Csa1G533670 (gene) Cucumber (Chinese Long) v2 | Cucurbit Genomics Database (CuGenDB)

Overview


Name	Csa1G533670
Type	gene
Organism	Cucumis. sativus (Cucumber (Chinese Long) v2)
Description	tRNA pseudouridine synthase
Location	Chr1 : 19040616 .. 19041134 (+)

Genome Viewer

Gene Expression

Sequences

The following sequences are available for this feature:

Gene sequence (with intron)

Legend: five_prime_UTRCDS

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

ATTTTGTTAGCCCCTCGAATTCCCGTCCCCCAAGAATAGGGTGCAATGTCAGTCTCTTCTTTGCGACTCCCACTTTCCCCATGGATAACCAAAGCTTCATCTTCATGTTTTCGTTTCCCCGACCCTGTTTTCGTTTCCCGGACTCCTCCTCTTAGGCCTGCACTGCTCCACTTTTTCTCATCTTCTACTGCCTCCACCGATGCTTTTTCCACTCGGTGCGCTCCGGATCAGCTCCGGAAATGGCAAGCTTTCCGTAAGAAAAAGGTCGTTTTGCGAATCGGCTATGTCGGGACTGATTATCGAGGTCCTCATTTCACGTTACTCTCTGTTTCTCTTGACCATCCTCTTGTGAATCCTTCACCATTTCTCATTAACTCACTAGTTTTGACAATTCAGGGCTACAAATGCAACGCAACCAACTGTCACATCCAAGTAAGTTTTTCTCTACATTATATCAGGAAAATTCCTATCGATGGATTGACCATGGCATCCCCTGAATATTCTGTTGCTGTGTTATGA

mRNA sequence

ATGTCAGTCTCTTCTTTGCGACTCCCACTTTCCCCATGGATAACCAAAGCTTCATCTTCATGTTTTCGTTTCCCCGACCCTGTTTTCGTTTCCCGGACTCCTCCTCTTAGGCCTGCACTGCTCCACTTTTTCTCATCTTCTACTGCCTCCACCGATGCTTTTTCCACTCGGTGCGCTCCGGATCAGCTCCGGAAATGGCAAGCTTTCCGTAAGAAAAAGGTCGTTTTGCGAATCGGCTATGTCGGGACTGATTATCGAGGTCCTCATTTCACGTTACTCTCTGTTTCTCTTGACCATCCTCTTGTGAATCCTTCACCATTTCTCATTAACTCACTAGTTTTGACAATTCAGGGCTACAAATGCAACGCAACCAACTGTCACATCCAAGTAAGTTTTTCTCTACATTATATCAGGAAAATTCCTATCGATGGATTGACCATGGCATCCCCTGAATATTCTGTTGCTGTGTTATGA

Coding sequence (CDS)

ATGTCAGTCTCTTCTTTGCGACTCCCACTTTCCCCATGGATAACCAAAGCTTCATCTTCATGTTTTCGTTTCCCCGACCCTGTTTTCGTTTCCCGGACTCCTCCTCTTAGGCCTGCACTGCTCCACTTTTTCTCATCTTCTACTGCCTCCACCGATGCTTTTTCCACTCGGTGCGCTCCGGATCAGCTCCGGAAATGGCAAGCTTTCCGTAAGAAAAAGGTCGTTTTGCGAATCGGCTATGTCGGGACTGATTATCGAGGTCCTCATTTCACGTTACTCTCTGTTTCTCTTGACCATCCTCTTGTGAATCCTTCACCATTTCTCATTAACTCACTAGTTTTGACAATTCAGGGCTACAAATGCAACGCAACCAACTGTCACATCCAAGTAAGTTTTTCTCTACATTATATCAGGAAAATTCCTATCGATGGATTGACCATGGCATCCCCTGAATATTCTGTTGCTGTGTTATGA

