Clc09G07935 (gene) Watermelon (cordophanus) v2

Overview
NameClc09G07935
Typegene
OrganismCitrullus lanatus subsp. cordophanus cv. cordophanus (Watermelon (cordophanus) v2)
DescriptionPentatricopeptide repeat-containing protein
LocationClcChr09: 6536525 .. 6537032 (+)
RNA-Seq ExpressionClc09G07935
SyntenyClc09G07935
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.
ATGGAAATGCCCGCCCCAACCCCTTCCATCACCCGTATACTACTTCAATTCACCGATTTCCTTTCAGCACCGGCTTCCAACCTTCTTACAAAATTGCACAATAGGTAACATTATTGCAACTGAAGCATTACATTTCTTTCATAATGATCGTTTACTTGCTGGACTTACTAACATTAAGCATTACTCTCAAGTATTTTCTCTCTATAATAAAATGCCTAATGTGGTTGTTTATACCTCTTTGATTTTCCTGTGGTGGAAACTGGAAGGAGGCTAAACATTCGTTAAATGAGATGGTGGATCAAGGTGTTCGACCAAATATGGTCACATTCAGTGTGTTGATTGATATGCTTTGCAAGGAAGGAAAGGTCATCCAGGCTCAAGAGTTGCTAGAGTGATGATTCACACAAACGTTCCAGATTCGTTTACTTATAATTCACTGATCGAGGGGTTTTGTTTGGTTGGTGACTTGAATAGTGCGAGGGAACTCTTTGTTAGTATACTATATTAA

mRNA sequence

ATGGAAATGCCCGCCCCAACCCCTTCCATCACCCGTATACTACTTCAATTCACCGATTTCCTTTCAGCACCGGCTTCCAACCTTCTTACAAAATTGCACAATAGGAAAGGTCATCCAGGCTCAAGAGTTGCTAGAGTGATGATTCACACAAACGTTCCAGATTCGTTTACTTATAATTCACTGATCGAGGGGTTTTGTTTGGTTGGTGACTTGAATAGTGCGAGGGAACTCTTTGTTAGTATACTATATTAA

Coding sequence (CDS)

ATGGAAATGCCCGCCCCAACCCCTTCCATCACCCGTATACTACTTCAATTCACCGATTTCCTTTCAGCACCGGCTTCCAACCTTCTTACAAAATTGCACAATAGGAAAGGTCATCCAGGCTCAAGAGTTGCTAGAGTGATGATTCACACAAACGTTCCAGATTCGTTTACTTATAATTCACTGATCGAGGGGTTTTGTTTGGTTGGTGACTTGAATAGTGCGAGGGAACTCTTTGTTAGTATACTATATTAA

Protein sequence

MEMPAPTPSITRILLQFTDFLSAPASNLLTKLHNRKGHPGSRVARVMIHTNVPDSFTYNSLIEGFCLVGDLNSARELFVSILY
Homology
BLAST of Clc09G07935 vs. NCBI nr
Match: XP_011659250.2 (pentatricopeptide repeat-containing protein At3g22470, mitochondrial isoform X1 [Cucumis sativus] >KAE8646286.1 hypothetical protein Csa_016185 [Cucumis sativus])

HSP 1 Score: 58.2 bits (139), Expect = 4.0e-05
Identity = 29/37 (78.38%), Postives = 32/37 (86.49%), Query Frame = 0

Query: 46  VMIHTN-VPDSFTYNSLIEGFCLVGDLNSARELFVSI 82
           VMI +  VPD  TYNSLIEGFC+VGDLNSARELFVS+
Sbjct: 356 VMIESGIVPDLVTYNSLIEGFCMVGDLNSARELFVSM 392

BLAST of Clc09G07935 vs. NCBI nr
Match: XP_011659251.1 (pentatricopeptide repeat-containing protein At3g22470, mitochondrial isoform X2 [Cucumis sativus])

HSP 1 Score: 58.2 bits (139), Expect = 4.0e-05
Identity = 29/37 (78.38%), Postives = 32/37 (86.49%), Query Frame = 0

Query: 46  VMIHTN-VPDSFTYNSLIEGFCLVGDLNSARELFVSI 82
           VMI +  VPD  TYNSLIEGFC+VGDLNSARELFVS+
Sbjct: 179 VMIESGIVPDLVTYNSLIEGFCMVGDLNSARELFVSM 215

BLAST of Clc09G07935 vs. NCBI nr
Match: XP_038877921.1 (pentatricopeptide repeat-containing protein At3g22470, mitochondrial-like isoform X2 [Benincasa hispida])

