Clc03G09860 (gene) Watermelon (cordophanus) v2

Overview
NameClc03G09860
Typegene
OrganismCitrullus lanatus subsp. cordophanus cv. cordophanus (Watermelon (cordophanus) v2)
DescriptionReverse transcriptase
LocationClcChr03: 12525706 .. 12526227 (+)
RNA-Seq ExpressionClc03G09860
SyntenyClc03G09860
Sequences
The following sequences are available for this feature:

Gene sequence (with intron)

Legend: exonCDSpolypeptide
Hold the cursor over a type above to highlight its positions in the sequence below.
ATGATTGAAACTGATGCGACTAATAATCTTTCAGCTCAGATCGCCAACATGACATCCTTGCTGCAAACAATTGCGTTGAACAACCAAGGTGAAGCAGCTGTGTCAATGGACGCAATGAACACGGTGAATGCAACAACATCTGTAAGCTGTGTGCAATGCGATGATGGCCACTTGTACGATATGTGTCCCTACAACCCACAATCTGTCTGTTATGTTTAGAATAACCCGTACTCTAAGACTTATAATCTGGGTTGGAGGAACCATCCTAACTTTGGATGGGGAGGAAACCAATCACAGACGCAGGGAACTGGACAACAGCCGCAGAGAAGCAATAACCCTGTGTACAACCAAGGTGTTCAAGGGCATCAAGCACAACGAAACGAGTCAGCAAATTCATCATCATCATCCCTTAAAGCACTTATCCGTCAAACTATCACCAAAAATGAAGAAACGCTTAAGTCATTGGAAGCGATGCTCCAAAACCAAATGGGTGAAATAAAAAGCCATGCCATTGCAATCTGA

mRNA sequence

ATGATTGAAACTGATGCGACTAATAATCTTTCAGCTCAGATCGCCAACATGACATCCTTGCTGCAAACAATTGCGTTGAACAACCAAGGTGAAGCAGCTGTGTCAATGGACGCAATGAACACGGTGAATGCAACAACATCTAATAACCCGTACTCTAAGACTTATAATCTGGGTTGGAGGAACCATCCTAACTTTGGATGGGGAGGAAACCAATCACAGACGCAGGGAACTGGACAACAGCCGCAGAGAAGCAATAACCCTGTGTACAACCAAGGTGTTCAAGGGCATCAAGCACAACGAAACGAGTCAGCAAATTCATCATCATCATCCCTTAAAGCACTTATCCGTCAAACTATCACCAAAAATGAAGAAACGCTTAAGTCATTGGAAGCGATGCTCCAAAACCAAATGGGTGAAATAAAAAGCCATGCCATTGCAATCTGA

Coding sequence (CDS)

ATGATTGAAACTGATGCGACTAATAATCTTTCAGCTCAGATCGCCAACATGACATCCTTGCTGCAAACAATTGCGTTGAACAACCAAGGTGAAGCAGCTGTGTCAATGGACGCAATGAACACGGTGAATGCAACAACATCTAATAACCCGTACTCTAAGACTTATAATCTGGGTTGGAGGAACCATCCTAACTTTGGATGGGGAGGAAACCAATCACAGACGCAGGGAACTGGACAACAGCCGCAGAGAAGCAATAACCCTGTGTACAACCAAGGTGTTCAAGGGCATCAAGCACAACGAAACGAGTCAGCAAATTCATCATCATCATCCCTTAAAGCACTTATCCGTCAAACTATCACCAAAAATGAAGAAACGCTTAAGTCATTGGAAGCGATGCTCCAAAACCAAATGGGTGAAATAAAAAGCCATGCCATTGCAATCTGA

Protein sequence

MIETDATNNLSAQIANMTSLLQTIALNNQGEAAVSMDAMNTVNATTSNNPYSKTYNLGWRNHPNFGWGGNQSQTQGTGQQPQRSNNPVYNQGVQGHQAQRNESANSSSSSLKALIRQTITKNEETLKSLEAMLQNQMGEIKSHAIAI
Homology
BLAST of Clc03G09860 vs. NCBI nr
Match: WP_217833202.1 (hypothetical protein, partial [Synechococcus sp. PCC 7002])