Protein sequence

MSVSSLRLPLSPWITKASSSCFRFPDPVFVSRTPPLRPALLHFFSSSTASTDAFSTRCAPDQLRKWQAFRKKKVVLRIGYVGTDYRGPHFTLLSVSLDHPLVNPSPFLINSLVLTIQGYKCNATNCHIQVSFSLHYIRKIPIDGLTMASPEYSVAVL*

Homology

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BLAST of Csa1G533670 vs. Swiss-Prot
Match: PUSH_ARATH (Putative tRNA pseudouridine synthase OS=Arabidopsis thaliana GN=At2g30320 PE=3 SV=1)

HSP 1 Score: 59.7 bits (143), Expect = 3.3e-08
Identity = 43/107 (40.19%), Postives = 56/107 (52.34%), Query Frame = 1


Query: 1   MSVSSLRLPLSPWITKASSSCFRFPDPVFVSRTPPLRPALLHFFSSSTASTDAFSTRCAP 60
           M+VS LR+P+        S  F +P     +R   + PALL F  SS+A+    ST  +P
Sbjct: 1   MAVSFLRIPIP-------SRVFWYP-----TRLIRVTPALLRF--SSSAAFQPSSTSLSP 60

Query: 61  DQ-----LRKWQAFRKKKVVLRIGYVGTDYRGPHFTLLSVSLDHPLV 103
                    KW+++RKKKVV+RIGYVGTDYRG     L +  D P +
Sbjct: 61  PSSDNFLADKWESYRKKKVVIRIGYVGTDYRG-----LQIQRDDPSI 88

[Close]

BLAST of Csa1G533670 vs. TrEMBL
Match: A0A0A0LVB6_CUCSA (Uncharacterized protein OS=Cucumis sativus GN=Csa_1G533670 PE=4 SV=1)

HSP 1 Score: 321.6 bits (823), Expect = 5.3e-85
Identity = 157/157 (100.00%), Postives = 157/157 (100.00%), Query Frame = 1


Query: 1   MSVSSLRLPLSPWITKASSSCFRFPDPVFVSRTPPLRPALLHFFSSSTASTDAFSTRCAP 60
           MSVSSLRLPLSPWITKASSSCFRFPDPVFVSRTPPLRPALLHFFSSSTASTDAFSTRCAP
Sbjct: 1   MSVSSLRLPLSPWITKASSSCFRFPDPVFVSRTPPLRPALLHFFSSSTASTDAFSTRCAP 60

Query: 61  DQLRKWQAFRKKKVVLRIGYVGTDYRGPHFTLLSVSLDHPLVNPSPFLINSLVLTIQGYK 120
           DQLRKWQAFRKKKVVLRIGYVGTDYRGPHFTLLSVSLDHPLVNPSPFLINSLVLTIQGYK
Sbjct: 61  DQLRKWQAFRKKKVVLRIGYVGTDYRGPHFTLLSVSLDHPLVNPSPFLINSLVLTIQGYK 120

Query: 121 CNATNCHIQVSFSLHYIRKIPIDGLTMASPEYSVAVL 158
           CNATNCHIQVSFSLHYIRKIPIDGLTMASPEYSVAVL
Sbjct: 121 CNATNCHIQVSFSLHYIRKIPIDGLTMASPEYSVAVL 157

[Close]

BLAST of Csa1G533670 vs. TrEMBL
Match: M5WP30_PRUPE (Uncharacterized protein OS=Prunus persica GN=PRUPE_ppa004352mg PE=4 SV=1)

HSP 1 Score: 75.1 bits (183), Expect = 8.6e-11
Identity = 41/87 (47.13%), Postives = 54/87 (62.07%), Query Frame = 1


Query: 1  MSVSSLRLPLSPWITKASSSCFRFPDPVFVSRTPPLRPALLHFFSSSTASTDAFSTRCAP 60
          M++SSLRLP S W+ +     FRF  P+      PLR  L++  SS +++    ST    
Sbjct: 1  MAISSLRLPFSLWLPRLPIQSFRFSKPIL-----PLRLNLIYCSSSISSTAQQTSTH--- 60