HSP 1 Score: 57.0 bits (136), Expect = 9.0e-05
Identity = 27/37 (72.97%), Postives = 30/37 (81.08%), Query Frame = 0

Query: 46  VMIHT-NVPDSFTYNSLIEGFCLVGDLNSARELFVSI 82
           +M H   +PD FTYNSLIEGFCLVGDLN A ELFVS+
Sbjct: 216 IMTHRGTLPDLFTYNSLIEGFCLVGDLNGANELFVSM 252

BLAST of Clc09G07935 vs. NCBI nr
Match: XP_038877920.1 (pentatricopeptide repeat-containing protein At1g63330-like isoform X1 [Benincasa hispida])

HSP 1 Score: 57.0 bits (136), Expect = 9.0e-05
Identity = 27/37 (72.97%), Postives = 30/37 (81.08%), Query Frame = 0

Query: 46  VMIHT-NVPDSFTYNSLIEGFCLVGDLNSARELFVSI 82
           +M H   +PD FTYNSLIEGFCLVGDLN A ELFVS+
Sbjct: 357 IMTHRGTLPDLFTYNSLIEGFCLVGDLNGANELFVSM 393

BLAST of Clc09G07935 vs. NCBI nr
Match: XP_038874245.1 (pentatricopeptide repeat-containing protein At3g22470, mitochondrial-like [Benincasa hispida] >XP_038874246.1 pentatricopeptide repeat-containing protein At3g22470, mitochondrial-like [Benincasa hispida] >XP_038874247.1 pentatricopeptide repeat-containing protein At3g22470, mitochondrial-like [Benincasa hispida])

HSP 1 Score: 56.6 bits (135), Expect = 1.2e-04
Identity = 27/41 (65.85%), Postives = 34/41 (82.93%), Query Frame = 0

Query: 42  RVARVMIHT-NVPDSFTYNSLIEGFCLVGDLNSARELFVSI 82
           ++  VMI   N+PD FTYN+L++GFCLVGDL+SARELF SI
Sbjct: 349 KLLEVMIQRGNIPDLFTYNTLMDGFCLVGDLHSARELFDSI 389

BLAST of Clc09G07935 vs. ExPASy TrEMBL
Match: A0A6J1DSW3 (pentatricopeptide repeat-containing protein At1g63330-like OS=Momordica charantia OX=3673 GN=LOC111022854 PE=4 SV=1)

HSP 1 Score: 56.6 bits (135), Expect = 5.7e-05
Identity = 23/31 (74.19%), Postives = 29/31 (93.55%), Query Frame = 0

Query: 51  NVPDSFTYNSLIEGFCLVGDLNSARELFVSI 82
           N PD FTYN+L++GFCLVGDLNSARELF+++
Sbjct: 362 NAPDLFTYNTLMDGFCLVGDLNSARELFINM 392

BLAST of Clc09G07935 vs. ExPASy TrEMBL
Match: A0A5A7UUW8 (Pentatricopeptide repeat-containing protein OS=Cucumis melo var. makuwa OX=1194695 GN=E5676_scaffold111G00730 PE=4 SV=1)

HSP 1 Score: 56.2 bits (134), Expect = 7.4e-05
Identity = 26/41 (63.41%), Postives = 35/41 (85.37%), Query Frame = 0

Query: 42  RVARVMIHTN-VPDSFTYNSLIEGFCLVGDLNSARELFVSI 82
           ++  +MI +  VP+ FTYNSL++GFC+VGDLNSARELFVS+
Sbjct: 277 KLLELMIESGIVPNVFTYNSLLKGFCMVGDLNSARELFVSM 317

BLAST of Clc09G07935 vs. ExPASy TrEMBL
Match: A0A5D3CCW0 (Pentatricopeptide repeat-containing protein OS=Cucumis melo var. makuwa OX=1194695 GN=E5676_scaffold886G00420 PE=4 SV=1)

HSP 1 Score: 56.2 bits (134), Expect = 7.4e-05
Identity = 26/32 (81.25%), Postives = 29/32 (90.62%), Query Frame = 0

Query: 51  NVPDSFTYNSLIEGFCLVGDLNSARELFVSIL 83
           +VP+  TYNSLIEGFCLVGDLNSARELF S+L
Sbjct: 343 SVPNLLTYNSLIEGFCLVGDLNSARELFFSML 374

BLAST of Clc09G07935 vs. ExPASy TrEMBL
Match: A0A1S4DYL3 (pentatricopeptide repeat-containing protein At1g63330-like isoform X3 OS=Cucumis melo OX=3656 GN=LOC103492587 PE=4 SV=1)