HSP 1 Score: 141.4 bits (355), Expect = 6.4e-30
Identity = 93/166 (56.02%), Postives = 107/166 (64.46%), Query Frame = 0

Query: 2   IETDATNNLSAQIANMTSLLQTIALNNQGEAAVSMDAMNTVNATTS-------------- 61
           IETDAT+NLSAQIANMTSLLQTIALNNQG    SMDAMNTVNAT S              
Sbjct: 1   IETDATSNLSAQIANMTSLLQTIALNNQGGTVASMDAMNTVNATASVSCVQCGEGHLYDM 60

Query: 62  ------------NNPYSKTYNLGWRNHPNFGWGGNQSQTQGTGQQPQRSNNPVYNQGVQG 121
                       NNPY+KTYN GWRNH NFGWG NQ QTQG  QQPQR N P +NQG QG
Sbjct: 61  CPYNPQSVCYVQNNPYAKTYNPGWRNHLNFGWGRNQQQTQGAEQQPQRGNPPGFNQGNQG 120

Query: 122 --HQAQRNESANSSSS--SLKALIRQTITKNEETLKSLEAMLQNQM 138
             HQ QR+  A++S+S  SL++L+R       E L + +AM Q+Q+
Sbjct: 121 QYHQFQRDPQADASTSFYSLESLLR-------ECLSTRDAMFQSQI 159

BLAST of Clc03G09860 vs. NCBI nr
Match: XP_038902511.1 (uncharacterized protein LOC120089170 [Benincasa hispida])

HSP 1 Score: 75.1 bits (183), Expect = 5.6e-10
Identity = 63/179 (35.20%), Postives = 92/179 (51.40%), Query Frame = 0

Query: 1   MIETDATNNLSAQIANMTSLLQTIALN----NQGEA--------------------AVSM 60
           +I  D    L+AQ+A +TSLLQ +A+N    +QG A                    +V M
Sbjct: 189 IIPVDIMTTLAAQMATVTSLLQMMAINHGTLSQGAAQDNTLAQVAVISCAQCGEGHSVEM 248

Query: 61  DAMNTVNA-TTSNNPYSKTYNLGWRNHPNFGWGGNQSQTQGTGQQ---PQRSNNPVYNQG 120
              N     +  NNPY+ TYN GWRNHPNF WGGN  Q      Q     R N PV++QG
Sbjct: 249 CPSNPQAVYSIQNNPYNNTYNPGWRNHPNFNWGGNNDQGGQRNLQNNSENRGNPPVFHQG 308

Query: 121 V--------QGHQAQRNESANSSSSSLKALIRQTITKNEETLKSLEAMLQN---QMGEI 141
           +        Q H    + + +++SSSL+AL++Q I KN+  ++S  + ++N   QMG++
Sbjct: 309 LNQSHHQSRQSHNQPSSSNFSTNSSSLEALLKQYIEKNDAVMQSQASSIRNLEVQMGQL 367

BLAST of Clc03G09860 vs. NCBI nr
Match: XP_030503898.1 (uncharacterized protein LOC115719117 [Cannabis sativa])

HSP 1 Score: 71.6 bits (174), Expect = 6.2e-09
Identity = 50/151 (33.11%), Postives = 89/151 (58.94%), Query Frame = 0

Query: 1   MIETDATNNLSAQIANMTSLLQTI--------ALNNQGEAAVSMDAMNTVNATTSNNPYS 60
           ++E DA   L+AQ+A+MT++L+ +        A +++GE +  +  +   N   +NNPYS
Sbjct: 228 VLEVDALTALTAQMASMTNILKNMNMGGSVQPARHSKGEISSFLCYVGNQNFNRNNNPYS 287

Query: 61  KTYNLGWRNHPNFGWGGNQSQTQGTGQQPQRSNNPVYNQGVQGHQAQRNESANSSSSSLK 120
            +YN  W++HPNF WGG  + + G   Q ++S  P ++Q  Q    Q ++   S +SSL+
Sbjct: 288 NSYNPAWKHHPNFSWGGQGASSSGAQGQGKQSFPPGFSQ--QPRPQQPHQPQGSQTSSLE 347