Query: 61 DQLRKWQAFRKKKVVLRIGYVGTDYRG 88
            L KWQ+ RKKKVVLR+GYVG+DYRG
Sbjct: 61 --LEKWQSVRKKKVVLRVGYVGSDYRG 77

[Close]

BLAST of Csa1G533670 vs. TrEMBL
Match: A0A068U688_COFCA (Uncharacterized protein OS=Coffea canephora GN=GSCOC_T00016610001 PE=4 SV=1)

HSP 1 Score: 74.3 bits (181), Expect = 1.5e-10
Identity = 43/96 (44.79%), Postives = 59/96 (61.46%), Query Frame = 1


Query: 1  MSVSSLRLPLSPWIT-KASSSCFRFPDPVFVSRTPPLRPALLHFFSSSTASTDAF----- 60
          M+V  LRLPLSPW+  +A+ +  +F +P       PL+P LL F +S+ AS  A      
Sbjct: 1  MAVIPLRLPLSPWLAARAAPTTLQFFNP-----NKPLKPFLLRFSTSAAASDAAAQDSVP 60

Query: 61 ---STRCAPDQLRKWQAFRKKKVVLRIGYVGTDYRG 88
             S+  +P    KW+ FRKKKVV+R+GYVG+DYRG
Sbjct: 61 LPPSSSPSPPPQNKWEPFRKKKVVMRVGYVGSDYRG 91

[Close]

BLAST of Csa1G533670 vs. TrEMBL
Match: F6GUG3_VITVI (Putative uncharacterized protein OS=Vitis vinifera GN=VIT_06s0004g07710 PE=4 SV=1)

HSP 1 Score: 72.8 bits (177), Expect = 4.3e-10
Identity = 42/88 (47.73%), Postives = 56/88 (63.64%), Query Frame = 1


Query: 1  MSVSSLRLPLSPWITKASSSCFRFPDPVFVSRTPPLRPALLHFFSSSTASTDAFSTRCAP 60
          M VSSLR PL PWI    +S  RF +P  + +        LH  SSS+++     T   P
Sbjct: 1  MVVSSLRFPLFPWIISNHTSNLRFSNPRILPQWS------LHCSSSSSSTV----TESNP 60

Query: 61 DQ-LRKWQAFRKKKVVLRIGYVGTDYRG 88
          DQ ++KW++FRKKKVV+R+GYVGT+YRG
Sbjct: 61 DQSVQKWESFRKKKVVMRVGYVGTNYRG 78

[Close]

BLAST of Csa1G533670 vs. TrEMBL
Match: A5C2V2_VITVI (Putative uncharacterized protein OS=Vitis vinifera GN=VITISV_034891 PE=4 SV=1)

HSP 1 Score: 72.8 bits (177), Expect = 4.3e-10
Identity = 42/88 (47.73%), Postives = 56/88 (63.64%), Query Frame = 1


Query: 1  MSVSSLRLPLSPWITKASSSCFRFPDPVFVSRTPPLRPALLHFFSSSTASTDAFSTRCAP 60
          M VSSLR PL PWI    +S  RF +P  + +        LH  SSS+++     T   P
Sbjct: 1  MVVSSLRFPLFPWIISNHTSNLRFSNPRILPQWS------LHCSSSSSSTV----TESNP 60

Query: 61 DQ-LRKWQAFRKKKVVLRIGYVGTDYRG 88
          DQ ++KW++FRKKKVV+R+GYVGT+YRG
Sbjct: 61 DQSVQKWESFRKKKVVMRVGYVGTNYRG 78

[Close]

BLAST of Csa1G533670 vs. TAIR10
Match: AT2G30320.1 (AT2G30320.1 Pseudouridine synthase family protein)

HSP 1 Score: 59.7 bits (143), Expect = 1.9e-09
Identity = 43/107 (40.19%), Postives = 56/107 (52.34%), Query Frame = 1


