NO05G01730, NO05G01730 (gene) Nannochloropsis oceanica

Overview
NameNO05G01730
Unique NameNO05G01730
Typegene
OrganismNannochloropsis oceanica (N. oceanica IMET1)
Sequence length2377
Alignment locationchr5:470212..472588 +

Link to JBrowse

Properties
Property NameValue
DescriptionU6 snRNA-associated Sm-like protein LSm6
Mutants
Expression

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Alignments
The following features are aligned
Aligned FeatureFeature TypeAlignment Location
chr5genomechr5:470212..472588 +
Analyses
This gene is derived from or has results from the following analyses
Analysis NameDate Performed
PRJNA7699582024-08-13
GSE1786722023-12-15
PRJNA9336932023-10-26
PRJNA9434492023-07-19
PXD0160542021-01-14
PXD0166992021-01-08
GSE1499042020-10-10
NoIMET1_WT_HS2020-09-29
GSE1396152020-03-11
PRJNA2413822020-03-11
BLASTP analysis of N. oceanica IMET1 genes2019-07-11
InterPro analysis for N. oceanica IMET1 genes2019-07-11
GO annotation for IMET1v2 genes2019-07-10
PXD0087212019-04-30
PRJNA1821802019-04-25
Gene prediction for N. oceanica IMET12017-10-24
Annotated Terms
The following terms have been associated with this gene:
Vocabulary: Cellular Component
TermDefinition
GO:0005732small nucleolar ribonucleoprotein complex
GO:0005634nucleus
GO:0005730nucleolus
Vocabulary: Biological Process
TermDefinition
GO:0000398mRNA splicing, via spliceosome
GO:0006139nucleobase-containing compound metabolic process
Vocabulary: INTERPRO
TermDefinition
IPR010920LSM_dom
IPR016487Lsm6/sSmF
IPR001163Ribonucl_LSM
Vocabulary: Molecular Function
TermDefinition
GO:0003723RNA binding
Homology
[Close]
BLAST of NO05G01730 vs. NCBI_GenBank
Match: XP_016543963.1 (PREDICTED: sm-like protein LSM36B [Capsicum annuum] >PHT43459.1 U6 snRNA-associated Sm-like protein LSm6 [Capsicum baccatum] >PHT63408.1 U6 snRNA-associated Sm-like protein LSm6 [Capsicum annuum] >PHU06148.1 U6 snRNA-associated Sm-like protein LSm6 [Capsicum chinense])

HSP 1 Score: 120.9 bits (302), Expect = 2.800e-24
Identity = 59/85 (69.41%), Postives = 66/85 (77.65%), Query Frame = 0 
Query:   21 ASEAKPAQNKKVTEFLKTILGRPVVVKLNSGVDYRGVLACLDSFMNIAMEQTEEYVHGQLKAKYGDCFIRGNNGTFIFLSRDVSG 106
            A E  PA  K   +FLK+I GRPVVVKLNSGVDYRG+LACLD +MNIAMEQTEEYV+GQLK KYGD FIRGNN  +I  S+   G
Sbjct:    4 AGEKGPATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSKRTLG 88
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BLAST of NO05G01730 vs. NCBI_GenBank
Match: GAX93734.1 (Hypothetical protein PINS_001617 [Pythium insidiosum])

HSP 1 Score: 120.2 bits (300), Expect = 4.800e-24
Identity = 53/72 (73.61%), Postives = 65/72 (90.28%), Query Frame = 0 
Query:   25 KPAQNKKVTEFLKTILGRPVVVKLNSGVDYRGVLACLDSFMNIAMEQTEEYVHGQLKAKYGDCFIRGNNGTF 97
            +P   K  ++FLK++LGRPV VKLN+GV+Y+GVLACLD FMNIAMEQT+EYV+GQLKA+YGDCFIRGNNGT+
Sbjct:    2 EPQAKKTPSDFLKSVLGRPVEVKLNNGVEYKGVLACLDGFMNIAMEQTQEYVNGQLKAQYGDCFIRGNNGTY 73
[Close]
BLAST of NO05G01730 vs. NCBI_GenBank
Match: KCW46066.1 (hypothetical protein EUGRSUZ_L00039 [Eucalyptus grandis])

