CSPI04G12390 (gene) Wild cucumber (PI 183967) | Cucurbit Genomics Database (CuGenDB)

Overview


Name	CSPI04G12390
Type	gene
Organism	Cucumis sativus (Wild cucumber (PI 183967))
Description	Retrotransposable element Tf2
Location	Chr4 : 10820667 .. 10821053 (+)

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.

GCCAGAGATGAGCTGCTGATTACTCTAAAGCATCACTTACAACACGCCCAAGCACAAATCAAGAAATTTGCGGATGTACACCATCGAGATGTGGTGTTCGACATTAGTGATTGGGTCTATTTAAAAATACAGTCGTATAGACAGCAGTCGTTGGCTAAAAAACGATGCGAAAAGCTGTCATCAAAATATTTTGGACCCTACATGGTATTAGGGAGGGTAGGGGAAGTGGCCTATCTACTAGATCTACCAGACACTGCTCGAATCCACCCCGTGTTCCACGTGTCACAACAAAAAAAAGGCTGTGGGAGACAAGCACCATGTGCAACTAGACATCTCCTTACTCAACGACCAAATGGAATTAGTCCTCGAGCCCGAAAATGTGACTGA

mRNA sequence

GCCAGAGATGAGCTGCTGATTACTCTAAAGCATCACTTACAACACGCCCAAGCACAAATCAAGAAATTTGCGGATGTACACCATCGAGATGTGGTGTTCGACATTAGTGATTGGGTCTATTTAAAAATACAGTCGTATAGACAGCAGTCGTTGGCTAAAAAACGATGCGAAAAGCTGTCATCAAAATATTTTGGACCCTACATGGTATTAGGGAGGGTAGGGGAAGTGGCCTATCTACTAGATCTACCAGACACTGCTCGAATCCACCCCGTGTTCCACGTGTCACAACAAAAAAAAGGCTGTGGGAGACAAGCACCATGTGCAACTAGACATCTCCTTACTCAACGACCAAATGGAATTAGTCCTCGAGCCCGAAAATGTGACTGA

Coding sequence (CDS)

GCCAGAGATGAGCTGCTGATTACTCTAAAGCATCACTTACAACACGCCCAAGCACAAATCAAGAAATTTGCGGATGTACACCATCGAGATGTGGTGTTCGACATTAGTGATTGGGTCTATTTAAAAATACAGTCGTATAGACAGCAGTCGTTGGCTAAAAAACGATGCGAAAAGCTGTCATCAAAATATTTTGGACCCTACATGGTATTAGGGAGGGTAGGGGAAGTGGCCTATCTACTAGATCTACCAGACACTGCTCGAATCCACCCCGTGTTCCACGTGTCACAACAAAAAAAAGGCTGTGGGAGACAAGCACCATGTGCAACTAGACATCTCCTTACTCAACGACCAAATGGAATTAGTCCTCGAGCCCGAAAATGTGACTGA

Homology

[Close]

BLAST of CSPI04G12390 vs. TrEMBL
Match: E5GC18_CUCME (Ty3-gypsy retrotransposon protein OS=Cucumis melo subsp. melo PE=4 SV=1)

HSP 1 Score: 156.4 bits (394), Expect = 2.4e-35
Identity = 72/89 (80.90%), Postives = 81/89 (91.01%), Query Frame = 1


Query: 2    RDELLITLKHHLQHAQAQIKKFADVHHRDVVFDISDWVYLKIQSYRQQSLAKKRCEKLSS 61
            RDE L TLK HLQHAQ Q+KKFA+VH RDVVFDI DWVYLK+Q YRQ+S+AK+RC+KLS 
Sbjct: 1084 RDETLATLKRHLQHAQDQMKKFANVHRRDVVFDIEDWVYLKLQPYRQKSVAKRRCDKLSP 1143

Query: 62   KYFGPYMVLGRVGEVAYLLDLPDTARIHP 91
            KYFGPYMV+GRVGEVAYLLDLPDTA+IHP
Sbjct: 1144 KYFGPYMVMGRVGEVAYLLDLPDTAKIHP 1172

[Close]

BLAST of CSPI04G12390 vs. TrEMBL
Match: Q9SQW9_ARATH (Putative retroelement pol polyprotein OS=Arabidopsis thaliana GN=F23H6.1 PE=4 SV=1)

HSP 1 Score: 121.3 bits (303), Expect = 8.5e-25
Identity = 56/98 (57.14%), Postives = 76/98 (77.55%), Query Frame = 1