Query: 1   MSVSSLRLPLSPWITKASSSCFRFPDPVFVSRTPPLRPALLHFFSSSTASTDAFSTRCAP 60
           M+VS LR+P+        S  F +P     +R   + PALL F  SS+A+    ST  +P
Sbjct: 1   MAVSFLRIPIP-------SRVFWYP-----TRLIRVTPALLRF--SSSAAFQPSSTSLSP 60

Query: 61  DQ-----LRKWQAFRKKKVVLRIGYVGTDYRGPHFTLLSVSLDHPLV 103
                    KW+++RKKKVV+RIGYVGTDYRG     L +  D P +
Sbjct: 61  PSSDNFLADKWESYRKKKVVIRIGYVGTDYRG-----LQIQRDDPSI 88

[Close]

BLAST of Csa1G533670 vs. NCBI nr
Match: gi|700210764|gb|KGN65860.1| (hypothetical protein Csa_1G533670 [Cucumis sativus])

HSP 1 Score: 321.6 bits (823), Expect = 7.5e-85
Identity = 157/157 (100.00%), Postives = 157/157 (100.00%), Query Frame = 1


Query: 1   MSVSSLRLPLSPWITKASSSCFRFPDPVFVSRTPPLRPALLHFFSSSTASTDAFSTRCAP 60
           MSVSSLRLPLSPWITKASSSCFRFPDPVFVSRTPPLRPALLHFFSSSTASTDAFSTRCAP
Sbjct: 1   MSVSSLRLPLSPWITKASSSCFRFPDPVFVSRTPPLRPALLHFFSSSTASTDAFSTRCAP 60

Query: 61  DQLRKWQAFRKKKVVLRIGYVGTDYRGPHFTLLSVSLDHPLVNPSPFLINSLVLTIQGYK 120
           DQLRKWQAFRKKKVVLRIGYVGTDYRGPHFTLLSVSLDHPLVNPSPFLINSLVLTIQGYK
Sbjct: 61  DQLRKWQAFRKKKVVLRIGYVGTDYRGPHFTLLSVSLDHPLVNPSPFLINSLVLTIQGYK 120

Query: 121 CNATNCHIQVSFSLHYIRKIPIDGLTMASPEYSVAVL 158
           CNATNCHIQVSFSLHYIRKIPIDGLTMASPEYSVAVL
Sbjct: 121 CNATNCHIQVSFSLHYIRKIPIDGLTMASPEYSVAVL 157

[Close]

BLAST of Csa1G533670 vs. NCBI nr
Match: gi|449454977|ref|XP_004145230.1| (PREDICTED: putative tRNA pseudouridine synthase [Cucumis sativus])

HSP 1 Score: 181.8 bits (460), Expect = 9.3e-43
Identity = 90/102 (88.24%), Postives = 92/102 (90.20%), Query Frame = 1


Query: 1   MSVSSLRLPLSPWITKASSSCFRFPDPVFVSRTPPLRPALLHFFSSSTASTDAFSTRCAP 60
           MSVSSLRLPLSPWITKASSSCFRFPDPVFVSRTPPLRPALLHFFSSSTASTDAFSTRCAP
Sbjct: 1   MSVSSLRLPLSPWITKASSSCFRFPDPVFVSRTPPLRPALLHFFSSSTASTDAFSTRCAP 60

Query: 61  DQLRKWQAFRKKKVVLRIGYVGTDYRGPHFTLLSVSLDHPLV 103
           DQLRKWQAFRKKKVVLRIGYVGTDYRG    +    L HP +
Sbjct: 61  DQLRKWQAFRKKKVVLRIGYVGTDYRG--LQMQRNQLSHPTI 100

[Close]

BLAST of Csa1G533670 vs. NCBI nr
Match: gi|659114949|ref|XP_008457308.1| (PREDICTED: putative tRNA pseudouridine synthase [Cucumis melo])

HSP 1 Score: 160.2 bits (404), Expect = 2.9e-36
Identity = 80/102 (78.43%), Postives = 86/102 (84.31%), Query Frame = 1


