Carg03028-RA (mRNA) Silver-seed gourd | Cucurbit Genomics Database (CuGenDB)

Overview


Name	Carg03028-RA
Type	mRNA
Organism	Cucurbita argyrosperma (Silver-seed gourd)
Description	50S ribosomal protein 6, chloroplastic
Location	Cucurbita_argyrosperma_scaffold_008 : 1456680 .. 1457003 (-)
Sequence length	324

Genome Viewer

Sequences

The following sequences are available for this feature:

Gene sequence (with intron)

Legend: polypeptideCDSexon

Hold the cursor over a type above to highlight its positions in the sequence below.

ATGTCGATTTCCACCTTTTTCGGCGGTAGGATTTCGGTTCCGCCATTGTTGAATTCATCGGCAAGCAAAACAGCTCCATGCTCCGGCGGGAATTTGGTGATTGAATGCTCGTCGAGGCCAAGCAAGAAGGCGACTGCACATCACATGAAAACGAGGCCACGGAAATCTCAGCCATGGGACATTCGGCGCAAGCCGACTGTATATCCTCCTCTGCCGCCTCTTCCACCGGACTGGACCGTGGTTTCATCAATCTCCAGCGATGAAATTGTCGAGGTAGCCGCTTCGAGTGCTTCGTCTGCTCAAGCACCGCCTACGACCGAGTAA

mRNA sequence

ATGTCGATTTCCACCTTTTTCGGCGGTAGGATTTCGGTTCCGCCATTGTTGAATTCATCGGCAAGCAAAACAGCTCCATGCTCCGGCGGGAATTTGGTGATTGAATGCTCGTCGAGGCCAAGCAAGAAGGCGACTGCACATCACATGAAAACGAGGCCACGGAAATCTCAGCCATGGGACATTCGGCGCAAGCCGACTGTATATCCTCCTCTGCCGCCTCTTCCACCGGACTGGACCGTGGTTTCATCAATCTCCAGCGATGAAATTGTCGAGGTAGCCGCTTCGAGTGCTTCGTCTGCTCAAGCACCGCCTACGACCGAGTAA

Coding sequence (CDS)

ATGTCGATTTCCACCTTTTTCGGCGGTAGGATTTCGGTTCCGCCATTGTTGAATTCATCGGCAAGCAAAACAGCTCCATGCTCCGGCGGGAATTTGGTGATTGAATGCTCGTCGAGGCCAAGCAAGAAGGCGACTGCACATCACATGAAAACGAGGCCACGGAAATCTCAGCCATGGGACATTCGGCGCAAGCCGACTGTATATCCTCCTCTGCCGCCTCTTCCACCGGACTGGACCGTGGTTTCATCAATCTCCAGCGATGAAATTGTCGAGGTAGCCGCTTCGAGTGCTTCGTCTGCTCAAGCACCGCCTACGACCGAGTAA

Protein sequence

MSISTFFGGRISVPPLLNSSASKTAPCSGGNLVIECSSRPSKKATAHHMKTRPRKSQPWDIRRKPTVYPPLPPLPPDWTVVSSISSDEIVEVAASSASSAQAPPTTE

Homology

[Close]

BLAST of Carg03028-RA vs. NCBI nr
Match: XP_023536142.1 (50S ribosomal protein 6, chloroplastic-like [Cucurbita pepo subsp. pepo])

HSP 1 Score: 144.8 bits (364), Expect = 1.7e-31
Identity = 70/71 (98.59%), Postives = 71/71 (100.00%), Query Frame = 0


Query: 1  MSISTFFGGRISVPPLLNSSASKTAPCSGGNLVIECSSRPSKKATAHHMKTRPRKSQPWD 60
          MSISTFFGGRISVPPLLNSSASKTAPCSGGNLVIECSSRP+KKATAHHMKTRPRKSQPWD
Sbjct: 1  MSISTFFGGRISVPPLLNSSASKTAPCSGGNLVIECSSRPNKKATAHHMKTRPRKSQPWD 60

Query: 61 IRRKPTVYPPL 72
          IRRKPTVYPPL
Sbjct: 61 IRRKPTVYPPL 71

[Close]

BLAST of Carg03028-RA vs. NCBI nr
Match: XP_022936242.1 (50S ribosomal protein 6, chloroplastic-like [Cucurbita moschata])

HSP 1 Score: 143.7 bits (361), Expect = 3.7e-31
Identity = 69/71 (97.18%), Postives = 71/71 (100.00%), Query Frame = 0


