CmoCh06G000220 (gene) Cucurbita moschata (Rifu) v1

Overview


Name	CmoCh06G000220
Type	gene
Organism	Cucurbita moschata (Cucurbita moschata (Rifu) v1)
Description	sigma factor binding protein 2, chloroplastic-like
Location	Cmo_Chr06: 145392 .. 145778 (+)
RNA-Seq Expression	CmoCh06G000220
Synteny	CmoCh06G000220

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.

ATGGAATCGAGTTTAGTTGGGAGGGACGTGGAAGAGGGGAGGAAAGAAAGGAGAAGGAACAGGAAACCCTGTGATCGGAAGAACCAACCTCTCAAAGTTGTGTACATATCCAACCCCATGAGGGTTCAAGCCAGTGCGGCTGAGTTTAGAGGCCTGGTTCAAGAACTCACCGGCCAAGATGCGCCCAAGTTTCCTCCTTCCGCCTCCTCGGCCTCCGTCCAGACTCCGGAGACTAATGTTCGAAAGATACAAGACGACGACGACGACGAACAACTCTTACTTCACTGGGCTGCAATGGAGGATTCCAGTGATGGTTTTCTTGGGGGTTCGTATGAGAGCTCGGAGGGTATTTTCATGAGGGATATGGTGGACAAATTGGCGGCTTGA

mRNA sequence

ATGGAATCGAGTTTAGTTGGGAGGGACGTGGAAGAGGGGAGGAAAGAAAGGAGAAGGAACAGGAAACCCTGTGATCGGAAGAACCAACCTCTCAAAGTTGTGTACATATCCAACCCCATGAGGGTTCAAGCCAGTGCGGCTGAGTTTAGAGGCCTGGTTCAAGAACTCACCGGCCAAGATGCGCCCAAGTTTCCTCCTTCCGCCTCCTCGGCCTCCGTCCAGACTCCGGAGACTAATGTTCGAAAGATACAAGACGACGACGACGACGAACAACTCTTACTTCACTGGGCTGCAATGGAGGATTCCAGTGATGGTTTTCTTGGGGGTTCGTATGAGAGCTCGGAGGGTATTTTCATGAGGGATATGGTGGACAAATTGGCGGCTTGA

Coding sequence (CDS)

ATGGAATCGAGTTTAGTTGGGAGGGACGTGGAAGAGGGGAGGAAAGAAAGGAGAAGGAACAGGAAACCCTGTGATCGGAAGAACCAACCTCTCAAAGTTGTGTACATATCCAACCCCATGAGGGTTCAAGCCAGTGCGGCTGAGTTTAGAGGCCTGGTTCAAGAACTCACCGGCCAAGATGCGCCCAAGTTTCCTCCTTCCGCCTCCTCGGCCTCCGTCCAGACTCCGGAGACTAATGTTCGAAAGATACAAGACGACGACGACGACGAACAACTCTTACTTCACTGGGCTGCAATGGAGGATTCCAGTGATGGTTTTCTTGGGGGTTCGTATGAGAGCTCGGAGGGTATTTTCATGAGGGATATGGTGGACAAATTGGCGGCTTGA

Protein sequence

MESSLVGRDVEEGRKERRRNRKPCDRKNQPLKVVYISNPMRVQASAAEFRGLVQELTGQDAPKFPPSASSASVQTPETNVRKIQDDDDDEQLLLHWAAMEDSSDGFLGGSYESSEGIFMRDMVDKLAA

Homology

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BLAST of CmoCh06G000220 vs. ExPASy Swiss-Prot
Match: Q9LDH1 (Sigma factor binding protein 1, chloroplastic OS=Arabidopsis thaliana OX=3702 GN=SIB1 PE=1 SV=1)

HSP 1 Score: 59.3 bits (142), Expect = 3.7e-08
Identity = 32/68 (47.06%), Postives = 43/68 (63.24%), Query Frame = 0


Query: 19 RNRKPCDRKNQPLKVVYISNPMRVQASAAEFRGLVQELTGQDA------PKFPPSASSAS 78
          + +K     N+P+KV YISNPMRVQ  A++FR LVQELTGQDA      P + PS+   +
Sbjct: 28 KQKKKTTSTNKPIKVRYISNPMRVQTCASKFRELVQELTGQDAVDLQPEPIYSPSSDDHN 87