Query: 1   MSVSSLRLPLSPWITKASSSCFRFPDPVFVSRTPPLRPALLHFFSSSTASTDAFSTRCAP 60
           MSVSSLRLPLSPWITK+SSSCFRFP PVFV RTP LRP LL+ FSS+ ASTDAFST+CAP
Sbjct: 1   MSVSSLRLPLSPWITKSSSSCFRFPYPVFVPRTPRLRPTLLYCFSSAAASTDAFSTQCAP 60

Query: 61  DQLRKWQAFRKKKVVLRIGYVGTDYRGPHFTLLSVSLDHPLV 103
           DQLRKWQAFRKKKVVLRIGYVGTDYRG    +    L HP +
Sbjct: 61  DQLRKWQAFRKKKVVLRIGYVGTDYRG--LQMQRNQLSHPTI 100

[Close]

BLAST of Csa1G533670 vs. NCBI nr
Match: gi|595837032|ref|XP_007207376.1| (hypothetical protein PRUPE_ppa004352mg [Prunus persica])

HSP 1 Score: 75.1 bits (183), Expect = 1.2e-10
Identity = 41/87 (47.13%), Postives = 54/87 (62.07%), Query Frame = 1


Query: 1  MSVSSLRLPLSPWITKASSSCFRFPDPVFVSRTPPLRPALLHFFSSSTASTDAFSTRCAP 60
          M++SSLRLP S W+ +     FRF  P+      PLR  L++  SS +++    ST    
Sbjct: 1  MAISSLRLPFSLWLPRLPIQSFRFSKPIL-----PLRLNLIYCSSSISSTAQQTSTH--- 60

Query: 61 DQLRKWQAFRKKKVVLRIGYVGTDYRG 88
            L KWQ+ RKKKVVLR+GYVG+DYRG
Sbjct: 61 --LEKWQSVRKKKVVLRVGYVGSDYRG 77

[Close]

BLAST of Csa1G533670 vs. NCBI nr
Match: gi|645215371|ref|XP_008229961.1| (PREDICTED: LOW QUALITY PROTEIN: putative tRNA pseudouridine synthase [Prunus mume])

HSP 1 Score: 74.3 bits (181), Expect = 2.1e-10
Identity = 41/87 (47.13%), Postives = 54/87 (62.07%), Query Frame = 1


Query: 1  MSVSSLRLPLSPWITKASSSCFRFPDPVFVSRTPPLRPALLHFFSSSTASTDAFSTRCAP 60
          M++SSLRLP S W+ +     FRF  P+      PLR  L++  SS +++    ST    
Sbjct: 1  MAISSLRLPFSLWLPRLPIQSFRFSKPIL-----PLRLNLIYCSSSISSTAQQTSTH--- 60

Query: 61 DQLRKWQAFRKKKVVLRIGYVGTDYRG 88
            L KWQ+ RKKKVVLR+GYVG+DYRG
Sbjct: 61 --LDKWQSVRKKKVVLRVGYVGSDYRG 77

The following BLAST results are available for this feature:

BLAST of Csa1G533670 vs. Swiss-Prot


Match Name	E-value	Identity	Description
PUSH_ARATH	3.3e-08	40.19	Putative tRNA pseudouridine synthase OS=Arabidopsis thaliana GN=At2g30320 PE=3 S...	[more]

BLAST of Csa1G533670 vs. TrEMBL


Match Name	E-value	Identity	Description
A0A0A0LVB6_CUCSA	5.3e-85	100.00	Uncharacterized protein OS=Cucumis sativus GN=Csa_1G533670 PE=4 SV=1	[more]
M5WP30_PRUPE	8.6e-11	47.13	Uncharacterized protein OS=Prunus persica GN=PRUPE_ppa004352mg PE=4 SV=1	[more]
A0A068U688_COFCA	1.5e-10	44.79	Uncharacterized protein OS=Coffea canephora GN=GSCOC_T00016610001 PE=4 SV=1	[more]
F6GUG3_VITVI	4.3e-10	47.73	Putative uncharacterized protein OS=Vitis vinifera GN=VIT_06s0004g07710 PE=4 SV=...	[more]
A5C2V2_VITVI	4.3e-10	47.73	Putative uncharacterized protein OS=Vitis vinifera GN=VITISV_034891 PE=4 SV=1	[more]

