKLKLNSIPFSLTCLLHKKYILADPTAEEESVMETIVTVVLDSSGQLVSFYKPGGSVLAYTSAVQKVDKKATGRK*

Homology

[Close]

BLAST of Cucsa.374740 vs. TrEMBL
Match: A0A0A0KYC2_CUCSA (Uncharacterized protein OS=Cucumis sativus GN=Csa_4G165890 PE=4 SV=1)

HSP 1 Score: 209.5 bits (532), Expect = 2.1e-51
Identity = 105/105 (100.00%), Postives = 105/105 (100.00%), Query Frame = 1


Query: 1   MPMINVQIPVVALNDDGKVVFVCEEEGGENFEKEPVNKENRKLKLNSIPFSLTCLLHKKY 60
           MPMINVQIPVVALNDDGKVVFVCEEEGGENFEKEPVNKENRKLKLNSIPFSLTCLLHKKY
Sbjct: 1   MPMINVQIPVVALNDDGKVVFVCEEEGGENFEKEPVNKENRKLKLNSIPFSLTCLLHKKY 60

Query: 61  ILADPTAEEESVMETIVTVVLDSSGQLVSFYKPGGSVLAYTSAVQ 106
           ILADPTAEEESVMETIVTVVLDSSGQLVSFYKPGGSVLAYTSAVQ
Sbjct: 61  ILADPTAEEESVMETIVTVVLDSSGQLVSFYKPGGSVLAYTSAVQ 105

[Close]

BLAST of Cucsa.374740 vs. TrEMBL
Match: U5FN09_POPTR (Uncharacterized protein OS=Populus trichocarpa GN=POPTR_0016s05590g PE=4 SV=1)

HSP 1 Score: 161.8 bits (408), Expect = 5.1e-37
Identity = 78/101 (77.23%), Postives = 90/101 (89.11%), Query Frame = 1


Query: 5   NVQIPVVALNDDGKVVFVCEEEGGENFEKEPVNKENRKLKLNSIPFSLTCLLHKKYILAD 64
           ++QIP+V+LNDDGK+V V EE+ G   EKEPVNKE RKL L+SIPFSLTC+LHK YILAD
Sbjct: 196 HLQIPIVSLNDDGKIVLVSEEDEGAKLEKEPVNKEKRKLTLSSIPFSLTCILHKNYILAD 255

Query: 65  PTAEEESVMETIVTVVLDSSGQLVSFYKPGGSVLAYTSAVQ 106
           PTAEEES+MET+VTVVLDSS +LVSFYKPGGSV AYTSAV+
Sbjct: 256 PTAEEESIMETLVTVVLDSSARLVSFYKPGGSVFAYTSAVK 296

[Close]

BLAST of Cucsa.374740 vs. TrEMBL
Match: B9II78_POPTR (3' exoribonuclease domain 1-containing family protein OS=Populus trichocarpa GN=POPTR_0016s05590g PE=4 SV=1)

HSP 1 Score: 161.8 bits (408), Expect = 5.1e-37
Identity = 78/101 (77.23%), Postives = 90/101 (89.11%), Query Frame = 1


Query: 5   NVQIPVVALNDDGKVVFVCEEEGGENFEKEPVNKENRKLKLNSIPFSLTCLLHKKYILAD 64
           ++QIP+V+LNDDGK+V V EE+ G   EKEPVNKE RKL L+SIPFSLTC+LHK YILAD
Sbjct: 196 HLQIPIVSLNDDGKIVLVSEEDEGAKLEKEPVNKEKRKLTLSSIPFSLTCILHKNYILAD 255

Query: 65  PTAEEESVMETIVTVVLDSSGQLVSFYKPGGSVLAYTSAVQ 106
           PTAEEES+MET+VTVVLDSS +LVSFYKPGGSV AYTSAV+
Sbjct: 256 PTAEEESIMETLVTVVLDSSARLVSFYKPGGSVFAYTSAVK 296

[Close]

BLAST of Cucsa.374740 vs. TrEMBL
Match: B9H9U8_POPTR (3' exoribonuclease domain 1-containing family protein OS=Populus trichocarpa GN=POPTR_0006s04970g PE=4 SV=1)

HSP 1 Score: 159.5 bits (402), Expect = 2.5e-36
Identity = 78/100 (78.00%), Postives = 88/100 (88.00%), Query Frame = 1


Query: 6   VQIPVVALNDDGKVVFVCEEEGGENFEKEPVNKENRKLKLNSIPFSLTCLLHKKYILADP 65
           VQIP+V+LNDDGK+V V EE+ G   E+EPVNKE RKL L+SIPFSLTC+LHK YILADP
Sbjct: 192 VQIPIVSLNDDGKIVLVSEEDDGTKLEEEPVNKEKRKLTLSSIPFSLTCILHKNYILADP 251