HSP 1 Score: 119.8 bits (299), Expect = 6.200e-24
Identity = 60/90 (66.67%), Postives = 68/90 (75.56%), Query Frame = 0 
Query:   15 GPGGPTASEAKPAQNKKVTEFLKTILGRPVVVKLNSGVDYRGVLACLDSFMNIAMEQTEEYVHGQLKAKYGDCFIRGNNGTFIFLSRDVS 105
            G GG   S    A  K   +FLK+I GRPVVVKLNSGVDYRG+LACLD +MNIAMEQTEEYV+GQLK KYGD FIRGNNG  ++   D+S
Sbjct:    3 GGGGEKGS----ATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNGNNVYKISDIS 88
[Close]
BLAST of NO05G01730 vs. NCBI_GenBank
Match: XP_011070291.1 (sm-like protein LSM36B [Sesamum indicum] >XP_011070293.1 sm-like protein LSM36B [Sesamum indicum])

HSP 1 Score: 119.0 bits (297), Expect = 1.100e-23
Identity = 56/77 (72.73%), Postives = 64/77 (83.12%), Query Frame = 0 
Query:   25 KPAQNKKVTEFLKTILGRPVVVKLNSGVDYRGVLACLDSFMNIAMEQTEEYVHGQLKAKYGDCFIRGNNGTFIFLSR 102
            KP+  K   +FLK+I GRPVVVKLNSGVDYRG+LACLD +MNIAMEQTEEYV+GQLK KYGD FIRGNN  +I  S+
Sbjct:    7 KPSTTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSK 83
[Close]
BLAST of NO05G01730 vs. NCBI_GenBank
Match: PIN08692.1 (Small nuclear ribonucleoprotein F [Handroanthus impetiginosus])

HSP 1 Score: 119.0 bits (297), Expect = 1.100e-23
Identity = 56/77 (72.73%), Postives = 64/77 (83.12%), Query Frame = 0 
Query:   25 KPAQNKKVTEFLKTILGRPVVVKLNSGVDYRGVLACLDSFMNIAMEQTEEYVHGQLKAKYGDCFIRGNNGTFIFLSR 102
            KP+  K   +FLK+I GRPVVVKLNSGVDYRG+LACLD +MNIAMEQTEEYV+GQLK KYGD FIRGNN  +I  S+
Sbjct:    7 KPSTTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSK 83
[Close]
BLAST of NO05G01730 vs. NCBI_GenBank
Match: XP_005851037.1 (hypothetical protein CHLNCDRAFT_34269 [Chlorella variabilis] >EFN58935.1 hypothetical protein CHLNCDRAFT_34269 [Chlorella variabilis])

HSP 1 Score: 117.9 bits (294), Expect = 2.400e-23
Identity = 54/72 (75.00%), Postives = 62/72 (86.11%), Query Frame = 0 
Query:   26 PAQNKKVTEFLKTILGRPVVVKLNSGVDYRGVLACLDSFMNIAMEQTEEYVHGQLKAKYGDCFIRGNNGTFI 98
            P+  K   +FLK+I G+PVVVKLNSGVDYRG+LACLD +MNIAMEQTEEYV+GQLK KYGDCFIRGNN  +I
Sbjct:    8 PSSAKTPADFLKSIKGKPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDCFIRGNNVLYI 79
[Close]
BLAST of NO05G01730 vs. NCBI_GenBank
Match: XP_024424862.1 (U6 snRNA-associated Sm-like protein LSm6 isoform X1 [Desmodus rotundus])

HSP 1 Score: 117.9 bits (294), Expect = 2.400e-23
Identity = 57/78 (73.08%), Postives = 65/78 (83.33%), Query Frame = 0 
Query:   33 TEFLKTILGRPVVVKLNSGVDYRGVLACLDSFMNIAMEQTEEYVHGQLKAKYGDCFIRGNNGTFIFLS-RDVSGCTYS 110
            ++FLK I+GRPVVVKLNSGVDYRGVLACLD +MNIA+EQTEEYV+GQLK KYGD FIRGNNG     S R+   CTY+
Sbjct:    9 SDFLKQIIGRPVVVKLNSGVDYRGVLACLDGYMNIALEQTEEYVNGQLKNKYGDAFIRGNNGGITESSRRERFNCTYT 86
[Close]
BLAST of NO05G01730 vs. NCBI_GenBank
Match: ETE72044.1 (U6 snRNA-associated Sm-like protein LSm6, partial [Ophiophagus hannah])