Query: 121 ALIRQTITKNEETLKSLEAMLQN---QMGEI 141
           +L+R  + KN+  ++S  A L+N   Q+G++
Sbjct: 348 SLMRDYMAKNDAVIQSQAASLRNLEVQLGQL 376

BLAST of Clc03G09860 vs. NCBI nr
Match: XP_024933238.1 (LOW QUALITY PROTEIN: uncharacterized protein LOC112492876, partial [Ziziphus jujuba])

HSP 1 Score: 67.0 bits (162), Expect = 1.5e-07
Identity = 49/139 (35.25%), Postives = 70/139 (50.36%), Query Frame = 0

Query: 21  LQTIALNNQGEAAVSMDAMNTVNA------TTSNNPYSKTYNLGWRNHPNFGWGGNQSQT 80
           ++ + +NN G A ++   M T+N          NNPYS TYNLGWRNHPNF W  N  Q 
Sbjct: 160 VEDVDINNLG-AQLATQFMKTLNTQFGNFQKQQNNPYSNTYNLGWRNHPNFSWSNNNQQG 219

Query: 81  QGTGQ----QPQRSNNPVYNQGVQGHQAQRNESANSSSSSLKALIRQT-------ITKNE 140
              GQ    Q Q+  +P Y +    H+ Q +  A +  SSL+  +++        + +NE
Sbjct: 220 SNQGQSGGFQRQQFQSPFYQKPQLAHKNQNSSQAQTQFSSLEQSLQELSNNTNSFMQRNE 279

Query: 141 ETLKSLEAMLQNQMGEIKS 143
           + L +   M  NQM  IKS
Sbjct: 280 QQLTNHSQMFNNQMAAIKS 297

BLAST of Clc03G09860 vs. NCBI nr
Match: XP_038895768.1 (uncharacterized protein LOC120083932 [Benincasa hispida])

HSP 1 Score: 66.2 bits (160), Expect = 2.6e-07
Identity = 57/174 (32.76%), Postives = 82/174 (47.13%), Query Frame = 0

Query: 2   IETDATNNLSAQIANMTSLLQTIALNNQG------------EAAVSMDAMNTVNA----- 61
           ++ +A   LS Q+A MTSLLQ I L N              +  VS      +++     
Sbjct: 54  VDANAIATLSTQVATMTSLLQNITLGNTSNQQKVNQVEAFEQPMVSCVGYGNLHSYDKCP 113

Query: 62  -------TTSNNPYSKTYNLGWRNHPNFGW-GGNQSQTQ-GTGQQPQRSNNPVYNQGVQG 121
                     NNP+SKTYN GWRNHPNF W GGNQ +   G   Q +    P + Q  Q 
Sbjct: 114 QNPQSVYFIKNNPFSKTYNPGWRNHPNFSWTGGNQQEHHPGANHQQRNGPPPAFQQTHQQ 173

Query: 122 HQAQRNESANSSS--SSLKALIRQTITKNEETLKSLEAMLQNQMGEIKSHAIAI 148
           HQ   N    +SS  S L+ L+++ I +N+  LKS  + + N   + + H + +
Sbjct: 174 HQQPFNRGGQASSLGSPLENLLKEYIAQNDVLLKSQASSITNLEIQEQCHVVTL 227

BLAST of Clc03G09860 vs. ExPASy TrEMBL
Match: A0A6P6GGJ1 (LOW QUALITY PROTEIN: uncharacterized protein LOC112492876 OS=Ziziphus jujuba OX=326968 GN=LOC112492876 PE=4 SV=1)

HSP 1 Score: 67.0 bits (162), Expect = 7.4e-08
Identity = 49/139 (35.25%), Postives = 70/139 (50.36%), Query Frame = 0

Query: 21  LQTIALNNQGEAAVSMDAMNTVNA------TTSNNPYSKTYNLGWRNHPNFGWGGNQSQT 80
           ++ + +NN G A ++   M T+N          NNPYS TYNLGWRNHPNF W  N  Q 
Sbjct: 160 VEDVDINNLG-AQLATQFMKTLNTQFGNFQKQQNNPYSNTYNLGWRNHPNFSWSNNNQQG 219

