Clc08G02090 (gene) Watermelon (cordophanus) v2

Overview


Name	Clc08G02090
Type	gene
Organism	Citrullus lanatus subsp. cordophanus cv. cordophanus (Watermelon (cordophanus) v2)
Description	Retrovirus-related Pol polyprotein from transposon TNT 1-94
Location	ClcChr08: 3886162 .. 3887653 (-)
RNA-Seq Expression	Clc08G02090
Synteny	Clc08G02090

Sequences

The following sequences are available for this feature:

Gene sequence (with intron)

Legend: exonfive_prime_UTRCDSpolypeptide

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

TCTCTTTGAGCTATCTCTGCATCAACAAATAGGGCTTGCGATTGGACTTTCTCTTCAAATACTCGGAGGTATCGACTTCCACTTCATTGTTTGTTTGTTTTGTTTTTTTTTCATTCTTCTTACTCTCTATCTTTCCTACTGATTTCTTCTATAAATATCCACTGATATAACTAAATTCATTGTCATTCAAATCCATCTCTCATGGTAAACATGTACCCTTGCTTATAACTTGTTTGATAAAATGCCTATGTGAACTGACTCATTCTATTTTTCATTTTATTTTATTTTATTTTTCTTTCCTCTCTTATGTTTCATTCACTTTAAAGTTTAAAGTTTGGCAAAATGCCATAAATTGGAGCACGGTACGTTGGAATGCCTTGAATCCTAAACCTAATTAGAATTGATATTTGATATATTTAATTATTTAAATATCTTCCTTCTCCACCTAGGGTTTAGAGAAGTGCACTATATAAACTCTCTAACCCTATAGGTTTCATTCATTCTGTACTCTTATAACATTTTCTCTAATAAAATTGTTCTCCCACTATCCCGTGGACGTAGATAACACATTGTTAGTGAACCACGTAAATTTTTGTGTAGATGTTTTTTATTTTTTATGTTCTTTTGTATTCTTTAATTGTCGATTTCATAACAAACTGGTATTAGAGCCTAATTGTTAGGGTTTCAAAATTCCGCATATATTCAACCATTAAAGATGTCTAGCATGAATGTAAAAATTGATAAATTCACCAGGAGGAACAATTTTTGTTTATGGTAGATCAAGATGTGATCCCTGCTCAAGCAGCAGGGGCTGTGGGCACCACTGACTGTTAAGTCAAAGAAGGTAGCCATGGATGACGCCGGAGAATGGCAGACTCTGGAAGAGAAGCCTCACTCAACGATCATGCTATGTTTGGCTGATGACGTCGTCATCGAGGTTGCAGATGAAGAAACTACCACTAGTCTGTGGTTAAAGTTGGAAAGTCTTTACATGATTAAGTCTTTAACCAAGAAGTTGTTTCTTAAGAAACGTTTGTATCATCTACATATGCAGGAAGGTACGTCTCTTCGAGATCATCTTGATCAGTTGAATAAAATTTTGTTAGATCTACGTAATATAGAAATTAAAGTTGATGATGAGGATGCTACCTTAATTCTATTGACGTCTTTGCCCTTGTCATATGAGACTTTCGTTTACTCGTATATTGGAGCTTGCCGGCCACACACGGCATCCATGCCAAAGACTTTCGGCCACCTTCCTCTCAACTACCTGCCTACTTGTTTTCCATCTTCCAAAGGTGAAAGTAGGGCTTACACGGGCTACTATTGCTTTCTTCCAGGGGAGTTTGGGTACCAACCTATTGGTTACAAGGACTTGACTGCTGAAATCTCTAAGATTGTTCGGTTTCATTGGCCTAAGGAATGTGTCAAGACTTATGTCGTCCTATTACTAGGGATGAGATCCAACATGTTCTATTTTTTCTCTGCTTAA

