NO13G01170, NO13G01170 (gene) Nannochloropsis oceanica

Overview
NameNO13G01170
Unique NameNO13G01170
Typegene
OrganismNannochloropsis oceanica (N. oceanica IMET1)
Sequence length1533
Alignment locationchr13:360094..361626 -

Link to JBrowse

Properties
Property NameValue
DescriptionU6 snRNA-associated Sm-like protein LSm4
Mutants
Expression

Hover the mouse over a column in the graph to view expression values.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

back to top
Alignments
The following features are aligned
Aligned FeatureFeature TypeAlignment Location
chr13genomechr13:360094..361626 -
Analyses
This gene is derived from or has results from the following analyses
Analysis NameDate Performed
GSE1786722023-12-15
PRJNA9336932023-10-26
PRJNA9434492023-07-19
PXD0160542021-01-14
GSE1499042020-10-10
NoIMET1_WT_HS2020-09-29
PXD0100302020-03-16
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: Biological Process
TermDefinition
GO:0006396RNA processing
GO:0009056catabolic process
GO:0006139nucleobase-containing compound metabolic process
Vocabulary: INTERPRO
TermDefinition
IPR010920LSM_dom
IPR027141LSm4/Sm_D1/D3
IPR001163Ribonucl_LSM
Vocabulary: Cellular Component
TermDefinition
GO:0005634nucleus
Vocabulary: Molecular Function
TermDefinition
GO:0003723RNA binding
Homology
[Close]
BLAST of NO13G01170 vs. NCBI_GenBank
Match: EWM21793.1 (u6 snrna-associated sm-like protein lsm4 [Nannochloropsis gaditana])

HSP 1 Score: 185.3 bits (469), Expect = 1.600e-43
Identity = 86/86 (100.00%), Postives = 86/86 (100.00%), Query Frame = 0 
Query:    1 MLPLSLLKTAQGHPMLVELKNGDTYNGRLVSCDTWMNITLRDVICTSRDGDRFWKIPECYVRGNSIKYLRVPEEVIDMVNEEDLER 87
            MLPLSLLKTAQGHPMLVELKNGDTYNGRLVSCDTWMNITLRDVICTSRDGDRFWKIPECYVRGNSIKYLRVPEEVIDMVNEEDLER
Sbjct:    1 MLPLSLLKTAQGHPMLVELKNGDTYNGRLVSCDTWMNITLRDVICTSRDGDRFWKIPECYVRGNSIKYLRVPEEVIDMVNEEDLER 86
[Close]
BLAST of NO13G01170 vs. NCBI_GenBank
Match: ETI45030.1 (U6 snRNA-associated Sm-like protein LSm4 [Phytophthora parasitica P1569] >ETK84999.1 U6 snRNA-associated Sm-like protein LSm4 [Phytophthora parasitica] >ETL38431.1 U6 snRNA-associated Sm-like protein LSm4 [Phytophthora parasitica] >ETL91546.1 U6 snRNA-associated Sm-like protein LSm4 [Phytophthora parasitica] >ETM44841.1 U6 snRNA-associated Sm-like protein LSm4 [Phytophthora parasitica] >ETO73624.1 U6 snRNA-associated Sm-like protein LSm4 [Phytophthora parasitica P1976] >ETP14830.1 U6 snRNA-associated Sm-like protein LSm4 [Phytophthora parasitica CJ01A1])

HSP 1 Score: 166.0 bits (419), Expect = 1.000e-37
Identity = 70/86 (81.40%), Postives = 81/86 (94.19%), Query Frame = 0 
Query:    1 MLPLSLLKTAQGHPMLVELKNGDTYNGRLVSCDTWMNITLRDVICTSRDGDRFWKIPECYVRGNSIKYLRVPEEVIDMVNEEDLER 87
            MLPLSLLKTAQGHPMLVELKNGDTYNG LV+CDTWMN+ LR+VICTS+DGDRFWK+PECY+RGN+IKY+RVP E++DMVNEED  +
Sbjct:    1 MLPLSLLKTAQGHPMLVELKNGDTYNGHLVNCDTWMNVNLREVICTSKDGDRFWKMPECYIRGNTIKYIRVPNEILDMVNEEDFNK 86
[Close]
BLAST of NO13G01170 vs. NCBI_GenBank
Match: XP_008893374.1 (hypothetical protein PPTG_01744 [Phytophthora parasitica INRA-310] >ETN21601.1 hypothetical protein PPTG_01744 [Phytophthora parasitica INRA-310] >ETP42871.1 hypothetical protein F442_10208 [Phytophthora parasitica P10297])