Query: 1  MSISTFFGGRISVPPLLNSSASKTAPCSGGNLVIECSSRPSKKATAHHMKTRPRKSQPWD 60
          MSIST+FGGRISVPPLLNSSASKTAPCSGGNLVIECSSRP+KKATAHHMKTRPRKSQPWD
Sbjct: 1  MSISTYFGGRISVPPLLNSSASKTAPCSGGNLVIECSSRPNKKATAHHMKTRPRKSQPWD 60

Query: 61 IRRKPTVYPPL 72
          IRRKPTVYPPL
Sbjct: 61 IRRKPTVYPPL 71

[Close]

BLAST of Carg03028-RA vs. NCBI nr
Match: XP_022975752.1 (50S ribosomal protein 6, chloroplastic [Cucurbita maxima])

HSP 1 Score: 141.7 bits (356), Expect = 1.4e-30
Identity = 69/71 (97.18%), Postives = 70/71 (98.59%), Query Frame = 0


Query: 1  MSISTFFGGRISVPPLLNSSASKTAPCSGGNLVIECSSRPSKKATAHHMKTRPRKSQPWD 60
          MSISTF GGRISVPPLLNSSASKTAPCSGGNLVIECSSRP+KKATAHHMKTRPRKSQPWD
Sbjct: 1  MSISTFSGGRISVPPLLNSSASKTAPCSGGNLVIECSSRPNKKATAHHMKTRPRKSQPWD 60

Query: 61 IRRKPTVYPPL 72
          IRRKPTVYPPL
Sbjct: 61 IRRKPTVYPPL 71

[Close]

BLAST of Carg03028-RA vs. NCBI nr
Match: XP_008466097.1 (PREDICTED: 50S ribosomal protein 6, chloroplastic [Cucumis melo])

HSP 1 Score: 132.5 bits (332), Expect = 8.5e-28
Identity = 64/71 (90.14%), Postives = 67/71 (94.37%), Query Frame = 0


Query: 1  MSISTFFGGRISVPPLLNSSASKTAPCSGGNLVIECSSRPSKKATAHHMKTRPRKSQPWD 60
          MSISTF G +ISVPPLLNSSASK APCSGGNL IECSSRP+KKATAHHMKTRP+KSQPWD
Sbjct: 1  MSISTFLGCKISVPPLLNSSASKAAPCSGGNLPIECSSRPNKKATAHHMKTRPKKSQPWD 60

Query: 61 IRRKPTVYPPL 72
          IRRKPTVYPPL
Sbjct: 61 IRRKPTVYPPL 71

[Close]

BLAST of Carg03028-RA vs. NCBI nr
Match: XP_011652886.1 (PREDICTED: 50S ribosomal protein 6, chloroplastic [Cucumis sativus] >KGN60302.1 hypothetical protein Csa_3G894500 [Cucumis sativus])

HSP 1 Score: 132.5 bits (332), Expect = 8.5e-28
Identity = 64/71 (90.14%), Postives = 67/71 (94.37%), Query Frame = 0


Query: 1  MSISTFFGGRISVPPLLNSSASKTAPCSGGNLVIECSSRPSKKATAHHMKTRPRKSQPWD 60
          MSISTF G +ISVPPLLNSSASK APCS GNL+IECSSRP+KKATAHHMKTRPRKSQPWD
Sbjct: 1  MSISTFLGCKISVPPLLNSSASKAAPCSAGNLLIECSSRPNKKATAHHMKTRPRKSQPWD 60

Query: 61 IRRKPTVYPPL 72
          IRRKPTVYPPL
Sbjct: 61 IRRKPTVYPPL 71

[Close]

BLAST of Carg03028-RA vs. TAIR10
Match: AT5G17870.1 (plastid-specific 50S ribosomal protein 6)

HSP 1 Score: 79.3 bits (194), Expect = 1.6e-15
Identity = 43/75 (57.33%), Postives = 51/75 (68.00%), Query Frame = 0


Query: 1  MSISTFFG-GRISV---PPLLNSSASKTAPCSGGNLVIECSSRPSKKATAHHMKTRPRKS 60
          MS+S  FG G ++V   P L      K     G  +VIECSSRP KK+TAHH KTRP+K+
Sbjct: 1  MSVSAIFGTGIVTVAASPVLRQFQVPKLGNGGGLGMVIECSSRPQKKSTAHHRKTRPKKT 60

Query: 61 QPWDIRRKPTVYPPL 72
          QPWDI+RKPTVY PL
Sbjct: 61 QPWDIKRKPTVYAPL 75

[Close]