HSP 1 Score: 117.5 bits (293), Expect = 3.100e-23
Identity = 52/66 (78.79%), Postives = 61/66 (92.42%), Query Frame = 0 
Query:   33 TEFLKTILGRPVVVKLNSGVDYRGVLACLDSFMNIAMEQTEEYVHGQLKAKYGDCFIRGNNGTFIF 99
            ++FLK I+GRPVVVKLNSGVDYRGVLACLD +MNIA+EQTEEYV+GQLK KYGD FIRGNNG +++
Sbjct:    9 SDFLKQIIGRPVVVKLNSGVDYRGVLACLDGYMNIALEQTEEYVNGQLKNKYGDAFIRGNNGKYVY 74
[Close]
BLAST of NO05G01730 vs. NCBI_GenBank
Match: XP_006442140.1 (sm-like protein LSM36B [Citrus clementina] >XP_006492754.1 PREDICTED: sm-like protein LSM36B [Citrus sinensis] >XP_002311269.3 sm-like protein LSM36B [Populus trichocarpa] >ABK93423.1 unknown [Populus trichocarpa] >ESR55380.1 hypothetical protein CICLE_v10023071mg [Citrus clementina] >KDO47989.1 hypothetical protein CISIN_1g034564mg [Citrus sinensis] >PNT23372.1 hypothetical protein POPTR_008G078400v3 [Populus trichocarpa] >PNT23373.1 hypothetical protein POPTR_008G078400v3 [Populus trichocarpa])

HSP 1 Score: 117.1 bits (292), Expect = 4.000e-23
Identity = 57/82 (69.51%), Postives = 64/82 (78.05%), Query Frame = 0 
Query:   20 TASEAKPAQNKKVTEFLKTILGRPVVVKLNSGVDYRGVLACLDSFMNIAMEQTEEYVHGQLKAKYGDCFIRGNNGTFIFLSR 102
            T  E   A  K   +FLK+I GRPVVVKLNSGVDYRG+LACLD +MNIAMEQTEEYV+GQLK KYGD FIRGNN  +I  S+
Sbjct:    3 TGGEKGSATTKTPADFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSK 84
[Close]
BLAST of NO05G01730 vs. NCBI_GenBank
Match: XP_002980839.1 (U6 snRNA-associated Sm-like protein LSm6 [Selaginella moellendorffii] >XP_002989366.1 U6 snRNA-associated Sm-like protein LSm6 [Selaginella moellendorffii] >EFJ09640.1 hypothetical protein SELMODRAFT_235757 [Selaginella moellendorffii] >EFJ18024.1 hypothetical protein SELMODRAFT_268399 [Selaginella moellendorffii])

HSP 1 Score: 117.1 bits (292), Expect = 4.000e-23
Identity = 55/74 (74.32%), Postives = 63/74 (85.14%), Query Frame = 0 
Query:   30 KKVTEFLKTILGRPVVVKLNSGVDYRGVLACLDSFMNIAMEQTEEYVHGQLKAKYGDCFIRGNNGTFIFLSRDV 104
            K  T+FL++I GRPVVVKLNSGVDYRG+LACLD +MNIAMEQTEEYV+GQLK KYGD FIRGNN  +I  S+ V
Sbjct:   12 KTPTDFLRSIKGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRGNNVLYISTSKKV 85
The following BLAST results are available for this feature:
BLAST of NO05G01730 vs. NCBI_GenBank
Analysis Date: 2019-07-11 (BLASTP analysis of N. oceanica IMET1 genes)
Total hits: 20
Match NameE-valueIdentityDescription
XP_016543963.12.800e-2469.41PREDICTED: sm-like protein LSM36B [Capsicum annuum... [more]
GAX93734.14.800e-2473.61Hypothetical protein PINS_001617 [Pythium insidios... [more]
KCW46066.16.200e-2466.67hypothetical protein EUGRSUZ_L00039 [Eucalyptus gr... [more]
XP_011070291.11.100e-2372.73sm-like protein LSM36B [Sesamum indicum] >XP_01107... [more]
PIN08692.11.100e-2372.73Small nuclear ribonucleoprotein F [Handroanthus im... [more]
XP_005851037.12.400e-2375.00hypothetical protein CHLNCDRAFT_34269 [Chlorella v... [more]
XP_024424862.12.400e-2373.08U6 snRNA-associated Sm-like protein LSm6 isoform X... [more]
ETE72044.13.100e-2378.79U6 snRNA-associated Sm-like protein LSm6, partial ... [more]
XP_006442140.14.000e-2369.51sm-like protein LSM36B [Citrus clementina] >XP_006... [more]
XP_002980839.14.000e-2374.32U6 snRNA-associated Sm-like protein LSm6 [Selagine... [more]

