CaUC04G068260 (gene) Watermelon (USVL246-FR2) v1

Overview


Name	CaUC04G068260
Type	gene
Organism	Citrullus amarus (Watermelon (USVL246-FR2) v1)
Description	transcription elongation factor B polypeptide 3
Location	Ciama_Chr04: 5722006 .. 5722360 (+)
RNA-Seq Expression	CaUC04G068260
Synteny	CaUC04G068260

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.

ATGAAAGTATAAAAGGAAGAGGAGAGGTTTGAATTATATATTTGCTTAAATCTTCCGCCACTCTTCTTCACACTTCAAACAATAAAAGTCTTAAACCATCAGATTCTTTGTTTGATCGCAACTAAGAAAGATGTGTGAAAAAGTAAGTAAAATCACTTCATCCTTCCTTACTTATCTTTCCATTAACAAAGCTATAGATAGTCTCAAGTTTCTTGGAGATGTTGGCAATACCGATTTAAATCTTCTTGATCGTATTTTACCACATTGTATTATTGACCAATTGATGCATATAGAGAACTCTTCCAAAGGAAGGGATCTCACACCTCTGACCGACAAATTATGGAAAAATTTCTAA

mRNA sequence

ATGAAAATGTGTGAAAAAGTAAGTAAAATCACTTCATCCTTCCTTACTTATCTTTCCATTAACAAAGCTATAGATAGTCTCAAGTTTCTTGGAGATGTTGGCAATACCGATTTAAATCTTCTTGATCGTATTTTACCACATTGTATTATTGACCAATTGATGCATATAGAGAACTCTTCCAAAGGAAGGGATCTCACACCTCTGACCGACAAATTATGGAAAAATTTCTAA

Coding sequence (CDS)

ATGAAAATGTGTGAAAAAGTAAGTAAAATCACTTCATCCTTCCTTACTTATCTTTCCATTAACAAAGCTATAGATAGTCTCAAGTTTCTTGGAGATGTTGGCAATACCGATTTAAATCTTCTTGATCGTATTTTACCACATTGTATTATTGACCAATTGATGCATATAGAGAACTCTTCCAAAGGAAGGGATCTCACACCTCTGACCGACAAATTATGGAAAAATTTCTAA

Protein sequence

MKMCEKVSKITSSFLTYLSINKAIDSLKFLGDVGNTDLNLLDRILPHCIIDQLMHIENSSKGRDLTPLTDKLWKNF

Homology

[Close]

BLAST of CaUC04G068260 vs. NCBI nr
Match: XP_038885873.1 (uncharacterized protein LOC120076176 [Benincasa hispida])

HSP 1 Score: 130.2 bits (326), Expect = 7.6e-27
Identity = 60/74 (81.08%), Postives = 71/74 (95.95%), Query Frame = 0


Query: 3  MCEKVSKITSSFLTYLSINKAIDSLKFLGDVGNTDLNLLDRILPHCIIDQLMHIENSSKG 62
          MCE+VSKI SSFL++ SIN+AIDSL+FLGDVG+TDL++L+RILPHC +DQLMHIENSSKG
Sbjct: 1  MCEEVSKIASSFLSHDSINEAIDSLRFLGDVGDTDLHVLERILPHCTVDQLMHIENSSKG 60

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

[Close]

BLAST of CaUC04G068260 vs. NCBI nr
Match: XP_038885879.1 (uncharacterized protein LOC120076185 [Benincasa hispida])

HSP 1 Score: 119.8 bits (299), Expect = 1.0e-23
Identity = 56/74 (75.68%), Postives = 68/74 (91.89%), Query Frame = 0


Query: 3  MCEKVSKITSSFLTYLSINKAIDSLKFLGDVGNTDLNLLDRILPHCIIDQLMHIENSSKG 62
          MCE+VSKI SSFL++ SIN+AID+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 CaUC04G068260 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: 106.7 bits (265), Expect = 9.1e-20
Identity = 50/71 (70.42%), Postives = 60/71 (84.51%), Query Frame = 0


Query: 6  KVSKITSSFLTYLSINKAIDSLKFLGDVGNTDLNLLDRILPHCIIDQLMHIENSSKGRDL 65
          +V KI S  L  L +NKAID+L+FLGDVG TD++LLDRILPHC +DQLMH+E SS+GRDL
Sbjct: 3  RVRKIPS--LVDLCVNKAIDNLRFLGDVGETDIHLLDRILPHCTVDQLMHVEKSSEGRDL 62

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

[Close]

BLAST of CaUC04G068260 vs. NCBI nr
Match: XP_038900481.1 (transcription elongation factor B polypeptide 3-like isoform X2 [Benincasa hispida])

HSP 1 Score: 106.7 bits (265), Expect = 9.1e-20
Identity = 50/71 (70.42%), Postives = 60/71 (84.51%), Query Frame = 0