BLAST of Carg03028-RA vs. Swiss-Prot
Match: sp|P82411|PSRP6_SPIOL (50S ribosomal protein 6, chloroplastic OS=Spinacia oleracea OX=3562 GN=PSRP6 PE=1 SV=1)

HSP 1 Score: 81.6 bits (200), Expect = 5.7e-15
Identity = 42/82 (51.22%), Postives = 53/82 (64.63%), Query Frame = 0


Query: 1  MSISTFFGGR-ISVPPLLNSSA----------SKTAPCSGGNLVIECSSRPSKKATAHHM 60
          MS+S  FG R +++P +L +S+          S    C GG + IECSSRP KK TAHHM
Sbjct: 1  MSVSAIFGARVVTIPSVLRTSSVDGRTVKLQPSTGGSCGGGVITIECSSRPQKKGTAHHM 60

Query: 61 KTRPRKSQPWDIRRKPTVYPPL 72
          KTRP+K+  WDI+R P VYPPL
Sbjct: 61 KTRPKKTARWDIKRGPAVYPPL 82

[Close]

BLAST of Carg03028-RA vs. Swiss-Prot
Match: sp|Q9FKP0|PSRP6_ARATH (50S ribosomal protein 6, chloroplastic OS=Arabidopsis thaliana OX=3702 GN=PSRP6 PE=3 SV=1)

HSP 1 Score: 79.3 bits (194), Expect = 2.8e-14
Identity = 43/75 (57.33%), Postives = 51/75 (68.00%), Query Frame = 0


Query: 1  MSISTFFG-GRISV---PPLLNSSASKTAPCSGGNLVIECSSRPSKKATAHHMKTRPRKS 60
          MS+S  FG G ++V   P L      K     G  +VIECSSRP KK+TAHH KTRP+K+
Sbjct: 1  MSVSAIFGTGIVTVAASPVLRQFQVPKLGNGGGLGMVIECSSRPQKKSTAHHRKTRPKKT 60

Query: 61 QPWDIRRKPTVYPPL 72
          QPWDI+RKPTVY PL
Sbjct: 61 QPWDIKRKPTVYAPL 75

[Close]

BLAST of Carg03028-RA vs. Swiss-Prot
Match: sp|P11892|PSRP6_PEA (50S ribosomal protein 6, chloroplastic OS=Pisum sativum OX=3888 GN=PSRP6 PE=3 SV=1)

HSP 1 Score: 71.6 bits (174), Expect = 5.9e-12
Identity = 40/73 (54.79%), Postives = 49/73 (67.12%), Query Frame = 0


Query: 2  SISTFFGGRISVPP---LLNSSASKTAPCSGGNLVIECSSRPSKKATAHHMKTRPRKSQP 61
          S+S+ FG  +S+ P   L N +       + G L+IECSSRP KK+TAHHMKTRPRKS+ 
Sbjct: 3  SVSSIFGCGVSMAPNSSLRNKAIRTERRSACGGLLIECSSRPQKKSTAHHMKTRPRKSRL 62

Query: 62 WDIRRKPTVYPPL 72
           D  RKPTVY PL
Sbjct: 63 SDRNRKPTVYAPL 75

[Close]

BLAST of Carg03028-RA vs. TrEMBL
Match: tr|A0A1S3CQF4|A0A1S3CQF4_CUCME (50S ribosomal protein 6, chloroplastic OS=Cucumis melo OX=3656 GN=LOC103503622 PE=4 SV=1)

HSP 1 Score: 132.5 bits (332), Expect = 5.7e-28
Identity = 64/71 (90.14%), Postives = 67/71 (94.37%), Query Frame = 0


Query: 1  MSISTFFGGRISVPPLLNSSASKTAPCSGGNLVIECSSRPSKKATAHHMKTRPRKSQPWD 60
          MSISTF G +ISVPPLLNSSASK APCSGGNL IECSSRP+KKATAHHMKTRP+KSQPWD
Sbjct: 1  MSISTFLGCKISVPPLLNSSASKAAPCSGGNLPIECSSRPNKKATAHHMKTRPKKSQPWD 60

Query: 61 IRRKPTVYPPL 72
          IRRKPTVYPPL
Sbjct: 61 IRRKPTVYPPL 71

[Close]

BLAST of Carg03028-RA vs. TrEMBL
Match: tr|A0A0A0LHS7|A0A0A0LHS7_CUCSA (Uncharacterized protein OS=Cucumis sativus OX=3659 GN=Csa_3G894500 PE=4 SV=1)

HSP 1 Score: 132.5 bits (332), Expect = 5.7e-28
Identity = 64/71 (90.14%), Postives = 67/71 (94.37%), Query Frame = 0