Query: 79 VQTPETNV 81
          +  P  N+
Sbjct: 88 LSPPAENL 95

[Close]

BLAST of CmoCh06G000220 vs. ExPASy Swiss-Prot
Match: O80669 (Sigma factor binding protein 2, chloroplastic OS=Arabidopsis thaliana OX=3702 GN=SIB2 PE=1 SV=1)

HSP 1 Score: 55.5 bits (132), Expect = 5.3e-07
Identity = 26/52 (50.00%), Postives = 37/52 (71.15%), Query Frame = 0


Query: 19 RNRKPCDRKNQPLKVVYISNPMRVQASAAEFRGLVQELTGQDAPKFPPSASS 71
          + ++     ++P+KV YISNPMRV+   ++FR LVQELTGQDA   PPS ++
Sbjct: 25 KQKRKSTTTHKPIKVRYISNPMRVETCPSKFRELVQELTGQDAADLPPSPTT 76

[Close]

BLAST of CmoCh06G000220 vs. ExPASy TrEMBL
Match: A0A6J1FKR4 (uncharacterized protein LOC111446639 OS=Cucurbita moschata OX=3662 GN=LOC111446639 PE=4 SV=1)

HSP 1 Score: 251.9 bits (642), Expect = 1.4e-63
Identity = 128/128 (100.00%), Postives = 128/128 (100.00%), Query Frame = 0


Query: 1   MESSLVGRDVEEGRKERRRNRKPCDRKNQPLKVVYISNPMRVQASAAEFRGLVQELTGQD 60
           MESSLVGRDVEEGRKERRRNRKPCDRKNQPLKVVYISNPMRVQASAAEFRGLVQELTGQD
Sbjct: 1   MESSLVGRDVEEGRKERRRNRKPCDRKNQPLKVVYISNPMRVQASAAEFRGLVQELTGQD 60

Query: 61  APKFPPSASSASVQTPETNVRKIQDDDDDEQLLLHWAAMEDSSDGFLGGSYESSEGIFMR 120
           APKFPPSASSASVQTPETNVRKIQDDDDDEQLLLHWAAMEDSSDGFLGGSYESSEGIFMR
Sbjct: 61  APKFPPSASSASVQTPETNVRKIQDDDDDEQLLLHWAAMEDSSDGFLGGSYESSEGIFMR 120

Query: 121 DMVDKLAA 129
           DMVDKLAA
Sbjct: 121 DMVDKLAA 128

[Close]

BLAST of CmoCh06G000220 vs. ExPASy TrEMBL
Match: A0A6J1D137 (sigma factor binding protein 2, chloroplastic-like OS=Momordica charantia OX=3673 GN=LOC111016633 PE=4 SV=1)

HSP 1 Score: 104.8 bits (260), Expect = 2.8e-19
Identity = 66/126 (52.38%), Postives = 86/126 (68.25%), Query Frame = 0


Query: 1   MESSLVGRDVEEGRKERRRNRKPCDRKNQPLKVVYISNPMRVQASAAEFRGLVQELTGQD 60
           M+ +L+  ++E  +KE R+ RK   +KNQPLKVVYISNPMRV  SA+EFR LVQELTG+D
Sbjct: 1   MDRNLIVSEMEPMKKETRK-RKLSVQKNQPLKVVYISNPMRVHTSASEFRALVQELTGRD 60

Query: 61  APKFPPSAS--SASVQTPETNVRKIQDDDDDEQLLLHWA-AMEDSSDGFLGGSYESSEGI 120
           A +FP  A    AS+   E N+ K ++ DDDE+  L  A  MEDS+D FL   YES E +
Sbjct: 61  A-EFPDPAKFHQASIDVGEMNLEKNREGDDDEEASLDVATTMEDSNDDFLESPYESFEEM 120

Query: 121 FMRDMV 124
            MR+M+
Sbjct: 121 LMREML 124

[Close]

BLAST of CmoCh06G000220 vs. ExPASy TrEMBL
Match: A0A5D3DPQ4 (Sigma factor binding protein 2 OS=Cucumis melo var. makuwa OX=1194695 GN=E5676_scaffold352G006730 PE=4 SV=1)