Query: 2    RDELLITLKHHLQHAQAQIKKFADVHHRDVVFDISDWVYLKIQSYRQQSLAKKRCEKLSS 61
            RD +L+ L+ +L+ AQAQ+KK AD   RDV F+I +WVYLK++ YRQ S+A ++ EKLS 
Sbjct: 1446 RDGMLVELRENLEIAQAQMKKAADKSRRDVAFEIDEWVYLKLRPYRQSSVAHRKNEKLSQ 1505

Query: 62   KYFGPYMVLGRVGEVAYLLDLPDTARIHPVFHVSQQKK 100
            +YFGP+ VL R+G+VAY L LP+ + IHPVFHVSQ K+
Sbjct: 1506 RYFGPFKVLHRIGQVAYKLQLPEHSTIHPVFHVSQLKR 1543

[Close]

BLAST of CSPI04G12390 vs. TrEMBL
Match: M4DN30_BRARP (Uncharacterized protein OS=Brassica rapa subsp. pekinensis PE=4 SV=1)

HSP 1 Score: 119.8 bits (299), Expect = 2.5e-24
Identity = 56/109 (51.38%), Postives = 76/109 (69.72%), Query Frame = 1


Query: 2    RDELLITLKHHLQHAQAQIKKFADVHHRDVVFDISDWVYLKIQSYRQQSLAKKRCEKLSS 61
            RDELL  LK HL+ +  ++K+ AD   RDV F + DWV+L++Q YRQ+++ ++  +KLS 
Sbjct: 1292 RDELLDELKQHLEASNNRMKQLADTKRRDVEFQVGDWVFLRLQPYRQKTVIRRTSQKLSH 1351

Query: 62   KYFGPYMVLGRVGEVAYLLDLPDTARIHPVFHVSQQKKGCGRQAPCATR 111
            +YFGP+ V  RVG+VAY L LP TARIHPVFHVS  KK  G   P + +
Sbjct: 1352 RYFGPFKVEARVGQVAYRLTLPTTARIHPVFHVSLLKKRIGDDEPASVQ 1400

[Close]

BLAST of CSPI04G12390 vs. TrEMBL
Match: A0A151SSE7_CAJCA (Retrotransposable element Tf2 (Fragment) OS=Cajanus cajan GN=KK1_003948 PE=4 SV=1)

HSP 1 Score: 119.4 bits (298), Expect = 3.2e-24
Identity = 57/101 (56.44%), Postives = 74/101 (73.27%), Query Frame = 1


Query: 2   RDELLITLKHHLQHAQAQIKKFADVHHRDVVFDISDWVYLKIQSYRQQSLAKKRCEKLSS 61
           R+E+L  LK HL+ AQ ++K+ AD H  D  F I D+VY+K+ SYRQ S+A + C KLS 
Sbjct: 246 REEMLKVLKFHLRRAQDRMKQIADKHRTDRQFVIGDFVYVKLHSYRQVSVAHRNCAKLSP 305

Query: 62  KYFGPYMVLGRVGEVAYLLDLPDTARIHPVFHVSQQKKGCG 103
           K+FGP+ VL R+G VAY LDLP ++RIHPVFHVSQ K+  G
Sbjct: 306 KFFGPFKVLDRIGAVAYKLDLPTSSRIHPVFHVSQLKRHIG 346

[Close]

BLAST of CSPI04G12390 vs. TrEMBL
Match: D1GEG7_BRARP (Disease resistance protein OS=Brassica rapa subsp. pekinensis PE=4 SV=1)

HSP 1 Score: 118.2 bits (295), Expect = 7.2e-24
Identity = 51/101 (50.50%), Postives = 73/101 (72.28%), Query Frame = 1


Query: 2    RDELLITLKHHLQHAQAQIKKFADVHHRDVVFDISDWVYLKIQSYRQQSLAKKRCEKLSS 61
            RD +L+ ++ HL  AQ  +K  AD H R++ F + DWVYLK++ +RQ ++ ++ C+KL++
Sbjct: 2521 RDAMLVQIQQHLLRAQHLMKASADKHRRELSFAVGDWVYLKLKPFRQHTVVRRYCQKLAA 2580

Query: 62   KYFGPYMVLGRVGEVAYLLDLPDTARIHPVFHVSQQKKGCG 103
            KYFGPY +  R+G+VAY L LPD ARIHPVFH+SQ K   G
Sbjct: 2581 KYFGPYEISERIGKVAYRLKLPDEARIHPVFHISQLKAALG 2621

[Close]

BLAST of CSPI04G12390 vs. NCBI nr
Match: gi|659130784|ref|XP_008465349.1| (PREDICTED: uncharacterized protein LOC103502989 [Cucumis melo])