BLAST of Csa1G533670 vs. TAIR10


Match Name	E-value	Identity	Description
AT2G30320.1	1.9e-09	40.19	Pseudouridine synthase family protein	[more]

BLAST of Csa1G533670 vs. NCBI nr


Match Name	E-value	Identity	Description
gi\|700210764\|gb\|KGN65860.1\|	7.5e-85	100.00	hypothetical protein Csa_1G533670 [Cucumis sativus]	[more]
gi\|449454977\|ref\|XP_004145230.1\|	9.3e-43	88.24	PREDICTED: putative tRNA pseudouridine synthase [Cucumis sativus]	[more]
gi\|659114949\|ref\|XP_008457308.1\|	2.9e-36	78.43	PREDICTED: putative tRNA pseudouridine synthase [Cucumis melo]	[more]
gi\|595837032\|ref\|XP_007207376.1\|	1.2e-10	47.13	hypothetical protein PRUPE_ppa004352mg [Prunus persica]	[more]
gi\|645215371\|ref\|XP_008229961.1\|	2.1e-10	47.13	PREDICTED: LOW QUALITY PROTEIN: putative tRNA pseudouridine synthase [Prunus mum...	[more]

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:0001522	pseudouridine synthesis
biological_process	GO:0008033	tRNA processing
biological_process	GO:0031119	tRNA pseudouridine synthesis
cellular_component	GO:0005575	cellular_component
molecular_function	GO:0003674	molecular_function
molecular_function	GO:0009982	pseudouridine synthase activity
molecular_function	GO:0003723	RNA binding

Unigene

This gene is associated with the following unigenes:


Unigene Name	Analysis Name	Sequence type in Unigene
CU141672	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
Csa1G533670.1	Csa1G533670.1	mRNA

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


Feature Name	Unique Name	Type
CU141672	CU141672	transcribed_cluster

Synteny

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


Gene	Orthologue	Organism	Block
Csa1G533670	Cla008112	Watermelon (97103) v1	cuwmB021
Csa1G533670	MELO3C020499	Melon (DHL92) v3.5.1	cumeB028
Csa1G533670	ClCG03G000200	Watermelon (Charleston Gray)	cuwcgB047
Csa1G533670	Lsi02G012250	Bottle gourd (USVL1VR-Ls)	culsiB030
Csa1G533670	MELO3C020498.2	Melon (DHL92) v3.6.1	cumedB023
Csa1G533670	Cla97C03G051010	Watermelon (97103) v2	cuwmbB043
Csa1G533670	Bhi08G000362	Wax gourd	cuwgoB048
Csa1G533670	CSPI01G24410	Wild cucumber (PI 183967)	cpicuB001
Csa1G533670	Cucsa.151990	Cucumber (Gy14) v1	cgycuB219
Csa1G533670	CmaCh13G000200	Cucurbita maxima (Rimu)	cmacuB213
Csa1G533670	CmoCh13G000110	Cucurbita moschata (Rifu)	cmocuB197
Csa1G533670	CsGy1G023890	Cucumber (Gy14) v2	cgybcuB002

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

None

The following block(s) are covering this gene:


Gene	Organism	Block
Csa1G533670	Cucurbita maxima (Rimu)	cmacuB219
Csa1G533670	Cucurbita maxima (Rimu)	cmacuB427
Csa1G533670	Cucurbita maxima (Rimu)	cmacuB433
Csa1G533670	Cucurbita moschata (Rifu)	cmocuB204
Csa1G533670	Cucurbita moschata (Rifu)	cmocuB416
Csa1G533670	Cucurbita pepo (Zucchini)	cpecuB507
Csa1G533670	Cucurbita pepo (Zucchini)	cpecuB532
Csa1G533670	Silver-seed gourd	carcuB0358
Csa1G533670	Silver-seed gourd	carcuB0548