Query: 1  MSISTFFGGRISVPPLLNSSASKTAPCSGGNLVIECSSRPSKKATAHHMKTRPRKSQPWD 60
          MSISTF G +ISVPPLLNSSASK APCS GNL+IECSSRP+KKATAHHMKTRPRKSQPWD
Sbjct: 1  MSISTFLGCKISVPPLLNSSASKAAPCSAGNLLIECSSRPNKKATAHHMKTRPRKSQPWD 60

Query: 61 IRRKPTVYPPL 72
          IRRKPTVYPPL
Sbjct: 61 IRRKPTVYPPL 71

[Close]

BLAST of Carg03028-RA vs. TrEMBL
Match: tr|A0A1U7ZDX7|A0A1U7ZDX7_NELNU (50S ribosomal protein 6, chloroplastic OS=Nelumbo nucifera OX=4432 GN=LOC104589113 PE=4 SV=1)

HSP 1 Score: 92.4 bits (228), Expect = 6.5e-16
Identity = 46/72 (63.89%), Postives = 53/72 (73.61%), Query Frame = 0


Query: 1  MSISTFFGGRISVP-PLLNSSASKTAPCSGGNLVIECSSRPSKKATAHHMKTRPRKSQPW 60
          MS+S  FG R+ VP   L   A K     G  +VIECSSRP KKATAHHMKTRP+K+QPW
Sbjct: 1  MSVSALFGTRVMVPNKSLAVGAPKGGRAGGMGMVIECSSRPKKKATAHHMKTRPKKTQPW 60

Query: 61 DIRRKPTVYPPL 72
          D+RR+PTVYPPL
Sbjct: 61 DVRRRPTVYPPL 72

[Close]

BLAST of Carg03028-RA vs. TrEMBL
Match: tr|A0A2R6QY39|A0A2R6QY39_ACTCH (50S ribosomal protein like OS=Actinidia chinensis var. chinensis OX=1590841 GN=CEY00_Acc12104 PE=4 SV=1)

HSP 1 Score: 90.5 bits (223), Expect = 2.5e-15
Identity = 52/83 (62.65%), Postives = 56/83 (67.47%), Query Frame = 0


Query: 1  MSISTFFGGRISV---PPLLNSS------ASKTAP---CSGGNLVIECSSRPSKKATAHH 60
          MS+S  FG ++     PP L SS      A K  P     GG LVIECSSRP KKATAHH
Sbjct: 1  MSVSAVFGPKMVTLPNPPSLTSSRFRYGGAIKAVPRIDGCGGGLVIECSSRPQKKATAHH 60

Query: 61 MKTRPRKSQPWDIRRKPTVYPPL 72
          MKTRPRK+QPWDIRRKP VYPPL
Sbjct: 61 MKTRPRKTQPWDIRRKPAVYPPL 83

[Close]

BLAST of Carg03028-RA vs. TrEMBL
Match: tr|V4SGY3|V4SGY3_9ROSI (Uncharacterized protein OS=Citrus clementina OX=85681 GN=CICLE_v10002778mg PE=4 SV=1)

HSP 1 Score: 90.1 bits (222), Expect = 3.2e-15
Identity = 47/71 (66.20%), Postives = 52/71 (73.24%), Query Frame = 0


Query: 1   MSISTFFGGRISVPPLLNSSASKTAPCSGGNLVIECSSRPSKKATAHHMKTRPRKSQPWD 60
           MSIS+FFG +I V P L+S            LVIE SSRP KKATAHHMKTRPRK+QPWD
Sbjct: 39  MSISSFFGSQIVVVPNLSSKKLGVEGKCNVGLVIENSSRPQKKATAHHMKTRPRKTQPWD 98

Query: 61  IRRKPTVYPPL 72
           + RKPTVYPPL
Sbjct: 99  VNRKPTVYPPL 109

The following BLAST results are available for this feature:

BLAST of Carg03028-RA vs. NCBI nr


Match Name	E-value	Identity	Description
XP_023536142.1	1.7e-31	98.59	50S ribosomal protein 6, chloroplastic-like [Cucurbita pepo subsp. pepo]	[more]
XP_022936242.1	3.7e-31	97.18	50S ribosomal protein 6, chloroplastic-like [Cucurbita moschata]	[more]
XP_022975752.1	1.4e-30	97.18	50S ribosomal protein 6, chloroplastic [Cucurbita maxima]	[more]
XP_008466097.1	8.5e-28	90.14	PREDICTED: 50S ribosomal protein 6, chloroplastic [Cucumis melo]	[more]
XP_011652886.1	8.5e-28	90.14	PREDICTED: 50S ribosomal protein 6, chloroplastic [Cucumis sativus] >KGN60302.1 ...	[more]