Query: 66  TAEEESVMETIVTVVLDSSGQLVSFYKPGGSVLAYTSAVQ 106
           TAEEES+MET+VTVVLDSS +LVSFYKPGG VLA TSAVQ
Sbjct: 252 TAEEESIMETLVTVVLDSSSRLVSFYKPGGPVLAQTSAVQ 291

[Close]

BLAST of Cucsa.374740 vs. TrEMBL
Match: U5G927_POPTR (Uncharacterized protein OS=Populus trichocarpa GN=POPTR_0006s04970g PE=4 SV=1)

HSP 1 Score: 158.7 bits (400), Expect = 4.3e-36
Identity = 77/101 (76.24%), Postives = 89/101 (88.12%), Query Frame = 1


Query: 5   NVQIPVVALNDDGKVVFVCEEEGGENFEKEPVNKENRKLKLNSIPFSLTCLLHKKYILAD 64
           ++QIP+V+LNDDGK+V V EE+ G   E+EPVNKE RKL L+SIPFSLTC+LHK YILAD
Sbjct: 176 HLQIPIVSLNDDGKIVLVSEEDDGTKLEEEPVNKEKRKLTLSSIPFSLTCILHKNYILAD 235

Query: 65  PTAEEESVMETIVTVVLDSSGQLVSFYKPGGSVLAYTSAVQ 106
           PTAEEES+MET+VTVVLDSS +LVSFYKPGG VLA TSAVQ
Sbjct: 236 PTAEEESIMETLVTVVLDSSSRLVSFYKPGGPVLAQTSAVQ 276

[Close]

BLAST of Cucsa.374740 vs. TAIR10
Match: AT1G60080.1 (AT1G60080.1 3'-5'-exoribonuclease family protein)

HSP 1 Score: 139.8 bits (351), Expect = 1.1e-33
Identity = 71/113 (62.83%), Postives = 89/113 (78.76%), Query Frame = 1


Query: 5   NVQIPVVALNDDGKVVFVCEEEGGENF---EKEPVNKENRKLKLNSIPFSLTCLLHKKYI 64
           N+QIP+VALND+G++V V  E+  +N    EKE VNKE RKL L +IPFSLTC+LHK YI
Sbjct: 176 NLQIPIVALNDNGRIVAVTGEKDQDNALITEKEAVNKEKRKLTLKNIPFSLTCILHKNYI 235

Query: 65  LADPTAEEESVMETIVTVVLDSSGQLVSFYKPGGSVLAYTSAVQKVDKKATGR 115
           LADPT EEES+M+T+VTVVLDSS Q+VSFYK GG+ LAY+SA++   + A  R
Sbjct: 236 LADPTTEEESIMDTLVTVVLDSSDQMVSFYKSGGAALAYSSAIKSCVELARKR 288

[Close]

BLAST of Cucsa.374740 vs. NCBI nr
Match: gi|700198686|gb|KGN53844.1| (hypothetical protein Csa_4G165890 [Cucumis sativus])

HSP 1 Score: 209.5 bits (532), Expect = 3.1e-51
Identity = 105/105 (100.00%), Postives = 105/105 (100.00%), Query Frame = 1


Query: 1   MPMINVQIPVVALNDDGKVVFVCEEEGGENFEKEPVNKENRKLKLNSIPFSLTCLLHKKY 60
           MPMINVQIPVVALNDDGKVVFVCEEEGGENFEKEPVNKENRKLKLNSIPFSLTCLLHKKY
Sbjct: 1   MPMINVQIPVVALNDDGKVVFVCEEEGGENFEKEPVNKENRKLKLNSIPFSLTCLLHKKY 60

Query: 61  ILADPTAEEESVMETIVTVVLDSSGQLVSFYKPGGSVLAYTSAVQ 106
           ILADPTAEEESVMETIVTVVLDSSGQLVSFYKPGGSVLAYTSAVQ
Sbjct: 61  ILADPTAEEESVMETIVTVVLDSSGQLVSFYKPGGSVLAYTSAVQ 105

[Close]

BLAST of Cucsa.374740 vs. NCBI nr
Match: gi|449463354|ref|XP_004149399.1| (PREDICTED: exosome complex component RRP43 [Cucumis sativus])

HSP 1 Score: 198.4 bits (503), Expect = 7.1e-48
Identity = 99/101 (98.02%), Postives = 101/101 (100.00%), Query Frame = 1


