Csa4G165880 (gene) Cucumber (Chinese Long) v2 | Cucurbit Genomics Database (CuGenDB)

Overview


Name	Csa4G165880
Type	gene
Organism	Cucumis. sativus (Cucumber (Chinese Long) v2)
Description	Unknown protein; contains IPR020568 (Ribosomal protein S5 domain 2-type fold)
Location	Chr4 : 8543767 .. 8544366 (+)

Genome Viewer

Gene Expression

Sequences

The following sequences are available for this feature:

Gene sequence (with intron)

Legend: CDSthree_prime_UTR

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

ATGGCTTACTTGGTATGTGCTTTAAATTCATGCATTGTCAATATATATATTTTTATTCTAGCAGTATCTTGGAGTTTGAAGTGAGGTTCCTTCACCAATATATCGTTATACTTTGTTTCTAAATTTTTTTCTTGCATCATCCTCACTTGTATTGGACATTTTCTCTCTATAGCTTGATTTTTAGACAGAATGCCAGTTTATTATTGCAGTTAATTGTTTTAGATGAGATAGCAACTTGACATGTGTTCCACAGGATATTTACTGTTTGGACGCTGATGGTTCTCTTTTTGATGCTGCACTTCTTTCTGCAGCAGCTGCATTTTCTCACTGTGAGGTTTCAGGCTCTCAACTTGTTCCCAACATGATATATTTCTGTGTAATTTGGTACATGTTATGCTTATGGCAGTAATGTCAATTATGGTGGGATAGGACATTTTGTCCTCCGTTAACACTAAGAATAGTTTTTCAGATTATAGATTGTTACTTTATGCTTTTAATCTTTTACATTTCTGATTTTTTTCCCTCTTTAGATTCCTTTTGTTATCAAAATTTATAGGGACACTTATGGCCCGTAACAACCAACTTTGGCAACCATACCCC

mRNA sequence

ATGGCTTACTTGGATATTTACTGTTTGGACGCTGATGGTTCTCTTTTTGATGCTGCACTTCTTTCTGCAGCAGCTGCATTTTCTCACTGTGAGGTTTCAGGCTCTCAACTTGTTCCCAACATGATATATTTCTGTGTAATTTGGTACATGTTATGCTTATGGCAGTAA

Coding sequence (CDS)

ATGGCTTACTTGGATATTTACTGTTTGGACGCTGATGGTTCTCTTTTTGATGCTGCACTTCTTTCTGCAGCAGCTGCATTTTCTCACTGTGAGGTTTCAGGCTCTCAACTTGTTCCCAACATGATATATTTCTGTGTAATTTGGTACATGTTATGCTTATGGCAGTAA

Protein sequence

MAYLDIYCLDADGSLFDAALLSAAAAFSHCEVSGSQLVPNMIYFCVIWYMLCLWQ*

Homology

[Close]

BLAST of Csa4G165880 vs. TrEMBL
Match: A0A0A0KWB3_CUCSA (Uncharacterized protein OS=Cucumis sativus GN=Csa_4G165880 PE=4 SV=1)

HSP 1 Score: 119.8 bits (299), Expect = 1.1e-24
Identity = 55/55 (100.00%), Postives = 55/55 (100.00%), Query Frame = 1


Query: 1  MAYLDIYCLDADGSLFDAALLSAAAAFSHCEVSGSQLVPNMIYFCVIWYMLCLWQ 56
          MAYLDIYCLDADGSLFDAALLSAAAAFSHCEVSGSQLVPNMIYFCVIWYMLCLWQ
Sbjct: 1  MAYLDIYCLDADGSLFDAALLSAAAAFSHCEVSGSQLVPNMIYFCVIWYMLCLWQ 55

[Close]

BLAST of Csa4G165880 vs. TrEMBL
Match: A0A103Y6N3_CYNCS (Exoribonuclease, phosphorolytic domain 2 OS=Cynara cardunculus var. scolymus GN=Ccrd_018206 PE=4 SV=1)