HSP 1 Score: 159.1 bits (401), Expect = 5.3e-36
Identity = 76/106 (71.70%), Postives = 86/106 (81.13%), Query Frame = 1


Query: 1   ARDELLITLKHHLQHAQAQIKKFADVHHRDVVFDISDWVYLKIQSYRQQSLAKKRCEKLS 60
           +RDE+L  LK HLQHAQ ++KKF D+H RDVVFDI D VYLK+Q YRQQS+ KKRCEKL 
Sbjct: 305 SRDEMLKALKRHLQHAQERMKKFVDIHRRDVVFDIGDKVYLKLQPYRQQSVTKKRCEKLL 364

Query: 61  SKYFGPYMVLGRVGEVAYLLDLPDTARIHPVFHVSQQKKGCGRQAP 107
            +YFGPY VLGRVGEVAYLLDL  TA+IHPVFHVSQ KK  G + P
Sbjct: 365 PRYFGPYTVLGRVGEVAYLLDLSKTAKIHPVFHVSQLKKAVGDKHP 410

[Close]

BLAST of CSPI04G12390 vs. NCBI nr
Match: gi|307136175|gb|ADN34016.1| (ty3-gypsy retrotransposon protein [Cucumis melo subsp. melo])

HSP 1 Score: 156.4 bits (394), Expect = 3.4e-35
Identity = 72/89 (80.90%), Postives = 81/89 (91.01%), Query Frame = 1


Query: 2    RDELLITLKHHLQHAQAQIKKFADVHHRDVVFDISDWVYLKIQSYRQQSLAKKRCEKLSS 61
            RDE L TLK HLQHAQ Q+KKFA+VH RDVVFDI DWVYLK+Q YRQ+S+AK+RC+KLS 
Sbjct: 1084 RDETLATLKRHLQHAQDQMKKFANVHRRDVVFDIEDWVYLKLQPYRQKSVAKRRCDKLSP 1143

Query: 62   KYFGPYMVLGRVGEVAYLLDLPDTARIHP 91
            KYFGPYMV+GRVGEVAYLLDLPDTA+IHP
Sbjct: 1144 KYFGPYMVMGRVGEVAYLLDLPDTAKIHP 1172

[Close]

BLAST of CSPI04G12390 vs. NCBI nr
Match: gi|922465109|ref|XP_013633118.1| (PREDICTED: uncharacterized protein LOC106338764 [Brassica oleracea var. oleracea])

HSP 1 Score: 124.8 bits (312), Expect = 1.1e-25
Identity = 56/109 (51.38%), Postives = 78/109 (71.56%), Query Frame = 1


Query: 2    RDELLITLKHHLQHAQAQIKKFADVHHRDVVFDISDWVYLKIQSYRQQSLAKKRCEKLSS 61
            RDELL  LKHHL+ +  ++K+ AD H RD+ F+I DWV+L++Q YRQ+++ ++  +KLS 
Sbjct: 1192 RDELLDELKHHLEASNNRMKQLADAHRRDIEFEIGDWVFLRLQPYRQKTVLRRSSQKLSH 1251

Query: 62   KYFGPYMVLGRVGEVAYLLDLPDTARIHPVFHVSQQKKGCGRQAPCATR 111
            +YFGP+ V  R+G+VAY L LP T RIHPVFHVS  KK  G   P + +
Sbjct: 1252 RYFGPFKVEARIGKVAYRLALPSTTRIHPVFHVSLLKKRVGTDEPVSVQ 1300

[Close]

BLAST of CSPI04G12390 vs. NCBI nr
Match: gi|922559973|ref|XP_013608212.1| (PREDICTED: uncharacterized protein LOC106314967 [Brassica oleracea var. oleracea])

HSP 1 Score: 123.6 bits (309), Expect = 2.5e-25
Identity = 56/107 (52.34%), Postives = 78/107 (72.90%), Query Frame = 1


Query: 2    RDELLITLKHHLQHAQAQIKKFADVHHRDVVFDISDWVYLKIQSYRQQSLAKKRCEKLSS 61
            RD++L  L+ H+ HAQ  +K+  D H R+VVF++ D VYLK++ YRQQ+LA++  EKLS+
Sbjct: 1445 RDDMLTLLREHIGHAQQVMKRQVDGHRREVVFEVGDKVYLKLRPYRQQTLARRANEKLSA 1504

Query: 62   KYFGPYMVLGRVGEVAYLLDLPDTARIHPVFHVSQQKKGCGRQAPCA 109
            +++GPY +  RVG+VAY L LP+ A+IHP FHVSQ KK  G   P A
Sbjct: 1505 RFYGPYEITARVGQVAYRLKLPEEAKIHPTFHVSQLKKAIGEDNPVA 1551