mRNA sequence

TCTCTTTGAGCTATCTCTGCATCAACAAATAGGGCTTGCGATTGGACTTTCTCTTCAAATACTCGGAGGAGGAACAATTTTTGTTTATGGTAGATCAAGATGTGATCCCTGCTCAAGCAGCAGGGGCTGTGGGCACCACTGACTGTTAAGTCAAAGAAGGTAGCCATGGATGACGCCGGAGAATGGCAGACTCTGGAAGAGAAGCCTCACTCAACGATCATGCTATGTTTGGCTGATGACGTCGTCATCGAGGTTGCAGATGAAGAAACTACCACTAGTCTGTGGTTAAAGTTGGAAAGTCTTTACATGATTAAGTCTTTAACCAAGAAGTTGTTTCTTAAGAAACGTTTGTATCATCTACATATGCAGGAAGGTACGTCTCTTCGAGATCATCTTGATCAGTTGAATAAAATTTTGTTAGATCTACGTAATATAGAAATTAAAGTTGATGATGAGGATGCTACCTTAATTCTATTGACGTCTTTGCCCTTGTCATATGAGACTTTCGTTTACTCGTATATTGGAGCTTGCCGGCCACACACGGCATCCATGCCAAAGACTTTCGGCCACCTTCCTCTCAACTACCTGCCTACTTGTTTTCCATCTTCCAAAGGTGAAAGTAGGGCTTACACGGGCTACTATTGCTTTCTTCCAGGGGAGTTTGGGTACCAACCTATTGGTTACAAGGACTTGACTGCTGAAATCTCTAAGATTGTTCGGTTTCATTGGCCTAAGGAATGTGTCAAGACTTATGTCGTCCTATTACTAGGGATGAGATCCAACATGTTCTATTTTTTCTCTGCTTAA

Coding sequence (CDS)

ATGGATGACGCCGGAGAATGGCAGACTCTGGAAGAGAAGCCTCACTCAACGATCATGCTATGTTTGGCTGATGACGTCGTCATCGAGGTTGCAGATGAAGAAACTACCACTAGTCTGTGGTTAAAGTTGGAAAGTCTTTACATGATTAAGTCTTTAACCAAGAAGTTGTTTCTTAAGAAACGTTTGTATCATCTACATATGCAGGAAGGTACGTCTCTTCGAGATCATCTTGATCAGTTGAATAAAATTTTGTTAGATCTACGTAATATAGAAATTAAAGTTGATGATGAGGATGCTACCTTAATTCTATTGACGTCTTTGCCCTTGTCATATGAGACTTTCGTTTACTCGTATATTGGAGCTTGCCGGCCACACACGGCATCCATGCCAAAGACTTTCGGCCACCTTCCTCTCAACTACCTGCCTACTTGTTTTCCATCTTCCAAAGGTGAAAGTAGGGCTTACACGGGCTACTATTGCTTTCTTCCAGGGGAGTTTGGGTACCAACCTATTGGTTACAAGGACTTGACTGCTGAAATCTCTAAGATTGTTCGGTTTCATTGGCCTAAGGAATGTGTCAAGACTTATGTCGTCCTATTACTAGGGATGAGATCCAACATGTTCTATTTTTTCTCTGCTTAA

Protein sequence

MDDAGEWQTLEEKPHSTIMLCLADDVVIEVADEETTTSLWLKLESLYMIKSLTKKLFLKKRLYHLHMQEGTSLRDHLDQLNKILLDLRNIEIKVDDEDATLILLTSLPLSYETFVYSYIGACRPHTASMPKTFGHLPLNYLPTCFPSSKGESRAYTGYYCFLPGEFGYQPIGYKDLTAEISKIVRFHWPKECVKTYVVLLLGMRSNMFYFFSA

Homology

[Close]

BLAST of Clc08G02090 vs. NCBI nr
Match: KAG6394709.1 (hypothetical protein SASPL_145299 [Salvia splendens])

HSP 1 Score: 160.6 bits (405), Expect = 1.5e-35
Identity = 81/114 (71.05%), Postives = 94/114 (82.46%), Query Frame = 0


Query: 6   EWQTLEEKPHSTIMLCLADDVVIEVADEETTTSLWLKLESLYMIKSLTKKLFLKKRLYHL 65
           EW TL+EK HSTIMLCL+DDV+IEV D E   +LW KLESLYM+KSLT KL LK+ L+ L
Sbjct: 29  EWVTLDEKAHSTIMLCLSDDVIIEVVDREIVAALWTKLESLYMMKSLTNKLLLKQPLFRL 88