HSP 1 Score: 62.4 bits (150), Expect = 2.0e-07
Identity = 28/31 (90.32%), Postives = 31/31 (100.00%), Query Frame = 1


Query: 1  MAYLDIYCLDADGSLFDAALLSAAAAFSHCE 32
          MAYLDIYCLDADG+LFDAALL+AAAAFSHC+
Sbjct: 17 MAYLDIYCLDADGALFDAALLAAAAAFSHCK 47

[Close]

BLAST of Csa4G165880 vs. TrEMBL
Match: A0A068UIP4_COFCA (Uncharacterized protein OS=Coffea canephora GN=GSCOC_T00027264001 PE=4 SV=1)

HSP 1 Score: 60.8 bits (146), Expect = 5.9e-07
Identity = 28/32 (87.50%), Postives = 30/32 (93.75%), Query Frame = 1


Query: 1   MAYLDIYCLDADGSLFDAALLSAAAAFSHCEV 33
           MAYLDIYCLDADGSLFDAALLSA AAFSH ++
Sbjct: 155 MAYLDIYCLDADGSLFDAALLSAVAAFSHLQI 186

[Close]

BLAST of Csa4G165880 vs. TrEMBL
Match: A0A068VEJ1_COFCA (Uncharacterized protein OS=Coffea canephora GN=GSCOC_T00012655001 PE=4 SV=1)

HSP 1 Score: 60.8 bits (146), Expect = 5.9e-07
Identity = 28/32 (87.50%), Postives = 30/32 (93.75%), Query Frame = 1


Query: 1  MAYLDIYCLDADGSLFDAALLSAAAAFSHCEV 33
          MAYLDIYCLDADGSLFDAALLSA AAFSH ++
Sbjct: 17 MAYLDIYCLDADGSLFDAALLSAVAAFSHLQI 48

[Close]

BLAST of Csa4G165880 vs. TrEMBL
Match: A0A0B0MVX7_GOSAR (Exosome complex component RRP43 OS=Gossypium arboreum GN=F383_26456 PE=4 SV=1)

HSP 1 Score: 60.5 bits (145), Expect = 7.7e-07
Identity = 27/31 (87.10%), Postives = 29/31 (93.55%), Query Frame = 1


Query: 1   MAYLDIYCLDADGSLFDAALLSAAAAFSHCE 32
           MAYLDIYCLDADG+LFD ALLSA AAFSHC+
Sbjct: 142 MAYLDIYCLDADGALFDTALLSAVAAFSHCK 172

[Close]

BLAST of Csa4G165880 vs. TAIR10
Match: AT1G60080.1 (AT1G60080.1 3'-5'-exoribonuclease family protein)

HSP 1 Score: 54.3 bits (129), Expect = 2.8e-08
Identity = 24/32 (75.00%), Postives = 27/32 (84.38%), Query Frame = 1


Query: 1   MAYLDIYCLDADGSLFDAALLSAAAAFSHCEV 33
           M YLDIYCLDADG+LFDAALL+A AAFS+ ++
Sbjct: 148 MGYLDIYCLDADGALFDAALLAAVAAFSNLQI 179

[Close]

BLAST of Csa4G165880 vs. NCBI nr
Match: gi|700198685|gb|KGN53843.1| (hypothetical protein Csa_4G165880 [Cucumis sativus])

HSP 1 Score: 119.8 bits (299), Expect = 1.5e-24
Identity = 55/55 (100.00%), Postives = 55/55 (100.00%), Query Frame = 1


Query: 1  MAYLDIYCLDADGSLFDAALLSAAAAFSHCEVSGSQLVPNMIYFCVIWYMLCLWQ 56
          MAYLDIYCLDADGSLFDAALLSAAAAFSHCEVSGSQLVPNMIYFCVIWYMLCLWQ
Sbjct: 1  MAYLDIYCLDADGSLFDAALLSAAAAFSHCEVSGSQLVPNMIYFCVIWYMLCLWQ 55