Query: 6  KVSKITSSFLTYLSINKAIDSLKFLGDVGNTDLNLLDRILPHCIIDQLMHIENSSKGRDL 65
          +V KI S  L  L +NKAID+L+FLGDVG TD++LLDRILPHC +DQLMH+E SS+GRDL
Sbjct: 3  RVRKIPS--LVDLCVNKAIDNLRFLGDVGETDIHLLDRILPHCTVDQLMHVEKSSEGRDL 62

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

[Close]

BLAST of CaUC04G068260 vs. NCBI nr
Match: XP_004143189.1 (transcription elongation factor B polypeptide 3 isoform X1 [Cucumis sativus] >KAE8646931.1 hypothetical protein Csa_021040 [Cucumis sativus])

HSP 1 Score: 106.3 bits (264), Expect = 1.2e-19
Identity = 50/71 (70.42%), Postives = 60/71 (84.51%), Query Frame = 0


Query: 6  KVSKITSSFLTYLSINKAIDSLKFLGDVGNTDLNLLDRILPHCIIDQLMHIENSSKGRDL 65
          +V KI S  L  L +NKAID+L+FLGDVG TD++LLDRILPHC +DQLMH+E SS+GRDL
Sbjct: 3  RVRKIPS--LVDLCVNKAIDNLRFLGDVGETDIHLLDRILPHCTVDQLMHVEKSSEGRDL 62

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

[Close]

BLAST of CaUC04G068260 vs. ExPASy TrEMBL
Match: A0A0A0KGZ5 (Uncharacterized protein OS=Cucumis sativus OX=3659 GN=Csa_6G169320 PE=4 SV=1)

HSP 1 Score: 106.3 bits (264), Expect = 5.7e-20
Identity = 50/71 (70.42%), Postives = 60/71 (84.51%), Query Frame = 0


Query: 6  KVSKITSSFLTYLSINKAIDSLKFLGDVGNTDLNLLDRILPHCIIDQLMHIENSSKGRDL 65
          +V KI S  L  L +NKAID+L+FLGDVG TD++LLDRILPHC +DQLMH+E SS+GRDL
Sbjct: 3  RVRKIPS--LVDLCVNKAIDNLRFLGDVGETDIHLLDRILPHCTVDQLMHVEKSSEGRDL 62

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

[Close]

BLAST of CaUC04G068260 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: 104.0 bits (258), Expect = 2.8e-19
Identity = 48/71 (67.61%), Postives = 60/71 (84.51%), Query Frame = 0


Query: 6  KVSKITSSFLTYLSINKAIDSLKFLGDVGNTDLNLLDRILPHCIIDQLMHIENSSKGRDL 65
          +V KI S  L  L +NKAID+++FLGDVG TD++LL+RILPHC +DQLMH+E SS+GRDL
Sbjct: 3  RVRKIPS--LVDLCVNKAIDNIRFLGDVGETDIHLLERILPHCTVDQLMHVEKSSEGRDL 62

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

[Close]

BLAST of CaUC04G068260 vs. ExPASy TrEMBL
Match: A0A5A7ULV4 (Transcription elongation factor B polypeptide 3 isoform X2 OS=Cucumis melo var. makuwa OX=1194695 GN=E6C27_scaffold24G003030 PE=4 SV=1)

HSP 1 Score: 104.0 bits (258), Expect = 2.8e-19
Identity = 48/71 (67.61%), Postives = 60/71 (84.51%), Query Frame = 0


Query: 6  KVSKITSSFLTYLSINKAIDSLKFLGDVGNTDLNLLDRILPHCIIDQLMHIENSSKGRDL 65
          +V KI S  L  L +NKAID+++FLGDVG TD++LL+RILPHC +DQLMH+E SS+GRDL
Sbjct: 3  RVRKIPS--LVDLCVNKAIDNIRFLGDVGETDIHLLERILPHCTVDQLMHVEKSSEGRDL 62

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

[Close]

BLAST of CaUC04G068260 vs. ExPASy TrEMBL
Match: A0A1S4E1U0 (transcription elongation factor B polypeptide 3 isoform X2 OS=Cucumis melo OX=3656 GN=LOC103496337 PE=4 SV=1)

HSP 1 Score: 104.0 bits (258), Expect = 2.8e-19
Identity = 48/71 (67.61%), Postives = 60/71 (84.51%), Query Frame = 0


Query: 6  KVSKITSSFLTYLSINKAIDSLKFLGDVGNTDLNLLDRILPHCIIDQLMHIENSSKGRDL 65
          +V KI S  L  L +NKAID+++FLGDVG TD++LL+RILPHC +DQLMH+E SS+GRDL
Sbjct: 3  RVRKIPS--LVDLCVNKAIDNIRFLGDVGETDIHLLERILPHCTVDQLMHVEKSSEGRDL 62

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

[Close]

BLAST of CaUC04G068260 vs. ExPASy TrEMBL
Match: A0A1S3C4D6 (transcription elongation factor B polypeptide 3 isoform X1 OS=Cucumis melo OX=3656 GN=LOC103496337 PE=4 SV=1)

HSP 1 Score: 104.0 bits (258), Expect = 2.8e-19
Identity = 48/71 (67.61%), Postives = 60/71 (84.51%), Query Frame = 0


