CcUC04G060590 (gene) Watermelon (PI 537277) v1

Overview


Name	CcUC04G060590
Type	gene
Organism	Citrullus colocynthis (Watermelon (PI 537277) v1)
Description	transcription elongation factor B polypeptide 3
Location	CicolChr04: 5224929 .. 5225283 (+)
RNA-Seq Expression	CcUC04G060590
Synteny	CcUC04G060590

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.

ATGAAAGTATAAAAGGAAGAGAAGAGGTTTGAATTATATATTTGCTTAAATCTTCCGCCACTCTTCTTCACACTTCAAATAGTAAAAGTCTTAAACCATCGGATTCTCTGTTTGATCACTACTAAGAAAGATGTGTGAAAAAGCAAGTAAAATCACTTCATCTTTTCTTACTTATCTTTCCATTAACGAAGCTACAGATAGTCTCAAGTTTCTTGGAGATGTTGGCAATACCGATTTAAATTTTCTTGATCGTATTTTACCACATTGTATTATTGACCAATTGATGCATATAGAGAACTCTTCCAAAGGAAGGGATCTCACACCTCTGACCGACAAATTATGGAAAAATTTCTAA

mRNA sequence

ATGAAAATGTGTGAAAAAGCAAGTAAAATCACTTCATCTTTTCTTACTTATCTTTCCATTAACGAAGCTACAGATAGTCTCAAGTTTCTTGGAGATGTTGGCAATACCGATTTAAATTTTCTTGATCGTATTTTACCACATTGTATTATTGACCAATTGATGCATATAGAGAACTCTTCCAAAGGAAGGGATCTCACACCTCTGACCGACAAATTATGGAAAAATTTCTAA

Coding sequence (CDS)

ATGAAAATGTGTGAAAAAGCAAGTAAAATCACTTCATCTTTTCTTACTTATCTTTCCATTAACGAAGCTACAGATAGTCTCAAGTTTCTTGGAGATGTTGGCAATACCGATTTAAATTTTCTTGATCGTATTTTACCACATTGTATTATTGACCAATTGATGCATATAGAGAACTCTTCCAAAGGAAGGGATCTCACACCTCTGACCGACAAATTATGGAAAAATTTCTAA

Protein sequence

MKMCEKASKITSSFLTYLSINEATDSLKFLGDVGNTDLNFLDRILPHCIIDQLMHIENSSKGRDLTPLTDKLWKNF

Homology

[Close]

BLAST of CcUC04G060590 vs. NCBI nr
Match: XP_038885873.1 (uncharacterized protein LOC120076176 [Benincasa hispida])

HSP 1 Score: 127.9 bits (320), Expect = 3.8e-26
Identity = 59/74 (79.73%), Postives = 68/74 (91.89%), Query Frame = 0


Query: 3  MCEKASKITSSFLTYLSINEATDSLKFLGDVGNTDLNFLDRILPHCIIDQLMHIENSSKG 62
          MCE+ SKI SSFL++ SINEA DSL+FLGDVG+TDL+ L+RILPHC +DQLMHIENSSKG
Sbjct: 1  MCEEVSKIASSFLSHDSINEAIDSLRFLGDVGDTDLHVLERILPHCTVDQLMHIENSSKG 60

Query: 63 RDLTPLTDKLWKNF 77
          RDLTP+TDKLWKNF
Sbjct: 61 RDLTPVTDKLWKNF 74

[Close]

BLAST of CcUC04G060590 vs. NCBI nr
Match: XP_038885879.1 (uncharacterized protein LOC120076185 [Benincasa hispida])

HSP 1 Score: 117.5 bits (293), Expect = 5.1e-23
Identity = 55/74 (74.32%), Postives = 65/74 (87.84%), Query Frame = 0


Query: 3  MCEKASKITSSFLTYLSINEATDSLKFLGDVGNTDLNFLDRILPHCIIDQLMHIENSSKG 62
          MCE+ SKI SSFL++ SINEA D+L+FL DVG+TDL+ L RILPHC +DQL+HIENSSKG
Sbjct: 1  MCEEVSKIASSFLSHDSINEAIDNLRFLRDVGDTDLHVLKRILPHCTVDQLLHIENSSKG 60

Query: 63 RDLTPLTDKLWKNF 77
          RDLT +TDKLWKNF
Sbjct: 61 RDLTLVTDKLWKNF 74

[Close]

BLAST of CcUC04G060590 vs. NCBI nr
Match: XP_022979571.1 (uncharacterized protein LOC111479252 [Cucurbita maxima])