Query: 66  HMQEGTSLRDHLDQLNKILLDLRNIEIKVDDEDATLILLTSLPLSYETFVYSYI 120
            MQEGT LRDHL+ LNKILLDLRN+E+KV+DEDA LILL SLP SYE FV S++
Sbjct: 89  RMQEGTPLRDHLENLNKILLDLRNVEVKVEDEDAALILLVSLPESYENFVESFM 142

[Close]

BLAST of Clc08G02090 vs. NCBI nr
Match: KAG6437869.1 (hypothetical protein SASPL_102799 [Salvia splendens])

HSP 1 Score: 159.8 bits (403), Expect = 2.5e-35
Identity = 80/114 (70.18%), Postives = 95/114 (83.33%), Query Frame = 0


Query: 6   EWQTLEEKPHSTIMLCLADDVVIEVADEETTTSLWLKLESLYMIKSLTKKLFLKKRLYHL 65
           EW TL+EK HSTIMLCL+DDV+IEV D+ET  +LW KLESLY  KSLT KL LK+RL+ L
Sbjct: 29  EWVTLDEKAHSTIMLCLSDDVIIEVVDQETAAALWTKLESLYRKKSLTNKLLLKQRLFRL 88

Query: 66  HMQEGTSLRDHLDQLNKILLDLRNIEIKVDDEDATLILLTSLPLSYETFVYSYI 120
            MQEGT LRDHL+ LNKILLDLRN+E+KV+D+DA +ILL SLP SYE FV S++
Sbjct: 89  SMQEGTPLRDHLENLNKILLDLRNVEVKVEDKDAAIILLVSLPESYENFVESFM 142

[Close]

BLAST of Clc08G02090 vs. NCBI nr
Match: KAG6437470.1 (hypothetical protein SASPL_102387 [Salvia splendens])

HSP 1 Score: 159.5 bits (402), Expect = 3.3e-35
Identity = 80/119 (67.23%), Postives = 96/119 (80.67%), Query Frame = 0


Query: 1   MDDAGEWQTLEEKPHSTIMLCLADDVVIEVADEETTTSLWLKLESLYMIKSLTKKLFLKK 60
           M+D  EW TL+EK HSTIMLCL+DDV+IEVA++ET  + W KLESLYM KSLT KL LK+
Sbjct: 1   MEDDEEWTTLDEKAHSTIMLCLSDDVIIEVAEQETAVAHWTKLESLYMTKSLTNKLLLKQ 60

Query: 61  RLYHLHMQEGTSLRDHLDQLNKILLDLRNIEIKVDDEDATLILLTSLPLSYETFVYSYI 120
           RL+ L MQEG  L+DHL+ LNKILLDLRN+++KV DED  LILL SLP SYE FV S++
Sbjct: 61  RLFRLRMQEGMPLQDHLENLNKILLDLRNVDVKVKDEDVALILLVSLPESYENFVESFM 119

[Close]

BLAST of Clc08G02090 vs. NCBI nr
Match: ABO36622.1 (copia LTR rider [Solanum lycopersicum] >ABO36636.1 copia LTR rider [Solanum lycopersicum])

HSP 1 Score: 156.4 bits (394), Expect = 2.8e-34
Identity = 79/114 (69.30%), Postives = 94/114 (82.46%), Query Frame = 0


Query: 6   EWQTLEEKPHSTIMLCLADDVVIEVADEETTTSLWLKLESLYMIKSLTKKLFLKKRLYHL 65
           E   LEEK HSTIMLCLADDV+ EV+DEET   LWLKLESLYM KSLT KL LK+RL+ L
Sbjct: 48  EMAILEEKAHSTIMLCLADDVITEVSDEETAAGLWLKLESLYMTKSLTNKLLLKQRLFGL 107

Query: 66  HMQEGTSLRDHLDQLNKILLDLRNIEIKVDDEDATLILLTSLPLSYETFVYSYI 120
            M EGT LR+HL+QLN +LL+LRNI++K++DEDA LILL SLP+S+E FV S+I
Sbjct: 108 RMAEGTQLREHLEQLNTLLLELRNIDVKIEDEDAALILLVSLPMSFENFVQSFI 161