HSP 1 Score: 166.0 bits (419), Expect = 1.000e-37
Identity = 70/86 (81.40%), Postives = 81/86 (94.19%), Query Frame = 0 
Query:    1 MLPLSLLKTAQGHPMLVELKNGDTYNGRLVSCDTWMNITLRDVICTSRDGDRFWKIPECYVRGNSIKYLRVPEEVIDMVNEEDLER 87
            MLPLSLLKTAQGHPMLVELKNGDTYNG LV+CDTWMN+ LR+VICTS+DGDRFWK+PECY+RGN+IKY+RVP E++DMVNEED  +
Sbjct:    1 MLPLSLLKTAQGHPMLVELKNGDTYNGHLVNCDTWMNVNLREVICTSKDGDRFWKMPECYIRGNTIKYIRVPNEILDMVNEEDFNK 86
[Close]
BLAST of NO13G01170 vs. NCBI_GenBank
Match: XP_024584582.1 (u6 snrna-associated sm-like protein lsm4 [Plasmopara halstedii] >CEG48213.1 u6 snrna-associated sm-like protein lsm4 [Plasmopara halstedii])

HSP 1 Score: 164.9 bits (416), Expect = 2.300e-37
Identity = 69/86 (80.23%), Postives = 82/86 (95.35%), Query Frame = 0 
Query:    1 MLPLSLLKTAQGHPMLVELKNGDTYNGRLVSCDTWMNITLRDVICTSRDGDRFWKIPECYVRGNSIKYLRVPEEVIDMVNEEDLER 87
            MLPLSLL+TAQGHPMLVELKNGDTYNG LV+CDTWMN+ LR+VICTS+DGDRFWK+PECY+RGN+IKY+RVP E++DMVNE+DL +
Sbjct:    1 MLPLSLLQTAQGHPMLVELKNGDTYNGHLVNCDTWMNVNLREVICTSKDGDRFWKMPECYIRGNTIKYIRVPNEILDMVNEDDLNK 86
[Close]
BLAST of NO13G01170 vs. NCBI_GenBank
Match: XP_009531179.1 (hypothetical protein PHYSODRAFT_347058 [Phytophthora sojae] >EGZ13750.1 hypothetical protein PHYSODRAFT_347058 [Phytophthora sojae])

HSP 1 Score: 164.5 bits (415), Expect = 2.900e-37
Identity = 69/85 (81.18%), Postives = 80/85 (94.12%), Query Frame = 0 
Query:    2 LPLSLLKTAQGHPMLVELKNGDTYNGRLVSCDTWMNITLRDVICTSRDGDRFWKIPECYVRGNSIKYLRVPEEVIDMVNEEDLER 87
            LPLSLLKTAQGHPMLVELKNGDTYNG LV+CDTWMN+ LR+VICTS+DGDRFWK+PECY+RGN+IKY+RVP E++DMVNEED  +
Sbjct:    4 LPLSLLKTAQGHPMLVELKNGDTYNGHLVNCDTWMNVNLREVICTSKDGDRFWKMPECYIRGNTIKYIRVPNEILDMVNEEDFSK 88
[Close]
BLAST of NO13G01170 vs. NCBI_GenBank
Match: GAQ92019.1 (U6 snRNA-associated Sm-like protein LSm4 [Klebsormidium nitens])