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Relationships

This gene is member of the following syntenic_region feature(s):

Feature NameUnique NameSpeciesType
nonsL086nonsL086Nannochloropsis oceanica (N. oceanica IMET1)syntenic_region
ncniR092ncniR092Nannochloropsis oceanica (N. oceanica IMET1)syntenic_region
ngnoR118ngnoR118Nannochloropsis oceanica (N. oceanica IMET1)syntenic_region


This gene is orthologous to the following gene feature(s):

Feature NameUnique NameSpeciesType
NSK003695NSK003695Nannochloropsis salina (N. salina CCMP1776)gene


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

Feature NameUnique NameSpeciesType
NO05G01730.1NO05G01730.1-proteinNannochloropsis oceanica (N. oceanica IMET1)polypeptide
NO05G01730.2NO05G01730.2-proteinNannochloropsis oceanica (N. oceanica IMET1)polypeptide


The following gene feature(s) are orthologous to this gene:

Feature NameUnique NameSpeciesType
jgi.p|Nanoce1779_2|583987gene_2961Nannochloropsis oceanica (N. oceanica CCMP1779)gene


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

Feature NameUnique NameSpeciesType
NO05G01730.1NO05G01730.1Nannochloropsis oceanica (N. oceanica IMET1)mRNA
NO05G01730.2NO05G01730.2Nannochloropsis oceanica (N. oceanica IMET1)mRNA


Sequences
The following sequences are available for this feature:

gene sequence

>NO05G01730 ID=NO05G01730|Name=NO05G01730|organism=Nannochloropsis oceanica|type=gene|length=2377bp
CTCCATGTACGCTTAGCTCTATCTTCATTCATTGCGCTCGCTTTTTACTT
TGTTGGGCTTTCCCACTAACCTTGAGTGAAGGAAAACGTTCCATCAAATT
ACAATTTCCACTCTTACGGAGTTTCTCTGACTCTACAAAACCCCTCAAAC
CAAACTCTCTCACCCGCCCGGCCCGCAACTATACTCACAATTAGTTATTT
TGTGAATACTTGTGTCCACACTTCTTGCTTAGACACTCATAAAACACCGT
CGACCCCTCATCCGCCGAACGCAGCTGCATGGTGTAAAAGCTCATCTCTG
GATGGCCACACTTCGGGCAAGGCTCGTCTACCTTGGCATGCCGGCTGTCC
CCTCCCTCGTCGTTTCCATCCTCGCATACCCCATCTGGTTTGGCAGCCGC
TGCCAGCTCCTGGTACCAGCGCGGCGCAGGTTTCTCGGCACTGGTGGTGA
TTATTTCTACTTGACCCAACTCTTTGTTTGAAAGAAGATGAATAGATGTA
TGTAGTGAGCTGTTTGGCTTCGATGTGGCGGGGTGGGAAGCAACGGGTAT
GGAGTTGACGGAGTTTTGAGGCGGGAAACGTACCGTCAAAGGTCGTGGAA
AATTTACAGATGCGGCAGACAATTGGGTCCTCATCCGGCAGATCCAGTAG
TGCATGGCATTCATCGCAAAAAGGCACGGCTCCGCCTGAGGCCATAGGCG
TGGAGGGATGGATCGTCGGAGATTCCAACTGAGATATGGAGGAATGGAGG
AGTCGTGGGGAGGTTAGAGCGGCGCCTACCAGATACTGATAAAGTCTGTG
GACTATAATCCATATGAAATGCATGTCGACATGAAATGTACGTAGATGTA
TCTGTGTGAGGGTTGGAGTGAAAATGAGGTGGCTGGAAGCCTCGTAAGAA
ATACTCGCCAGTTACCAAGTAGTGTCTATCTTGAGATTTGGGCCGAAGAA
ATAATTTGGGCCGGAGAGATGAATTTGGGCCTCGGTTCGCAGCTTGTTTC
AGAACTCAATCCCTGTCATACACACAAACAACCACAGTAACGACAAACCA
AAGGTCATGTCTGACGCATCACCGTCTACCACGACGACGGCAGCGCAAGG
CCCCGGTGGCCCCACAGCGTCCGAGGCCAAGCCTGCTCAGgtgaggaagc
aatggaagaattgtgatgatgatgcggattggaggatcgaatgacacgtc
tgtgtgagctagaagtgcgctaggcagccaatttcacccagtaaggacaa
ccacgatcaaatcatgtggtggtggtcgtgcagtcgctgtattggcatgg
tgcctccaagcatgccgttcatttctgctccccctagctctctccctcac
acccttcctccctcgttttccaaaccattaccacctgccccgacagAACA
AAAAAGTGACTGAGTTCCTTAAAACCATCTTGGGCCGCCCCGTGGTGGTT
AAGCTGAACTCGGGCGTGGACTATCGAGgtacgttgggctattagggtga
gggtgggggcgaggtcgggcatgtggcgggtgcagcaaagccccaggtgt
gcatcgaaaagaataaagatgcgatggacaacagcttgctgtccatcaat
gtgtgctggcacagattctttgagaaggtagcaggtcgtcaccgtcttat
actctccctatcaaccactcttcctgcctttgagttaagGCGTGCTGGCC
TGTTTGGACAGCTTCATGAATATTGCCATGGAGCAAACGGAGGAGTACGT
GCATGGACAGCTGAAGGCTAAGTACGGTGATTGTTTCATTCGCGGAAATA
ATGgtacgtttatttttcttagcagggatgtgagtggatgcacttatagt
acatacttgcaaggcagccttcttccgcgccttgcatcggcctcacgtcc
ttgattgaaatttagtcaatttcgccacatgcctacaggtgcgacaaata
tagtgcatcgtgcgtcttcgtgggcgtgttgaatgtgtcttgaggctttc
atgcctgaaaatccgtttttaaacctccttttaaccctcaccctttcatc
ctccgccatttggacccccaaccttcaacacagTTTTGTATATCTCTACG
CAAAAGCGGAGGTAGCATCTTCTCCCCTTAAATGGTGCATTTGAGAGAAG
GGCGGGCACTAAGTGATGGGCACGTAAAGCTCATTGAACGGAGGGGAGAG
AAGCAAGTCTATGTTTATTAAAGAGCGCGTGCAATCACCAATACGGGCCA
CCGGCCAAAGGACAAAGAGGGAAAGTATAGAAGTAGGGATTATTGTTTGT
TTTCCCGCTTTTGATCGCGGTGCAAAGTATGGCTGCCGGTCCTGCGTTGT
AATAAAATAACAACAGATACAAACCCA
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protein sequence of NO05G01730.1

>NO05G01730.1-protein ID=NO05G01730.1-protein|Name=NO05G01730.1|organism=Nannochloropsis oceanica|type=polypeptide|length=104bp
MSDASPSTTTTAAQGPGGPTASEAKPAQNKKVTEFLKTILGRPVVVKLNS
GVDYRGVLACLDSFMNIAMEQTEEYVHGQLKAKYGDCFIRGNNVLYISTQ
KRR*
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protein sequence of NO05G01730.2

>NO05G01730.2-protein ID=NO05G01730.2-protein|Name=NO05G01730.2|organism=Nannochloropsis oceanica|type=polypeptide|length=127bp
MSDASPSTTTTAAQGPGGPTASEAKPAQNKKVTEFLKTILGRPVVVKLNS
GVDYRGVLACLDSFMNIAMEQTEEYVHGQLKAKYGDCFIRGNNGTFIFLS
RDVSGCTYSTYLQGSLLPRLASASRP*
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Synonyms
Publications