[Close]

BLAST of Clc08G02090 vs. NCBI nr
Match: KAG6390907.1 (hypothetical protein SASPL_148652 [Salvia splendens])

HSP 1 Score: 156.0 bits (393), Expect = 3.6e-34
Identity = 79/114 (69.30%), Postives = 94/114 (82.46%), Query Frame = 0


Query: 6   EWQTLEEKPHSTIMLCLADDVVIEVADEETTTSLWLKLESLYMIKSLTKKLFLKKRLYHL 65
           +W TL EK HSTIMLCL+DDV+IEVA++ET  +LW KLESLYM KSLT KL LK+RL+ L
Sbjct: 29  KWVTLAEKAHSTIMLCLSDDVIIEVANQETAVALWTKLESLYMTKSLTNKLLLKQRLFRL 88

Query: 66  HMQEGTSLRDHLDQLNKILLDLRNIEIKVDDEDATLILLTSLPLSYETFVYSYI 120
           H QEG  LRDHL+ LNKILLDLRN+E+KV+DEDA LILL SL  SY+ FV S++
Sbjct: 89  HKQEGKPLRDHLENLNKILLDLRNVEVKVEDEDAALILLVSLLKSYKNFVESFM 142

[Close]

BLAST of Clc08G02090 vs. ExPASy Swiss-Prot
Match: P10978 (Retrovirus-related Pol polyprotein from transposon TNT 1-94 OS=Nicotiana tabacum OX=4097 PE=2 SV=1)

HSP 1 Score: 109.4 bits (272), Expect = 5.1e-23
Identity = 53/109 (48.62%), Postives = 76/109 (69.72%), Query Frame = 0


Query: 4   AGEWQTLEEKPHSTIMLCLADDVVIEVADEETTTSLWLKLESLYMIKSLTKKLFLKKRLY 63
           A +W  L+E+  S I L L+DDVV  + DE+T   +W +LESLYM K+LT KL+LKK+LY
Sbjct: 49  AEDWADLDERAASAIRLHLSDDVVNNIIDEDTARGIWTRLESLYMSKTLTNKLYLKKQLY 108

Query: 64  HLHMQEGTSLRDHLDQLNKILLDLRNIEIKVDDEDATLILLTSLPLSYE 113
            LHM EGT+   HL+  N ++  L N+ +K+++ED  ++LL SLP SY+
Sbjct: 109 ALHMSEGTNFLSHLNVFNGLITQLANLGVKIEEEDKAILLLNSLPSSYD 157

[Close]

BLAST of Clc08G02090 vs. ExPASy TrEMBL
Match: B1N668 (Copia LTR rider OS=Solanum lycopersicum OX=4081 GN=LYC_68t000004 PE=4 SV=1)

HSP 1 Score: 156.4 bits (394), Expect = 1.4e-34
Identity = 79/114 (69.30%), Postives = 94/114 (82.46%), Query Frame = 0


Query: 6   EWQTLEEKPHSTIMLCLADDVVIEVADEETTTSLWLKLESLYMIKSLTKKLFLKKRLYHL 65
           E   LEEK HSTIMLCLADDV+ EV+DEET   LWLKLESLYM KSLT KL LK+RL+ L
Sbjct: 48  EMAILEEKAHSTIMLCLADDVITEVSDEETAAGLWLKLESLYMTKSLTNKLLLKQRLFGL 107

Query: 66  HMQEGTSLRDHLDQLNKILLDLRNIEIKVDDEDATLILLTSLPLSYETFVYSYI 120
            M EGT LR+HL+QLN +LL+LRNI++K++DEDA LILL SLP+S+E FV S+I
Sbjct: 108 RMAEGTQLREHLEQLNTLLLELRNIDVKIEDEDAALILLVSLPMSFENFVQSFI 161

[Close]

BLAST of Clc08G02090 vs. ExPASy TrEMBL
Match: A0A6D2K463 (CCHC-type domain-containing protein OS=Microthlaspi erraticum OX=1685480 GN=MERR_LOCUS19845 PE=4 SV=1)

HSP 1 Score: 154.5 bits (389), Expect = 5.1e-34
Identity = 79/117 (67.52%), Postives = 94/117 (80.34%), Query Frame = 0