Query: 81  QGTGQ----QPQRSNNPVYNQGVQGHQAQRNESANSSSSSLKALIRQT-------ITKNE 140
              GQ    Q Q+  +P Y +    H+ Q +  A +  SSL+  +++        + +NE
Sbjct: 220 SNQGQSGGFQRQQFQSPFYQKPQLAHKNQNSSQAQTQFSSLEQSLQELSNNTNSFMQRNE 279

Query: 141 ETLKSLEAMLQNQMGEIKS 143
           + L +   M  NQM  IKS
Sbjct: 280 QQLTNHSQMFNNQMAAIKS 297

BLAST of Clc03G09860 vs. ExPASy TrEMBL
Match: A0A6A3BRM8 (Reverse transcriptase OS=Hibiscus syriacus OX=106335 GN=F3Y22_tig00109972pilonHSYRG00035 PE=4 SV=1)

HSP 1 Score: 59.3 bits (142), Expect = 1.6e-05
Identity = 44/153 (28.76%), Postives = 80/153 (52.29%), Query Frame = 0

Query: 3   ETDATNNLSAQIANMTSLLQTIALNNQGEAAVSMDAMNTVNATTSNNPYSKTYNLGWRNH 62
           E +A +++S Q++ +T++L+ +  +                   +NNPYS TYN GWR H
Sbjct: 460 ELEAKDSVSTQLSAITNMLKNLQCSTD----------------VNNNPYSNTYNAGWRQH 519

Query: 63  PNFGWGGNQSQTQGTGQQPQRSNNP-VYNQGVQGHQAQRNESANSSSSSLKALIRQ---- 122
           PNF WG   +       + Q  N P  Y   +  H + +  S+++S SSL+A I++    
Sbjct: 520 PNFSWGNQGAHNANQPTRQQNHNEPQSYQNAMPCHNSNKGASSSASISSLEATIQEFIST 579

Query: 123 --TITKNEET-LKSLEAMLQNQMGEIKSHAIAI 148
             T+ +N  T +K+  A+L +Q   ++SH++++
Sbjct: 580 TKTMLQNHSTSIKNQGALLYSQGALLQSHSLSL 596

BLAST of Clc03G09860 vs. ExPASy TrEMBL
Match: A0A6A2WPT7 (LRRNT_2 domain-containing protein OS=Hibiscus syriacus OX=106335 GN=F3Y22_tig00117007pilonHSYRG00066 PE=4 SV=1)

HSP 1 Score: 58.9 bits (141), Expect = 2.0e-05
Identity = 46/164 (28.05%), Postives = 79/164 (48.17%), Query Frame = 0

Query: 3   ETDATNNLSAQIANMTSLLQTIAL--------------------NNQGEAAVSMDAMNTV 62
           E +A +++SAQ++ +T++L+ +                      +++ E   + +++N V
Sbjct: 218 ELEAKDSVSAQLSAITNMLKNLQCFTDVKEVKTTSLACLLCQGNHHESECPTNHESINFV 277

Query: 63  N--ATTSNNPYSKTYNLGWRNHPNFGWGGNQSQTQGTGQQPQRSNNP-VYNQGVQGHQAQ 122
                 SNNPYS TYN GWR HPNF WG   +       + Q  N P  Y   +  H A 
Sbjct: 278 GNYNRCSNNPYSNTYNTGWRQHPNFSWGNQGAHNANQPTRQQNHNEPQSYQNAMPWHNAN 337

Query: 123 RNESANSSSSSLKALIRQTITKNEETLKSLEAMLQNQMGEIKSH 144
           +  S+ +S SSL+A I++ I+  +  L+     ++NQ   +  H
Sbjct: 338 KGASSLASISSLEATIQEFISTTKTKLQDHSTSIKNQGALLHKH 381

BLAST of Clc03G09860 vs. ExPASy TrEMBL
Match: A0A6J1EEI2 (uncharacterized protein LOC111433394 OS=Cucurbita moschata OX=3662 GN=LOC111433394 PE=4 SV=1)

HSP 1 Score: 58.9 bits (141), Expect = 2.0e-05
Identity = 49/189 (25.93%), Postives = 86/189 (45.50%), Query Frame = 0