[Close]

BLAST of Csa4G165880 vs. NCBI nr
Match: gi|659121683|ref|XP_008460773.1| (PREDICTED: exosome complex component RRP43 isoform X2 [Cucumis melo])

HSP 1 Score: 62.4 bits (150), Expect = 2.9e-07
Identity = 29/32 (90.62%), Postives = 31/32 (96.88%), Query Frame = 1


Query: 1   MAYLDIYCLDADGSLFDAALLSAAAAFSHCEV 33
           MAYLDIYCLDADGSLFDAALLSAAAAFSH ++
Sbjct: 149 MAYLDIYCLDADGSLFDAALLSAAAAFSHLQI 180

[Close]

BLAST of Csa4G165880 vs. NCBI nr
Match: gi|449463354|ref|XP_004149399.1| (PREDICTED: exosome complex component RRP43 [Cucumis sativus])

HSP 1 Score: 62.4 bits (150), Expect = 2.9e-07
Identity = 29/32 (90.62%), Postives = 31/32 (96.88%), Query Frame = 1


Query: 1   MAYLDIYCLDADGSLFDAALLSAAAAFSHCEV 33
           MAYLDIYCLDADGSLFDAALLSAAAAFSH ++
Sbjct: 149 MAYLDIYCLDADGSLFDAALLSAAAAFSHLQI 180

[Close]

BLAST of Csa4G165880 vs. NCBI nr
Match: gi|976918298|gb|KVI03487.1| (Exoribonuclease, phosphorolytic domain 2 [Cynara cardunculus var. scolymus])

HSP 1 Score: 62.4 bits (150), Expect = 2.9e-07
Identity = 28/31 (90.32%), Postives = 31/31 (100.00%), Query Frame = 1


Query: 1  MAYLDIYCLDADGSLFDAALLSAAAAFSHCE 32
          MAYLDIYCLDADG+LFDAALL+AAAAFSHC+
Sbjct: 17 MAYLDIYCLDADGALFDAALLAAAAAFSHCK 47

[Close]

BLAST of Csa4G165880 vs. NCBI nr
Match: gi|659121681|ref|XP_008460772.1| (PREDICTED: exosome complex component RRP43 isoform X1 [Cucumis melo])

HSP 1 Score: 62.4 bits (150), Expect = 2.9e-07
Identity = 29/32 (90.62%), Postives = 31/32 (96.88%), Query Frame = 1


Query: 1   MAYLDIYCLDADGSLFDAALLSAAAAFSHCEV 33
           MAYLDIYCLDADGSLFDAALLSAAAAFSH ++
Sbjct: 161 MAYLDIYCLDADGSLFDAALLSAAAAFSHLQI 192

The following BLAST results are available for this feature:

BLAST of Csa4G165880 vs. TrEMBL


Match Name	E-value	Identity	Description
A0A0A0KWB3_CUCSA	1.1e-24	100.00	Uncharacterized protein OS=Cucumis sativus GN=Csa_4G165880 PE=4 SV=1	[more]
A0A103Y6N3_CYNCS	2.0e-07	90.32	Exoribonuclease, phosphorolytic domain 2 OS=Cynara cardunculus var. scolymus GN=...	[more]
A0A068UIP4_COFCA	5.9e-07	87.50	Uncharacterized protein OS=Coffea canephora GN=GSCOC_T00027264001 PE=4 SV=1	[more]
A0A068VEJ1_COFCA	5.9e-07	87.50	Uncharacterized protein OS=Coffea canephora GN=GSCOC_T00012655001 PE=4 SV=1	[more]
A0A0B0MVX7_GOSAR	7.7e-07	87.10	Exosome complex component RRP43 OS=Gossypium arboreum GN=F383_26456 PE=4 SV=1	[more]

BLAST of Csa4G165880 vs. TAIR10


Match Name	E-value	Identity	Description
AT1G60080.1	2.8e-08	75.00	3'-5'-exoribonuclease family protein	[more]