Query: 3   DAGEWQTLEEKPHSTIMLCLADDVVIEVADEETTTSLWLKLESLYMIKSLTKKLFLKKRL 62
           DA    +LEEK H+TI+LCLADDV+IEV+ E T   LW KLESLYM KSLT KL LK+RL
Sbjct: 43  DAAAMTSLEEKAHATILLCLADDVIIEVSSETTAAGLWGKLESLYMTKSLTNKLLLKQRL 102

Query: 63  YHLHMQEGTSLRDHLDQLNKILLDLRNIEIKVDDEDATLILLTSLPLSYETFVYSYI 120
           + L M EGT LRDHLDQLN +LL+LRNI++KV+DEDA L+LL SLPLSYE +V S+I
Sbjct: 103 FALRMDEGTQLRDHLDQLNTLLLELRNIDVKVEDEDAALLLLVSLPLSYEHYVQSFI 159

[Close]

BLAST of Clc08G02090 vs. ExPASy TrEMBL
Match: A0A0D3BRH8 (Uncharacterized protein OS=Brassica oleracea var. oleracea OX=109376 PE=4 SV=1)

HSP 1 Score: 153.7 bits (387), Expect = 8.8e-34
Identity = 78/116 (67.24%), Postives = 94/116 (81.03%), Query Frame = 0


Query: 6   EWQTLEEKPHSTIMLCLADDVVIEVADEETTTSLWLKLESLYMIKSLTKKLFLKKRLYHL 65
           E +  EEK +STI+LCLAD+++IEV+  +    LWLKLESLYM KSLTKKL LK+RL+ L
Sbjct: 48  EMEVTEEKAYSTILLCLADEIIIEVSGVDAAADLWLKLESLYMTKSLTKKLLLKQRLFAL 107

Query: 66  HMQEGTSLRDHLDQLNKILLDLRNIEIKVDDEDATLILLTSLPLSYETFVYSYIGA 122
            MQEGT L+DHLD LN ILLDLRNI++KV+DEDA LILL SLP SYE FV S+IG+
Sbjct: 108 RMQEGTQLQDHLDSLNSILLDLRNIDVKVEDEDAALILLVSLPNSYENFVQSFIGS 163

[Close]

BLAST of Clc08G02090 vs. ExPASy TrEMBL
Match: A0A6P6S469 (disease resistance protein RGA2-like OS=Coffea arabica OX=13443 GN=LOC113687246 PE=4 SV=1)

HSP 1 Score: 153.3 bits (386), Expect = 1.1e-33
Identity = 80/115 (69.57%), Postives = 93/115 (80.87%), Query Frame = 0


Query: 6   EWQTLEEKPHSTIMLCLADDVVIEVADEETTTSLWLKLESLYMIKSLTKKLFLKKRLYHL 65
           E  +LEEK HSTIML L DDV+ EVA EET T LW+KLESLYM KSLT KL LK+RL+ L
Sbjct: 479 ESMSLEEKAHSTIMLFLTDDVITEVAGEETATGLWVKLESLYMTKSLTNKLLLKQRLFGL 538

Query: 66  HMQEGTSLRDHLDQLNKILLDLRNIEIKVDDEDATLILLTSLPLSYETFVYSYIG 121
            MQEGT L++HLDQLN ILL+LRNI++K++DED  LILL SL LSYE FV S+IG
Sbjct: 539 RMQEGTPLQEHLDQLNTILLELRNIDVKIEDEDTALILLVSLSLSYENFVQSFIG 593

[Close]

BLAST of Clc08G02090 vs. ExPASy TrEMBL
Match: A0A0D3CQC5 (CCHC-type domain-containing protein OS=Brassica oleracea var. oleracea OX=109376 PE=4 SV=1)

HSP 1 Score: 149.8 bits (377), Expect = 1.3e-32
Identity = 77/117 (65.81%), Postives = 95/117 (81.20%), Query Frame = 0


Query: 3   DAGEWQTLEEKPHSTIMLCLADDVVIEVADEETTTSLWLKLESLYMIKSLTKKLFLKKRL 62
           +A + +TLEEK  STI+LCLAD+++IEV+DE+T  SLW KLESLYM KSLT KL LK+RL
Sbjct: 43  EAADLETLEEKAFSTILLCLADEIIIEVSDEKTIASLWQKLESLYMTKSLTNKLLLKQRL 102