[Close]

BLAST of CSPI04G12390 vs. NCBI nr
Match: gi|6466937|gb|AAF13073.1|AC011621_1 (putative retroelement pol polyprotein [Arabidopsis thaliana])

HSP 1 Score: 121.3 bits (303), Expect = 1.2e-24
Identity = 56/98 (57.14%), Postives = 76/98 (77.55%), Query Frame = 1


Query: 2    RDELLITLKHHLQHAQAQIKKFADVHHRDVVFDISDWVYLKIQSYRQQSLAKKRCEKLSS 61
            RD +L+ L+ +L+ AQAQ+KK AD   RDV F+I +WVYLK++ YRQ S+A ++ EKLS 
Sbjct: 1446 RDGMLVELRENLEIAQAQMKKAADKSRRDVAFEIDEWVYLKLRPYRQSSVAHRKNEKLSQ 1505

Query: 62   KYFGPYMVLGRVGEVAYLLDLPDTARIHPVFHVSQQKK 100
            +YFGP+ VL R+G+VAY L LP+ + IHPVFHVSQ K+
Sbjct: 1506 RYFGPFKVLHRIGQVAYKLQLPEHSTIHPVFHVSQLKR 1543

The following BLAST results are available for this feature:

BLAST of CSPI04G12390 vs. Swiss-Prot


Match Name	E-value	Identity	Description

BLAST of CSPI04G12390 vs. TrEMBL


Match Name	E-value	Identity	Description
E5GC18_CUCME	2.4e-35	80.90	Ty3-gypsy retrotransposon protein OS=Cucumis melo subsp. melo PE=4 SV=1	[more]
Q9SQW9_ARATH	8.5e-25	57.14	Putative retroelement pol polyprotein OS=Arabidopsis thaliana GN=F23H6.1 PE=4 SV...	[more]
M4DN30_BRARP	2.5e-24	51.38	Uncharacterized protein OS=Brassica rapa subsp. pekinensis PE=4 SV=1	[more]
A0A151SSE7_CAJCA	3.2e-24	56.44	Retrotransposable element Tf2 (Fragment) OS=Cajanus cajan GN=KK1_003948 PE=4 SV=...	[more]
D1GEG7_BRARP	7.2e-24	50.50	Disease resistance protein OS=Brassica rapa subsp. pekinensis PE=4 SV=1	[more]

BLAST of CSPI04G12390 vs. TAIR10


Match Name	E-value	Identity	Description

BLAST of CSPI04G12390 vs. NCBI nr


Match Name	E-value	Identity	Description
gi\|659130784\|ref\|XP_008465349.1\|	5.3e-36	71.70	PREDICTED: uncharacterized protein LOC103502989 [Cucumis melo]	[more]
gi\|307136175\|gb\|ADN34016.1\|	3.4e-35	80.90	ty3-gypsy retrotransposon protein [Cucumis melo subsp. melo]	[more]
gi\|922465109\|ref\|XP_013633118.1\|	1.1e-25	51.38	PREDICTED: uncharacterized protein LOC106338764 [Brassica oleracea var. oleracea...	[more]
gi\|922559973\|ref\|XP_013608212.1\|	2.5e-25	52.34	PREDICTED: uncharacterized protein LOC106314967 [Brassica oleracea var. oleracea...	[more]
gi\|6466937\|gb\|AAF13073.1\|AC011621_1	1.2e-24	57.14	putative retroelement pol polyprotein [Arabidopsis thaliana]	[more]

Annotated Terms

The following terms have been associated with this gene:

Vocabulary: **INTERPRO**
Term	Definition

GO Annotation

GO Assignments

This gene is annotated with the following GO terms.

Category	Term Accession	Term Name
biological_process	GO:0015074	DNA integration
cellular_component	GO:0005575	cellular_component
molecular_function	GO:0003676	nucleic acid binding

Relationships

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


Feature Name	Unique Name	Type
CSPI04G12390.1	CSPI04G12390.1	mRNA

InterPro

Analysis Name: InterPro Annotations of cucumber (PI183967)
Date Performed: 2017-01-17


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
None	No IPR available	PANTHER	PTHR24559	FAMILY NOT NAMED	coord: 2..99 score: 3.9
None	No IPR available	PANTHER	PTHR24559:SF186	SUBFAMILY NOT NAMED	coord: 2..99 score: 3.9

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
CSPI04G12390	Cucumber (Gy14) v2	cgybcpiB171
CSPI04G12390	Cucumber (Chinese Long) v3	cpicucB216
CSPI04G12390	Cucumber (Chinese Long) v2	cpicuB181