Query: 5   NVQIPVVALNDDGKVVFVCEEEGGENFEKEPVNKENRKLKLNSIPFSLTCLLHKKYILAD 64
           ++QIPVVALNDDGKVVFVCEEEGGENFEKEPVNKENRKLKLNSIPFSLTCLLHKKYILAD
Sbjct: 177 HLQIPVVALNDDGKVVFVCEEEGGENFEKEPVNKENRKLKLNSIPFSLTCLLHKKYILAD 236

Query: 65  PTAEEESVMETIVTVVLDSSGQLVSFYKPGGSVLAYTSAVQ 106
           PTAEEESVMETIVTVVLDSSGQLVSFYKPGGSVLAYTSAVQ
Sbjct: 237 PTAEEESVMETIVTVVLDSSGQLVSFYKPGGSVLAYTSAVQ 277

[Close]

BLAST of Cucsa.374740 vs. NCBI nr
Match: gi|659121683|ref|XP_008460773.1| (PREDICTED: exosome complex component RRP43 isoform X2 [Cucumis melo])

HSP 1 Score: 190.7 bits (483), Expect = 1.5e-45
Identity = 95/101 (94.06%), Postives = 99/101 (98.02%), Query Frame = 1


Query: 5   NVQIPVVALNDDGKVVFVCEEEGGENFEKEPVNKENRKLKLNSIPFSLTCLLHKKYILAD 64
           ++QIPVVALNDDG+VVFV EEEGGENFEKEPVNKE RKLKLNS+PFSLTCLLHKKYILAD
Sbjct: 177 HLQIPVVALNDDGRVVFVSEEEGGENFEKEPVNKEKRKLKLNSVPFSLTCLLHKKYILAD 236

Query: 65  PTAEEESVMETIVTVVLDSSGQLVSFYKPGGSVLAYTSAVQ 106
           PTAEEESVMETIVTVVLDSSGQLVSFYKPGGSVLAYTSAVQ
Sbjct: 237 PTAEEESVMETIVTVVLDSSGQLVSFYKPGGSVLAYTSAVQ 277

[Close]

BLAST of Cucsa.374740 vs. NCBI nr
Match: gi|659121681|ref|XP_008460772.1| (PREDICTED: exosome complex component RRP43 isoform X1 [Cucumis melo])

HSP 1 Score: 190.7 bits (483), Expect = 1.5e-45
Identity = 95/101 (94.06%), Postives = 99/101 (98.02%), Query Frame = 1


Query: 5   NVQIPVVALNDDGKVVFVCEEEGGENFEKEPVNKENRKLKLNSIPFSLTCLLHKKYILAD 64
           ++QIPVVALNDDG+VVFV EEEGGENFEKEPVNKE RKLKLNS+PFSLTCLLHKKYILAD
Sbjct: 189 HLQIPVVALNDDGRVVFVSEEEGGENFEKEPVNKEKRKLKLNSVPFSLTCLLHKKYILAD 248

Query: 65  PTAEEESVMETIVTVVLDSSGQLVSFYKPGGSVLAYTSAVQ 106
           PTAEEESVMETIVTVVLDSSGQLVSFYKPGGSVLAYTSAVQ
Sbjct: 249 PTAEEESVMETIVTVVLDSSGQLVSFYKPGGSVLAYTSAVQ 289

[Close]

BLAST of Cucsa.374740 vs. NCBI nr
Match: gi|224138050|ref|XP_002322717.1| (3' exoribonuclease domain 1-containing family protein [Populus trichocarpa])

HSP 1 Score: 161.8 bits (408), Expect = 7.3e-37
Identity = 78/101 (77.23%), Postives = 90/101 (89.11%), Query Frame = 1


Query: 5   NVQIPVVALNDDGKVVFVCEEEGGENFEKEPVNKENRKLKLNSIPFSLTCLLHKKYILAD 64
           ++QIP+V+LNDDGK+V V EE+ G   EKEPVNKE RKL L+SIPFSLTC+LHK YILAD
Sbjct: 196 HLQIPIVSLNDDGKIVLVSEEDEGAKLEKEPVNKEKRKLTLSSIPFSLTCILHKNYILAD 255

Query: 65  PTAEEESVMETIVTVVLDSSGQLVSFYKPGGSVLAYTSAVQ 106
           PTAEEES+MET+VTVVLDSS +LVSFYKPGGSV AYTSAV+
Sbjct: 256 PTAEEESIMETLVTVVLDSSARLVSFYKPGGSVFAYTSAVK 296

The following BLAST results are available for this feature:

BLAST of Cucsa.374740 vs. TrEMBL


Match Name	E-value	Identity	Description
A0A0A0KYC2_CUCSA	2.1e-51	100.00	Uncharacterized protein OS=Cucumis sativus GN=Csa_4G165890 PE=4 SV=1	[more]
U5FN09_POPTR	5.1e-37	77.23	Uncharacterized protein OS=Populus trichocarpa GN=POPTR_0016s05590g PE=4 SV=1	[more]
B9II78_POPTR	5.1e-37	77.23	3' exoribonuclease domain 1-containing family protein OS=Populus trichocarpa GN=...	[more]
B9H9U8_POPTR	2.5e-36	78.00	3' exoribonuclease domain 1-containing family protein OS=Populus trichocarpa GN=...	[more]
U5G927_POPTR	4.3e-36	76.24	Uncharacterized protein OS=Populus trichocarpa GN=POPTR_0006s04970g PE=4 SV=1	[more]

BLAST of Cucsa.374740 vs. TAIR10


Match Name	E-value	Identity	Description
AT1G60080.1	1.1e-33	62.83	3'-5'-exoribonuclease family protein	[more]

BLAST of Cucsa.374740 vs. NCBI nr


Match Name	E-value	Identity	Description
gi\|700198686\|gb\|KGN53844.1\|	3.1e-51	100.00	hypothetical protein Csa_4G165890 [Cucumis sativus]	[more]
gi\|449463354\|ref\|XP_004149399.1\|	7.1e-48	98.02	PREDICTED: exosome complex component RRP43 [Cucumis sativus]	[more]
gi\|659121683\|ref\|XP_008460773.1\|	1.5e-45	94.06	PREDICTED: exosome complex component RRP43 isoform X2 [Cucumis melo]	[more]
gi\|659121681\|ref\|XP_008460772.1\|	1.5e-45	94.06	PREDICTED: exosome complex component RRP43 isoform X1 [Cucumis melo]	[more]
gi\|224138050\|ref\|XP_002322717.1\|	7.3e-37	77.23	3' exoribonuclease domain 1-containing family protein [Populus trichocarpa]	[more]

Annotated Terms

The following terms have been associated with this gene:

Vocabulary: **INTERPRO**
Term	Definition
IPR015847	ExoRNase_PH_dom2

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 gene is annotated with the following GO terms.

Category	Term Accession	Term Name
biological_process	GO:0009058	biosynthetic process
biological_process	GO:0090305	nucleic acid phosphodiester bond hydrolysis
biological_process	GO:0006401	RNA catabolic process
biological_process	GO:0006396	RNA processing
cellular_component	GO:0005829	cytosol
cellular_component	GO:0000178	exosome (RNase complex)
molecular_function	GO:0004527	exonuclease activity

Relationships

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


Feature Name	Unique Name	Type
Cucsa.374740.1	Cucsa.374740.1	mRNA

InterPro

Analysis Name: InterPro Annotations of cucumber (Gy14)
Date Performed: 2017-01-17


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
IPR015847	Exoribonuclease, phosphorolytic domain 2	PFAM	PF03725	RNase_PH_C	coord: 49..96 score: 9.
IPR015847	Exoribonuclease, phosphorolytic domain 2	unknown	SSF55666	Ribonuclease PH domain 2-like	coord: 43..102 score: 1.54
None	No IPR available	PANTHER	PTHR11097	EXOSOME COMPLEX EXONUCLEASE RIBOSOMAL RNA PROCESSING PROTEIN	coord: 5..114 score: 9.7

Synteny

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


Gene	Orthologue	Organism	Block
Cucsa.374740	Cla002766	Watermelon (97103) v1	cgywmB676
Cucsa.374740	Csa4G165890	Cucumber (Chinese Long) v2	cgycuB524
Cucsa.374740	ClCG04G000120	Watermelon (Charleston Gray)	cgywcgB639
Cucsa.374740	CSPI04G10590	Wild cucumber (PI 183967)	cgycpiB553
Cucsa.374740	Cp4.1LG10g11590	Cucurbita pepo (Zucchini)	cgycpeB0988
Cucsa.374740	Cla97C04G068550	Watermelon (97103) v2	cgywmbB643

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

None

The following block(s) are covering this gene:


Gene	Organism	Block
Cucsa.374740	Cucumber (Chinese Long) v3	cgycucB568
Cucsa.374740	Melon (DHL92) v3.5.1	cgymeB608
Cucsa.374740	Bottle gourd (USVL1VR-Ls)	cgylsiB606
Cucsa.374740	Melon (DHL92) v3.6.1	cgymedB605