HSP 1 Score: 87.8 bits (216), Expect = 3.5e-14
Identity = 56/122 (45.90%), Postives = 73/122 (59.84%), Query Frame = 0


Query: 14  RKERRRNRKPCDRKNQPLKVVYISNPMRVQASAAEFRGLVQELTGQDA-----PKFPPSA 73
           +K+  R RK C+   QPLKVVYISNPMRV  SA+EFR LVQELTG+DA      KF P++
Sbjct: 17  KKKTTRKRKSCEENKQPLKVVYISNPMRVHTSASEFRALVQELTGRDAEFPDPSKFYPAS 76

Query: 74  SSASVQTPETNVRKIQDDDDDEQLLLHWAAMEDSS--DGFLGGSYESSEGIFMRDMVDKL 129
               +   E  V   Q +DD+++LL+      DSS  D F   S+ES E I  RD+++  
Sbjct: 77  CEIVMNDLEKKVVADQGEDDEQELLI------DSSCDDDFWRSSFESLEDILRRDVMENF 132

[Close]

BLAST of CmoCh06G000220 vs. ExPASy TrEMBL
Match: A0A1S3B8H6 (uncharacterized protein LOC103487167 OS=Cucumis melo OX=3656 GN=LOC103487167 PE=4 SV=1)

HSP 1 Score: 87.8 bits (216), Expect = 3.5e-14
Identity = 56/122 (45.90%), Postives = 73/122 (59.84%), Query Frame = 0


Query: 14  RKERRRNRKPCDRKNQPLKVVYISNPMRVQASAAEFRGLVQELTGQDA-----PKFPPSA 73
           +K+  R RK C+   QPLKVVYISNPMRV  SA+EFR LVQELTG+DA      KF P++
Sbjct: 17  KKKTTRKRKSCEENKQPLKVVYISNPMRVHTSASEFRALVQELTGRDAEFPDPSKFYPAS 76

Query: 74  SSASVQTPETNVRKIQDDDDDEQLLLHWAAMEDSS--DGFLGGSYESSEGIFMRDMVDKL 129
               +   E  V   Q +DD+++LL+      DSS  D F   S+ES E I  RD+++  
Sbjct: 77  CEIVMNDLEKKVVADQGEDDEQELLI------DSSCDDDFWRSSFESLEDILRRDVMENF 132

[Close]

BLAST of CmoCh06G000220 vs. ExPASy TrEMBL
Match: A0A0A0LFH5 (VQ domain-containing protein OS=Cucumis sativus OX=3659 GN=Csa_3G820480 PE=4 SV=1)

HSP 1 Score: 87.4 bits (215), Expect = 4.6e-14
Identity = 57/120 (47.50%), Postives = 74/120 (61.67%), Query Frame = 0


Query: 19  RNRKPCDRKNQPLKVVYISNPMRVQASAAEFRGLVQELTGQDA-----PKFPPSASSASV 78
           R RK C+   QPLKVVYISNPMRV  SA+EFR LVQELTG+DA      KF P ASS  +
Sbjct: 22  RKRKSCEENKQPLKVVYISNPMRVHTSASEFRALVQELTGRDAEFPDPTKFYP-ASSCEI 81

Query: 79  QTPETNVRKI---QDDDDDEQLLLHWAAMEDSS--DGFLGGSYESSEGIFMRDMVDKLAA 129
              +   +K+   + ++D+++LL+      DSS  D FL  SYES E I  RD+++   A
Sbjct: 82  MNDDDVEKKVVAAEGEEDEQELLI------DSSCDDDFLRSSYESLEDILRRDVMENFGA 134

[Close]

BLAST of CmoCh06G000220 vs. TAIR 10
Match: AT3G56710.1 (sigma factor binding protein 1 )

HSP 1 Score: 59.3 bits (142), Expect = 2.6e-09
Identity = 32/68 (47.06%), Postives = 43/68 (63.24%), Query Frame = 0