HSP 1 Score: 102.8 bits (255), Expect = 1.3e-18
Identity = 44/57 (77.19%), Postives = 51/57 (89.47%), Query Frame = 0


Query: 20 INEATDSLKFLGDVGNTDLNFLDRILPHCIIDQLMHIENSSKGRDLTPLTDKLWKNF 77
          +N+A DSL+FLGDVG TDLNFL+ ILPHC +DQLMHIEN SKGRDLTP+T+KLWK F
Sbjct: 5  VNKAIDSLRFLGDVGQTDLNFLEHILPHCTVDQLMHIENCSKGRDLTPITNKLWKTF 61

[Close]

BLAST of CcUC04G060590 vs. NCBI nr
Match: XP_038900478.1 (transcription elongation factor B polypeptide 3-like isoform X1 [Benincasa hispida] >XP_038900479.1 transcription elongation factor B polypeptide 3-like isoform X1 [Benincasa hispida] >XP_038900480.1 transcription elongation factor B polypeptide 3-like isoform X1 [Benincasa hispida])

HSP 1 Score: 100.9 bits (250), Expect = 5.0e-18
Identity = 43/62 (69.35%), Postives = 53/62 (85.48%), Query Frame = 0


Query: 15 LTYLSINEATDSLKFLGDVGNTDLNFLDRILPHCIIDQLMHIENSSKGRDLTPLTDKLWK 74
          L  L +N+A D+L+FLGDVG TD++ LDRILPHC +DQLMH+E SS+GRDLTP+TDKLWK
Sbjct: 10 LVDLCVNKAIDNLRFLGDVGETDIHLLDRILPHCTVDQLMHVEKSSEGRDLTPITDKLWK 69

Query: 75 NF 77
           F
Sbjct: 70 KF 71

[Close]

BLAST of CcUC04G060590 vs. NCBI nr
Match: XP_038900481.1 (transcription elongation factor B polypeptide 3-like isoform X2 [Benincasa hispida])

HSP 1 Score: 100.9 bits (250), Expect = 5.0e-18
Identity = 43/62 (69.35%), Postives = 53/62 (85.48%), Query Frame = 0


Query: 15 LTYLSINEATDSLKFLGDVGNTDLNFLDRILPHCIIDQLMHIENSSKGRDLTPLTDKLWK 74
          L  L +N+A D+L+FLGDVG TD++ LDRILPHC +DQLMH+E SS+GRDLTP+TDKLWK
Sbjct: 10 LVDLCVNKAIDNLRFLGDVGETDIHLLDRILPHCTVDQLMHVEKSSEGRDLTPITDKLWK 69

Query: 75 NF 77
           F
Sbjct: 70 KF 71

[Close]

BLAST of CcUC04G060590 vs. ExPASy TrEMBL
Match: A0A6J1IR58 (uncharacterized protein LOC111479252 OS=Cucurbita maxima OX=3661 GN=LOC111479252 PE=4 SV=1)

HSP 1 Score: 102.8 bits (255), Expect = 6.3e-19
Identity = 44/57 (77.19%), Postives = 51/57 (89.47%), Query Frame = 0


Query: 20 INEATDSLKFLGDVGNTDLNFLDRILPHCIIDQLMHIENSSKGRDLTPLTDKLWKNF 77
          +N+A DSL+FLGDVG TDLNFL+ ILPHC +DQLMHIEN SKGRDLTP+T+KLWK F
Sbjct: 5  VNKAIDSLRFLGDVGQTDLNFLEHILPHCTVDQLMHIENCSKGRDLTPITNKLWKTF 61

[Close]

BLAST of CcUC04G060590 vs. ExPASy TrEMBL
Match: A0A0A0KGZ5 (Uncharacterized protein OS=Cucumis sativus OX=3659 GN=Csa_6G169320 PE=4 SV=1)

HSP 1 Score: 100.5 bits (249), Expect = 3.1e-18
Identity = 43/62 (69.35%), Postives = 53/62 (85.48%), Query Frame = 0


Query: 15 LTYLSINEATDSLKFLGDVGNTDLNFLDRILPHCIIDQLMHIENSSKGRDLTPLTDKLWK 74
          L  L +N+A D+L+FLGDVG TD++ LDRILPHC +DQLMH+E SS+GRDLTP+TDKLWK
Sbjct: 10 LVDLCVNKAIDNLRFLGDVGETDIHLLDRILPHCTVDQLMHVEKSSEGRDLTPVTDKLWK 69