Query: 63  YHLHMQEGTSLRDHLDQLNKILLDLRNIEIKVDDEDATLILLTSLPLSYETFVYSYI 120
           + L MQEG  LRDHLD+LN ILL+LRNI++KV+DEDA LILL  LP S+E FV  +I
Sbjct: 103 FALRMQEGIELRDHLDKLNTILLELRNIDVKVEDEDAALILLVYLPNSFENFVQLFI 159

The following BLAST results are available for this feature:

BLAST of Clc08G02090 vs. NCBI nr


Match Name	E-value	Identity	Description
KAG6394709.1	1.5e-35	71.05	hypothetical protein SASPL_145299 [Salvia splendens]	[more]
KAG6437869.1	2.5e-35	70.18	hypothetical protein SASPL_102799 [Salvia splendens]	[more]
KAG6437470.1	3.3e-35	67.23	hypothetical protein SASPL_102387 [Salvia splendens]	[more]
ABO36622.1	2.8e-34	69.30	copia LTR rider [Solanum lycopersicum] >ABO36636.1 copia LTR rider [Solanum lyco...	[more]
KAG6390907.1	3.6e-34	69.30	hypothetical protein SASPL_148652 [Salvia splendens]	[more]

BLAST of Clc08G02090 vs. ExPASy Swiss-Prot


Match Name	E-value	Identity	Description
P10978	5.1e-23	48.62	Retrovirus-related Pol polyprotein from transposon TNT 1-94 OS=Nicotiana tabacum...	[more]

BLAST of Clc08G02090 vs. ExPASy TrEMBL


Match Name	E-value	Identity	Description
B1N668	1.4e-34	69.30	Copia LTR rider OS=Solanum lycopersicum OX=4081 GN=LYC_68t000004 PE=4 SV=1	[more]
A0A6D2K463	5.1e-34	67.52	CCHC-type domain-containing protein OS=Microthlaspi erraticum OX=1685480 GN=MERR...	[more]
A0A0D3BRH8	8.8e-34	67.24	Uncharacterized protein OS=Brassica oleracea var. oleracea OX=109376 PE=4 SV=1	[more]
A0A6P6S469	1.1e-33	69.57	disease resistance protein RGA2-like OS=Coffea arabica OX=13443 GN=LOC113687246 ...	[more]
A0A0D3CQC5	1.3e-32	65.81	CCHC-type domain-containing protein OS=Brassica oleracea var. oleracea OX=109376...	[more]

BLAST of Clc08G02090 vs. ExPASy TrEMBL


Match Name	E-value	Identity	Description

InterPro

Analysis Name: InterPro Annotations of Watermelon (cordophanus) v2
Date Performed: 2022-01-31


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
None	No IPR available	PFAM	PF14223	Retrotran_gag_2	coord: 7..116 e-value: 5.2E-29 score: 100.8
None	No IPR available	PANTHER	PTHR34676:SF12	ZINC FINGER, CCHC-TYPE, RIBONUCLEASE H-LIKE DOMAIN, GAG-PRE-INTEGRASE DOMAIN PROTEIN-RELATED	coord: 4..117
None	No IPR available	PANTHER	PTHR34676	FAMILY NOT NAMED	coord: 4..117

Relationships

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


Feature Name	Unique Name	Type
Clc08G02090.1	Clc08G02090.1	mRNA

GO Annotation

GO Assignments

This gene is annotated with the following GO terms.

Category	Term Accession	Term Name
biological_process	GO:0009734	auxin-activated signaling pathway
biological_process	GO:0006952	defense response
biological_process	GO:0071897	DNA biosynthetic process
biological_process	GO:0015074	DNA integration
biological_process	GO:0055085	transmembrane transport
cellular_component	GO:0016021	integral component of membrane
molecular_function	GO:0043531	ADP binding
molecular_function	GO:0003887	DNA-directed DNA polymerase activity
molecular_function	GO:0003676	nucleic acid binding
molecular_function	GO:0008270	zinc ion binding