Query: 1   MIETDATNNLSAQIANMTSLLQTIALNNQGEAAVSMDAMNTVNATTS------------- 60
           ++E DA ++++AQ+A++T++LQ +AL         +  +  +N T +             
Sbjct: 272 VLEVDALSSINAQLASVTNILQNLALGQDSMIKAPVHTVAVINQTAAESCVYCGEEHTFD 331

Query: 61  ----------------------NNPYSKTYNLGWRNHPNFGWGGNQSQTQGTGQQPQRSN 120
                                 NNP+S TYN GWRNHPNF W G  S  Q   Q P ++N
Sbjct: 332 QCPSNPASIFYVGNQASQGNPKNNPFSNTYNPGWRNHPNFSWKGQGSYNQ---QMPPKAN 391

Query: 121 NPVYNQGVQGHQAQRNESANSS-----------SSSLKALIRQTITKNEETLKSLEAMLQ 144
            P    G+Q   A  ++  N+             +S+++LI++ + KN+  +++ +A L+
Sbjct: 392 YPP-GFGLQNQLAYSSQQVNTQGKGIPQAQYTLGTSIESLIKEYMAKNDVVIQNQQASLR 451

BLAST of Clc03G09860 vs. ExPASy TrEMBL
Match: A0A2Z6MHA8 (Retrotrans_gag domain-containing protein OS=Trifolium subterraneum OX=3900 GN=TSUD_315860 PE=4 SV=1)

HSP 1 Score: 58.5 bits (140), Expect = 2.6e-05
Identity = 39/108 (36.11%), Postives = 56/108 (51.85%), Query Frame = 0

Query: 35  SMDAMNTVNATTSNNPYSKTYNLGWRNHPNFGWGGNQSQTQGTGQQPQRSNNPVYNQGVQ 94
           +M   N   + T+NNPYS TYN GWRNHPNFGWGGNQ+Q+Q   Q P +++ P     ++
Sbjct: 323 AMYLSNFKKSNTTNNPYSNTYNPGWRNHPNFGWGGNQNQSQ--QQAPSQNSQPRQQSPLE 382

Query: 95  GHQAQRNESANSSSSSLKALIRQTITKNEETLKSLEAMLQNQMGEIKS 143
              AQ  +    +   +K    Q     E+   + +   +N    IKS
Sbjct: 383 DALAQFIKVTQGNFEEMKISQNQLKANQEQMKVNQDIANKNHEASIKS 428

The following BLAST results are available for this feature:
Match NameE-valueIdentityDescription
WP_217833202.16.4e-3056.02hypothetical protein, partial [Synechococcus sp. PCC 7002][more]
XP_038902511.15.6e-1035.20uncharacterized protein LOC120089170 [Benincasa hispida][more]
XP_030503898.16.2e-0933.11uncharacterized protein LOC115719117 [Cannabis sativa][more]
XP_024933238.11.5e-0735.25LOW QUALITY PROTEIN: uncharacterized protein LOC112492876, partial [Ziziphus juj... [more]
XP_038895768.12.6e-0732.76uncharacterized protein LOC120083932 [Benincasa hispida][more]
Match NameE-valueIdentityDescription
Match NameE-valueIdentityDescription
A0A6P6GGJ17.4e-0835.25LOW QUALITY PROTEIN: uncharacterized protein LOC112492876 OS=Ziziphus jujuba OX=... [more]
A0A6A3BRM81.6e-0528.76Reverse transcriptase OS=Hibiscus syriacus OX=106335 GN=F3Y22_tig00109972pilonHS... [more]
A0A6A2WPT72.0e-0528.05LRRNT_2 domain-containing protein OS=Hibiscus syriacus OX=106335 GN=F3Y22_tig001... [more]
A0A6J1EEI22.0e-0525.93uncharacterized protein LOC111433394 OS=Cucurbita moschata OX=3662 GN=LOC1114333... [more]
A0A2Z6MHA82.6e-0536.11Retrotrans_gag domain-containing protein OS=Trifolium subterraneum OX=3900 GN=TS... [more]
Match NameE-valueIdentityDescription
InterPro
Analysis Name: InterPro Annotations of Watermelon (cordophanus) v2
Date Performed: 2022-01-31
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 119..139
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 62..111

Relationships

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

Feature NameUnique NameType
Clc03G09860.1Clc03G09860.1mRNA