Query: 75 NF 77
           F
Sbjct: 70 KF 71

[Close]

BLAST of CcUC04G060590 vs. ExPASy TrEMBL
Match: A0A6J1D807 (transcription elongation factor B polypeptide 3 OS=Momordica charantia OX=3673 GN=LOC111018119 PE=4 SV=1)

HSP 1 Score: 100.5 bits (249), Expect = 3.1e-18
Identity = 47/71 (66.20%), Postives = 57/71 (80.28%), Query Frame = 0


Query: 6  KASKITSSFLTYLSINEATDSLKFLGDVGNTDLNFLDRILPHCIIDQLMHIENSSKGRDL 65
          +A KI S  L  L +N A D+L+FLGDVG TD++ L+RILPHC +DQLMH+E SSKGRDL
Sbjct: 3  RARKIPS--LVDLCVNTAIDNLRFLGDVGETDIHLLERILPHCTLDQLMHVEKSSKGRDL 62

Query: 66 TPLTDKLWKNF 77
          TP+TDKLWK F
Sbjct: 63 TPVTDKLWKKF 71

[Close]

BLAST of CcUC04G060590 vs. ExPASy TrEMBL
Match: A0A6J1ITM2 (uncharacterized protein LOC111479243 OS=Cucurbita maxima OX=3661 GN=LOC111479243 PE=4 SV=1)

HSP 1 Score: 99.8 bits (247), Expect = 5.4e-18
Identity = 43/57 (75.44%), Postives = 51/57 (89.47%), Query Frame = 0


Query: 20 INEATDSLKFLGDVGNTDLNFLDRILPHCIIDQLMHIENSSKGRDLTPLTDKLWKNF 77
          +N+A DSL+FLGDVG TDLNFL+ ILPHC ++QLM IENSSKGRDLTP+T+KLWK F
Sbjct: 5  VNKAIDSLRFLGDVGQTDLNFLEHILPHCTVEQLMRIENSSKGRDLTPVTNKLWKTF 61

[Close]

BLAST of CcUC04G060590 vs. ExPASy TrEMBL
Match: A0A5D3BGR1 (Transcription elongation factor B polypeptide 3 isoform X2 OS=Cucumis melo var. makuwa OX=1194695 GN=E5676_scaffold203G00180 PE=4 SV=1)

HSP 1 Score: 98.2 bits (243), Expect = 1.6e-17
Identity = 41/62 (66.13%), Postives = 53/62 (85.48%), Query Frame = 0


Query: 15 LTYLSINEATDSLKFLGDVGNTDLNFLDRILPHCIIDQLMHIENSSKGRDLTPLTDKLWK 74
          L  L +N+A D+++FLGDVG TD++ L+RILPHC +DQLMH+E SS+GRDLTP+TDKLWK
Sbjct: 10 LVDLCVNKAIDNIRFLGDVGETDIHLLERILPHCTVDQLMHVEKSSEGRDLTPVTDKLWK 69

Query: 75 NF 77
           F
Sbjct: 70 KF 71

[Close]

BLAST of CcUC04G060590 vs. TAIR 10
Match: AT2G42780.1 (FUNCTIONS IN: molecular_function unknown; INVOLVED IN: regulation of transcription; LOCATED IN: integral to membrane, nucleus; EXPRESSED IN: 20 plant structures; EXPRESSED DURING: 11 growth stages; CONTAINS InterPro DOMAIN/s: RNA polymerase II transcription factor SIII, subunit A (InterPro:IPR010684); Has 187 Blast hits to 186 proteins in 77 species: Archae - 0; Bacteria - 0; Metazoa - 104; Fungi - 29; Plants - 38; Viruses - 0; Other Eukaryotes - 16 (source: NCBI BLink). )

HSP 1 Score: 69.3 bits (168), Expect = 1.5e-12
Identity = 28/62 (45.16%), Postives = 43/62 (69.35%), Query Frame = 0


Query: 15 LTYLSINEATDSLKFLGDVGNTDLNFLDRILPHCIIDQLMHIENSSKGRDLTPLTDKLWK 74
          L  L + +A D++K++G VG  D   L++IL HC ++QL HIE+++   DL+P+TDK WK
Sbjct: 13 LVDLCVRKAIDNVKYIGYVGGVDFQLLEQILQHCTLEQLKHIEDATDDTDLSPITDKFWK 72

Query: 75 NF 77
           F
Sbjct: 73 GF 74

[Close]