BLAST of Carg03028-RA vs. TAIR10


Match Name	E-value	Identity	Description
AT5G17870.1	1.6e-15	57.33	plastid-specific 50S ribosomal protein 6	[more]

BLAST of Carg03028-RA vs. Swiss-Prot


Match Name	E-value	Identity	Description
sp\|P82411\|PSRP6_SPIOL	5.7e-15	51.22	50S ribosomal protein 6, chloroplastic OS=Spinacia oleracea OX=3562 GN=PSRP6 PE=...	[more]
sp\|Q9FKP0\|PSRP6_ARATH	2.8e-14	57.33	50S ribosomal protein 6, chloroplastic OS=Arabidopsis thaliana OX=3702 GN=PSRP6 ...	[more]
sp\|P11892\|PSRP6_PEA	5.9e-12	54.79	50S ribosomal protein 6, chloroplastic OS=Pisum sativum OX=3888 GN=PSRP6 PE=3 SV...	[more]

BLAST of Carg03028-RA vs. TrEMBL


Match Name	E-value	Identity	Description
tr\|A0A1S3CQF4\|A0A1S3CQF4_CUCME	5.7e-28	90.14	50S ribosomal protein 6, chloroplastic OS=Cucumis melo OX=3656 GN=LOC103503622 P...	[more]
tr\|A0A0A0LHS7\|A0A0A0LHS7_CUCSA	5.7e-28	90.14	Uncharacterized protein OS=Cucumis sativus OX=3659 GN=Csa_3G894500 PE=4 SV=1	[more]
tr\|A0A1U7ZDX7\|A0A1U7ZDX7_NELNU	6.5e-16	63.89	50S ribosomal protein 6, chloroplastic OS=Nelumbo nucifera OX=4432 GN=LOC1045891...	[more]
tr\|A0A2R6QY39\|A0A2R6QY39_ACTCH	2.5e-15	62.65	50S ribosomal protein like OS=Actinidia chinensis var. chinensis OX=1590841 GN=C...	[more]
tr\|V4SGY3\|V4SGY3_9ROSI	3.2e-15	66.20	Uncharacterized protein OS=Citrus clementina OX=85681 GN=CICLE_v10002778mg PE=4 ...	[more]

Annotated Terms

The following terms have been associated with this mRNA:

Vocabulary: **Molecular Function**
Term	Definition
GO:0019843	rRNA binding
GO:0003735	structural constituent of ribosome

Vocabulary: **Cellular Component**
Term	Definition
GO:0009507	chloroplast
GO:0005840	ribosome

Vocabulary: **Biological Process**
Term	Definition
GO:0006412	translation

Vocabulary: **INTERPRO**
Term	Definition
IPR020526	Ribosomal_L6_chp

GO Annotation

GO Assignments

This mRNA is annotated with the following GO terms.

Category	Term Accession	Term Name
biological_process	GO:0006412	translation
biological_process	GO:0042254	ribosome biogenesis
cellular_component	GO:0009507	chloroplast
cellular_component	GO:0005840	ribosome
molecular_function	GO:0019843	rRNA binding
molecular_function	GO:0003735	structural constituent of ribosome

Relationships

This mRNA is a part of the following gene feature(s):


Feature Name	Unique Name	Type
Carg03028	Carg03028	gene

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


Feature Name	Unique Name	Type
Carg03028-RA.CDS.1	Carg03028-RA.CDS.1	CDS

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


Feature Name	Unique Name	Type
Carg03028-RA.exon.1	Carg03028-RA.exon.1	exon

The following polypeptide feature(s) derives from this mRNA:


Feature Name	Unique Name	Type
Carg03028-RA	Carg03028-RA-protein	polypeptide

InterPro

Analysis Name: InterPro Annotations of silver-seed gourd
Date Performed: 2019-03-07


IPR Term	IPR Description	Source	Source Term	Source Description	Alignment
IPR020526	Ribosomal protein L6, chloroplast	PFAM	PF17257	DUF5323	coord: 28..86 e-value: 9.5E-37 score: 124.6
IPR020526	Ribosomal protein L6, chloroplast	PANTHER	PTHR36798	FAMILY NOT NAMED	coord: 19..90
IPR020526	Ribosomal protein L6, chloroplast	PRODOM	PD069352		coord: 2..79 e-value: 1.0E-14 score: 188.0
None	No IPR available	MOBIDB_LITE	mobidb-lite	disorder_prediction	coord: 39..72