BLAST of Csa4G165880 vs. NCBI nr


Match Name	E-value	Identity	Description
gi\|700198685\|gb\|KGN53843.1\|	1.5e-24	100.00	hypothetical protein Csa_4G165880 [Cucumis sativus]	[more]
gi\|659121683\|ref\|XP_008460773.1\|	2.9e-07	90.63	PREDICTED: exosome complex component RRP43 isoform X2 [Cucumis melo]	[more]
gi\|449463354\|ref\|XP_004149399.1\|	2.9e-07	90.63	PREDICTED: exosome complex component RRP43 [Cucumis sativus]	[more]
gi\|976918298\|gb\|KVI03487.1\|	2.9e-07	90.32	Exoribonuclease, phosphorolytic domain 2 [Cynara cardunculus var. scolymus]	[more]
gi\|659121681\|ref\|XP_008460772.1\|	2.9e-07	90.63	PREDICTED: exosome complex component RRP43 isoform X1 [Cucumis melo]	[more]

Annotated Terms

The following terms have been associated with this gene:

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

GO Annotation

GO Assignments

This gene is annotated with the following GO terms.

Category	Term Accession	Term Name
biological_process	GO:0008150	biological_process
biological_process	GO:0006401	RNA catabolic process
biological_process	GO:0006396	RNA processing
cellular_component	GO:0005575	cellular_component
cellular_component	GO:0000178	exosome (RNase complex)
molecular_function	GO:0003674	molecular_function

Unigene

This gene is associated with the following unigenes:


Unigene Name	Analysis Name	Sequence type in Unigene
CU089451	cucumber EST collection version 3.0	transcribed_cluster

Relationships

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


Feature Name	Unique Name	Type
Csa4G165880.1	Csa4G165880.1	mRNA

The following transcribed_cluster feature(s) are associated with this gene:


Feature Name	Unique Name	Type
CU089451	CU089451	transcribed_cluster

InterPro

Analysis Name: InterPro Annotations of cucumber (Chinese Long)
Date Performed: 2016-09-28


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
IPR020568	Ribosomal protein S5 domain 2-type fold	unknown	SSF54211	Ribosomal protein S5 domain 2-like	coord: 2..38 score: 3.3

Synteny

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

None

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

None

The following block(s) are covering this gene:


Gene	Organism	Block
Csa4G165880	Cucumber (Gy14) v2	cgybcuB165
Csa4G165880	Melon (DHL92) v3.6.1	cumedB313
Csa4G165880	Silver-seed gourd	carcuB0213
Csa4G165880	Silver-seed gourd	carcuB0214
Csa4G165880	Silver-seed gourd	carcuB0313
Csa4G165880	Watermelon (97103) v2	cuwmbB302
Csa4G165880	Wax gourd	cuwgoB392
Csa4G165880	Cucumber (Gy14) v1	cgycuB524
Csa4G165880	Cucurbita maxima (Rimu)	cmacuB666
Csa4G165880	Cucurbita maxima (Rimu)	cmacuB673
Csa4G165880	Cucurbita maxima (Rimu)	cmacuB868
Csa4G165880	Cucurbita moschata (Rifu)	cmocuB654
Csa4G165880	Cucurbita moschata (Rifu)	cmocuB662
Csa4G165880	Cucurbita moschata (Rifu)	cmocuB857
Csa4G165880	Melon (DHL92) v3.5.1	cumeB331
Csa4G165880	Watermelon (Charleston Gray)	cuwcgB305
Csa4G165880	Watermelon (97103) v1	cuwmB335
Csa4G165880	Cucurbita pepo (Zucchini)	cpecuB074
Csa4G165880	Cucurbita pepo (Zucchini)	cpecuB080
Csa4G165880	Cucurbita pepo (Zucchini)	cpecuB489
Csa4G165880	Bottle gourd (USVL1VR-Ls)	culsiB260