BLAST of CcUC04G060590 vs. TAIR 10
Match: AT2G42780.2 (FUNCTIONS IN: molecular_function unknown; INVOLVED IN: regulation of transcription; LOCATED IN: integral to membrane, nucleus; EXPRESSED IN: 20 plant structures; EXPRESSED DURING: 11 growth stages; CONTAINS InterPro DOMAIN/s: RNA polymerase II transcription factor SIII, subunit A (InterPro:IPR010684). )

HSP 1 Score: 69.3 bits (168), Expect = 1.5e-12
Identity = 28/62 (45.16%), Postives = 43/62 (69.35%), Query Frame = 0


Query: 15 LTYLSINEATDSLKFLGDVGNTDLNFLDRILPHCIIDQLMHIENSSKGRDLTPLTDKLWK 74
          L  L + +A D++K++G VG  D   L++IL HC ++QL HIE+++   DL+P+TDK WK
Sbjct: 13 LVDLCVRKAIDNVKYIGYVGGVDFQLLEQILQHCTLEQLKHIEDATDDTDLSPITDKFWK 72

Query: 75 NF 77
           F
Sbjct: 73 GF 74

The following BLAST results are available for this feature:

BLAST of CcUC04G060590 vs. NCBI nr


Match Name	E-value	Identity	Description
XP_038885873.1	3.8e-26	79.73	uncharacterized protein LOC120076176 [Benincasa hispida]	[more]
XP_038885879.1	5.1e-23	74.32	uncharacterized protein LOC120076185 [Benincasa hispida]	[more]
XP_022979571.1	1.3e-18	77.19	uncharacterized protein LOC111479252 [Cucurbita maxima]	[more]
XP_038900478.1	5.0e-18	69.35	transcription elongation factor B polypeptide 3-like isoform X1 [Benincasa hispi...	[more]
XP_038900481.1	5.0e-18	69.35	transcription elongation factor B polypeptide 3-like isoform X2 [Benincasa hispi...	[more]

BLAST of CcUC04G060590 vs. NCBI nr


Match Name	E-value	Identity	Description

BLAST of CcUC04G060590 vs. ExPASy TrEMBL


Match Name	E-value	Identity	Description
A0A6J1IR58	6.3e-19	77.19	uncharacterized protein LOC111479252 OS=Cucurbita maxima OX=3661 GN=LOC111479252...	[more]
A0A0A0KGZ5	3.1e-18	69.35	Uncharacterized protein OS=Cucumis sativus OX=3659 GN=Csa_6G169320 PE=4 SV=1	[more]
A0A6J1D807	3.1e-18	66.20	transcription elongation factor B polypeptide 3 OS=Momordica charantia OX=3673 G...	[more]
A0A6J1ITM2	5.4e-18	75.44	uncharacterized protein LOC111479243 OS=Cucurbita maxima OX=3661 GN=LOC111479243...	[more]
A0A5D3BGR1	1.6e-17	66.13	Transcription elongation factor B polypeptide 3 isoform X2 OS=Cucumis melo var. ...	[more]

BLAST of CcUC04G060590 vs. TAIR 10


Match Name	E-value	Identity	Description
AT2G42780.1	1.5e-12	45.16	FUNCTIONS IN: molecular_function unknown; INVOLVED IN: regulation of transcripti...	[more]
AT2G42780.2	1.5e-12	45.16	FUNCTIONS IN: molecular_function unknown; INVOLVED IN: regulation of transcripti...	[more]

InterPro

Analysis Name: InterPro Annotations of Watermelon (PI 537277) v1
Date Performed: 2022-01-31


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
None	No IPR available	GENE3D	6.10.250.3180		coord: 25..76 e-value: 9.1E-10 score: 40.6
None	No IPR available	PANTHER	PTHR47543	OS08G0169600 PROTEIN	coord: 5..76
IPR010684	RNA polymerase II transcription factor SIII, subunit A	PFAM	PF06881	Elongin_A	coord: 31..76 e-value: 8.5E-10 score: 39.1

Relationships

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


Feature Name	Unique Name	Type
CcUC04G060590.1	CcUC04G060590.1	mRNA

GO Annotation

GO Assignments

This gene is annotated with the following GO terms.

Category	Term Accession	Term Name
biological_process	GO:0006368	transcription elongation from RNA polymerase II promoter
biological_process	GO:0006414	translational elongation
cellular_component	GO:0070449	elongin complex
cellular_component	GO:0005634	nucleus
molecular_function	GO:0003746	translation elongation factor activity