Query: 19 RNRKPCDRKNQPLKVVYISNPMRVQASAAEFRGLVQELTGQDA------PKFPPSASSAS 78
          + +K     N+P+KV YISNPMRVQ  A++FR LVQELTGQDA      P + PS+   +
Sbjct: 28 KQKKKTTSTNKPIKVRYISNPMRVQTCASKFRELVQELTGQDAVDLQPEPIYSPSSDDHN 87

Query: 79 VQTPETNV 81
          +  P  N+
Sbjct: 88 LSPPAENL 95

[Close]

BLAST of CmoCh06G000220 vs. TAIR 10
Match: AT2G41180.1 (VQ motif-containing protein )

HSP 1 Score: 55.5 bits (132), Expect = 3.8e-08
Identity = 26/52 (50.00%), Postives = 37/52 (71.15%), Query Frame = 0


Query: 19 RNRKPCDRKNQPLKVVYISNPMRVQASAAEFRGLVQELTGQDAPKFPPSASS 71
          + ++     ++P+KV YISNPMRV+   ++FR LVQELTGQDA   PPS ++
Sbjct: 25 KQKRKSTTTHKPIKVRYISNPMRVETCPSKFRELVQELTGQDAADLPPSPTT 76

The following BLAST results are available for this feature:

BLAST of CmoCh06G000220 vs. ExPASy Swiss-Prot


Match Name	E-value	Identity	Description
Q9LDH1	3.7e-08	47.06	Sigma factor binding protein 1, chloroplastic OS=Arabidopsis thaliana OX=3702 GN...	[more]
O80669	5.3e-07	50.00	Sigma factor binding protein 2, chloroplastic OS=Arabidopsis thaliana OX=3702 GN...	[more]

BLAST of CmoCh06G000220 vs. ExPASy TrEMBL


Match Name	E-value	Identity	Description
A0A6J1FKR4	1.4e-63	100.00	uncharacterized protein LOC111446639 OS=Cucurbita moschata OX=3662 GN=LOC1114466...	[more]
A0A6J1D137	2.8e-19	52.38	sigma factor binding protein 2, chloroplastic-like OS=Momordica charantia OX=367...	[more]
A0A5D3DPQ4	3.5e-14	45.90	Sigma factor binding protein 2 OS=Cucumis melo var. makuwa OX=1194695 GN=E5676_s...	[more]
A0A1S3B8H6	3.5e-14	45.90	uncharacterized protein LOC103487167 OS=Cucumis melo OX=3656 GN=LOC103487167 PE=...	[more]
A0A0A0LFH5	4.6e-14	47.50	VQ domain-containing protein OS=Cucumis sativus OX=3659 GN=Csa_3G820480 PE=4 SV=...	[more]

BLAST of CmoCh06G000220 vs. TAIR 10


Match Name	E-value	Identity	Description
AT3G56710.1	2.6e-09	47.06	sigma factor binding protein 1	[more]
AT2G41180.1	3.8e-08	50.00	VQ motif-containing protein	[more]

InterPro

Analysis Name: InterPro Annotations of Cucurbita moschata (Rifu) v1
Date Performed: 2021-10-25

Position :

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IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
IPR008889	VQ	PFAM	PF05678	VQ	coord: 36..62 e-value: 1.2E-10 score: 40.7
None	No IPR available	MOBIDB_LITE	mobidb-lite	disorder_prediction	coord: 58..84
None	No IPR available	MOBIDB_LITE	mobidb-lite	disorder_prediction	coord: 63..79
None	No IPR available	MOBIDB_LITE	mobidb-lite	disorder_prediction	coord: 1..30
None	No IPR available	MOBIDB_LITE	mobidb-lite	disorder_prediction	coord: 1..19
None	No IPR available	PANTHER	PTHR33624:SF2	SIGMA FACTOR BINDING PROTEIN 1, CHLOROPLASTIC	coord: 14..125
IPR039335	Sigma factor binding protein 1/2	PANTHER	PTHR33624	SIGMA FACTOR BINDING PROTEIN 1, CHLOROPLASTIC	coord: 14..125

Relationships

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


Feature Name	Unique Name	Type
CmoCh06G000220.1	CmoCh06G000220.1	mRNA

GO Annotation

GO Assignments

This gene is annotated with the following GO terms.

Category	Term Accession	Term Name
biological_process	GO:0051091	positive regulation of DNA-binding transcription factor activity