Query: 6  KVSKITSSFLTYLSINKAIDSLKFLGDVGNTDLNLLDRILPHCIIDQLMHIENSSKGRDL 65
          +V KI S  L  L +NKAID+++FLGDVG TD++LL+RILPHC +DQLMH+E SS+GRDL
Sbjct: 3  RVRKIPS--LVDLCVNKAIDNIRFLGDVGETDIHLLERILPHCTVDQLMHVEKSSEGRDL 62

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

[Close]

BLAST of CaUC04G068260 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: 73.9 bits (180), Expect = 6.1e-14
Identity = 34/72 (47.22%), Postives = 51/72 (70.83%), Query Frame = 0


Query: 5  EKVSKITSSFLTYLSINKAIDSLKFLGDVGNTDLNLLDRILPHCIIDQLMHIENSSKGRD 64
          E+++K   S L  L + KAID++K++G VG  D  LL++IL HC ++QL HIE+++   D
Sbjct: 4  ERLTKKPPS-LVDLCVRKAIDNVKYIGYVGGVDFQLLEQILQHCTLEQLKHIEDATDDTD 63

Query: 65 LTPLTDKLWKNF 77
          L+P+TDK WK F
Sbjct: 64 LSPITDKFWKGF 74

[Close]

BLAST of CaUC04G068260 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: 73.9 bits (180), Expect = 6.1e-14
Identity = 34/72 (47.22%), Postives = 51/72 (70.83%), Query Frame = 0


Query: 5  EKVSKITSSFLTYLSINKAIDSLKFLGDVGNTDLNLLDRILPHCIIDQLMHIENSSKGRD 64
          E+++K   S L  L + KAID++K++G VG  D  LL++IL HC ++QL HIE+++   D
Sbjct: 4  ERLTKKPPS-LVDLCVRKAIDNVKYIGYVGGVDFQLLEQILQHCTLEQLKHIEDATDDTD 63

Query: 65 LTPLTDKLWKNF 77
          L+P+TDK WK F
Sbjct: 64 LSPITDKFWKGF 74

The following BLAST results are available for this feature:

BLAST of CaUC04G068260 vs. NCBI nr


Match Name	E-value	Identity	Description
XP_038885873.1	7.6e-27	81.08	uncharacterized protein LOC120076176 [Benincasa hispida]	[more]
XP_038885879.1	1.0e-23	75.68	uncharacterized protein LOC120076185 [Benincasa hispida]	[more]
XP_038900478.1	9.1e-20	70.42	transcription elongation factor B polypeptide 3-like isoform X1 [Benincasa hispi...	[more]
XP_038900481.1	9.1e-20	70.42	transcription elongation factor B polypeptide 3-like isoform X2 [Benincasa hispi...	[more]
XP_004143189.1	1.2e-19	70.42	transcription elongation factor B polypeptide 3 isoform X1 [Cucumis sativus] >KA...	[more]

BLAST of CaUC04G068260 vs. NCBI nr


Match Name	E-value	Identity	Description

BLAST of CaUC04G068260 vs. ExPASy TrEMBL


Match Name	E-value	Identity	Description
A0A0A0KGZ5	5.7e-20	70.42	Uncharacterized protein OS=Cucumis sativus OX=3659 GN=Csa_6G169320 PE=4 SV=1	[more]
A0A5D3BGR1	2.8e-19	67.61	Transcription elongation factor B polypeptide 3 isoform X2 OS=Cucumis melo var. ...	[more]
A0A5A7ULV4	2.8e-19	67.61	Transcription elongation factor B polypeptide 3 isoform X2 OS=Cucumis melo var. ...	[more]
A0A1S4E1U0	2.8e-19	67.61	transcription elongation factor B polypeptide 3 isoform X2 OS=Cucumis melo OX=36...	[more]
A0A1S3C4D6	2.8e-19	67.61	transcription elongation factor B polypeptide 3 isoform X1 OS=Cucumis melo OX=36...	[more]

BLAST of CaUC04G068260 vs. TAIR 10


Match Name	E-value	Identity	Description
AT2G42780.1	6.1e-14	47.22	FUNCTIONS IN: molecular_function unknown; INVOLVED IN: regulation of transcripti...	[more]
AT2G42780.2	6.1e-14	47.22	FUNCTIONS IN: molecular_function unknown; INVOLVED IN: regulation of transcripti...	[more]

InterPro

Analysis Name: InterPro Annotations of Watermelon (USVL246-FR2) v1
Date Performed: 2022-01-31


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
IPR010684	RNA polymerase II transcription factor SIII, subunit A	PFAM	PF06881	Elongin_A	coord: 31..76 e-value: 2.5E-10 score: 40.8
None	No IPR available	GENE3D	6.10.250.3180		coord: 26..76 e-value: 2.5E-10 score: 42.4
None	No IPR available	PANTHER	PTHR47543	OS08G0169600 PROTEIN	coord: 6..76

Relationships

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


Feature Name	Unique Name	Type
CaUC04G068260.1	CaUC04G068260.1	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