HSP 1 Score: 56.2 bits (134), Expect = 7.4e-05
Identity = 26/32 (81.25%), Postives = 29/32 (90.62%), Query Frame = 0

Query: 51  NVPDSFTYNSLIEGFCLVGDLNSARELFVSIL 83
           +VP+  TYNSLIEGFCLVGDLNSARELF S+L
Sbjct: 343 SVPNLLTYNSLIEGFCLVGDLNSARELFFSML 374

BLAST of Clc09G07935 vs. ExPASy TrEMBL
Match: A0A5A7TFD7 (Pentatricopeptide repeat-containing protein OS=Cucumis melo var. makuwa OX=1194695 GN=E5676_scaffold306G001070 PE=4 SV=1)

HSP 1 Score: 55.5 bits (132), Expect = 1.3e-04
Identity = 25/36 (69.44%), Postives = 31/36 (86.11%), Query Frame = 0

Query: 46  VMIHTNVPDSFTYNSLIEGFCLVGDLNSARELFVSI 82
           +M+   VPD FTY SLIEGFCLVGDL+SA+ELF+S+
Sbjct: 298 MMLRGIVPDLFTYTSLIEGFCLVGDLDSAKELFLSM 333

BLAST of Clc09G07935 vs. TAIR 10
Match: AT1G12300.1 (Tetratricopeptide repeat (TPR)-like superfamily protein )

HSP 1 Score: 40.4 bits (93), Expect = 8.1e-04
Identity = 17/27 (62.96%), Postives = 22/27 (81.48%), Query Frame = 0

Query: 52  VPDSFTYNSLIEGFCLVGDLNSARELF 79
           V D+ TYN+LI+GFC +G LN A+ELF
Sbjct: 435 VADTVTYNTLIQGFCELGKLNVAKELF 461

The following BLAST results are available for this feature:
Match NameE-valueIdentityDescription
XP_011659250.24.0e-0578.38pentatricopeptide repeat-containing protein At3g22470, mitochondrial isoform X1 ... [more]
XP_011659251.14.0e-0578.38pentatricopeptide repeat-containing protein At3g22470, mitochondrial isoform X2 ... [more]
XP_038877921.19.0e-0572.97pentatricopeptide repeat-containing protein At3g22470, mitochondrial-like isofor... [more]
XP_038877920.19.0e-0572.97pentatricopeptide repeat-containing protein At1g63330-like isoform X1 [Benincasa... [more]
XP_038874245.11.2e-0465.85pentatricopeptide repeat-containing protein At3g22470, mitochondrial-like [Benin... [more]
Match NameE-valueIdentityDescription
Match NameE-valueIdentityDescription
A0A6J1DSW35.7e-0574.19pentatricopeptide repeat-containing protein At1g63330-like OS=Momordica charanti... [more]
A0A5A7UUW87.4e-0563.41Pentatricopeptide repeat-containing protein OS=Cucumis melo var. makuwa OX=11946... [more]
A0A5D3CCW07.4e-0581.25Pentatricopeptide repeat-containing protein OS=Cucumis melo var. makuwa OX=11946... [more]
A0A1S4DYL37.4e-0581.25pentatricopeptide repeat-containing protein At1g63330-like isoform X3 OS=Cucumis... [more]
A0A5A7TFD71.3e-0469.44Pentatricopeptide repeat-containing protein OS=Cucumis melo var. makuwa OX=11946... [more]
Match NameE-valueIdentityDescription
AT1G12300.18.1e-0462.96Tetratricopeptide repeat (TPR)-like superfamily protein [more]
InterPro
Analysis Name: InterPro Annotations of Watermelon (cordophanus) v2
Date Performed: 2022-01-31
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR002885Pentatricopeptide repeatTIGRFAMTIGR00756TIGR00756coord: 56..79
e-value: 3.9E-5
score: 21.5
IPR002885Pentatricopeptide repeatPFAMPF12854PPR_1coord: 52..78
e-value: 3.9E-10
score: 39.3
IPR002885Pentatricopeptide repeatPROSITEPS51375PPRcoord: 54..83
score: 9.536388
IPR011990Tetratricopeptide-like helical domain superfamilyGENE3D1.25.40.10Tetratricopeptide repeat domaincoord: 25..82
e-value: 6.3E-6
score: 27.8

Relationships

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

Feature NameUnique NameType
Clc09G07935.1Clc09G07935.1mRNA


GO Annotation
GO Assignments
This gene is annotated with the following GO terms.
Category Term Accession Term Name
molecular_function GO:0005515 protein binding