HSP 1 Score: 161.0 bits (406), Expect = 3.300e-36
Identity = 71/86 (82.56%), Postives = 81/86 (94.19%), Query Frame = 0 
Query:    1 MLPLSLLKTAQGHPMLVELKNGDTYNGRLVSCDTWMNITLRDVICTSRDGDRFWKIPECYVRGNSIKYLRVPEEVIDMVNEEDLER 87
            MLPLSLLKTAQGHPMLVELKNG+TYNG LV+CDTWMNI LR+VICTS+DGDRFW++PECYVRGN+IKYLRVP+EVID V EE ++R
Sbjct:    1 MLPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYVRGNTIKYLRVPDEVIDKVQEETIKR 86
[Close]
BLAST of NO13G01170 vs. NCBI_GenBank
Match: XP_024394039.1 (sm-like protein LSM4 [Physcomitrella patens] >PNR40941.1 hypothetical protein PHYPA_018344 [Physcomitrella patens])

HSP 1 Score: 160.2 bits (404), Expect = 5.500e-36
Identity = 70/86 (81.40%), Postives = 81/86 (94.19%), Query Frame = 0 
Query:    1 MLPLSLLKTAQGHPMLVELKNGDTYNGRLVSCDTWMNITLRDVICTSRDGDRFWKIPECYVRGNSIKYLRVPEEVIDMVNEEDLER 87
            MLPLSLLKTAQGHPMLVELKNG+TYNG LV+CDTWMNI LR+VICTS+DGDRFW++PECY+RGN+IKYLRVP+EVID V EE ++R
Sbjct:    1 MLPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVPDEVIDKVQEETVKR 86
[Close]
BLAST of NO13G01170 vs. NCBI_GenBank
Match: OIV91290.1 (hypothetical protein TanjilG_01821 [Lupinus angustifolius])

HSP 1 Score: 159.1 bits (401), Expect = 1.200e-35
Identity = 70/86 (81.40%), Postives = 79/86 (91.86%), Query Frame = 0 
Query:    1 MLPLSLLKTAQGHPMLVELKNGDTYNGRLVSCDTWMNITLRDVICTSRDGDRFWKIPECYVRGNSIKYLRVPEEVIDMVNEEDLER 87
            MLPLSLLKTAQGHPMLVELKNG+TYNG LV+CDTWMNI LR+VICTS+DGDRFW++PECY+RGN+IKYLRVP+EVID V EE   R
Sbjct:    1 MLPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVPDEVIDKVQEESKSR 86
[Close]
BLAST of NO13G01170 vs. NCBI_GenBank
Match: XP_019426976.1 (PREDICTED: sm-like protein LSM4 [Lupinus angustifolius])

HSP 1 Score: 159.1 bits (401), Expect = 1.200e-35
Identity = 70/86 (81.40%), Postives = 79/86 (91.86%), Query Frame = 0 
Query:    1 MLPLSLLKTAQGHPMLVELKNGDTYNGRLVSCDTWMNITLRDVICTSRDGDRFWKIPECYVRGNSIKYLRVPEEVIDMVNEEDLER 87
            MLPLSLLKTAQGHPMLVELKNG+TYNG LV+CDTWMNI LR+VICTS+DGDRFW++PECY+RGN+IKYLRVP+EVID V EE   R
Sbjct:    1 MLPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVPDEVIDKVQEESKSR 86
[Close]
BLAST of NO13G01170 vs. NCBI_GenBank
Match: ACU14927.1 (unknown [Glycine max])

HSP 1 Score: 158.7 bits (400), Expect = 1.600e-35
Identity = 70/86 (81.40%), Postives = 79/86 (91.86%), Query Frame = 0 
Query:    1 MLPLSLLKTAQGHPMLVELKNGDTYNGRLVSCDTWMNITLRDVICTSRDGDRFWKIPECYVRGNSIKYLRVPEEVIDMVNEEDLER 87
            MLPLSLLKTAQGHPMLVELKNG+TYNG LV+CDTWMNI LR+VICTS+DGDRFW++PECY+RGN+IKYLRVP+EVID V EE   R
Sbjct:    1 MLPLSLLKTAQGHPMLVELKNGETYNGHLVNCDTWMNIHLREVICTSKDGDRFWRMPECYIRGNTIKYLRVPDEVIDKVQEETKSR 86
The following BLAST results are available for this feature:
BLAST of NO13G01170 vs. NCBI_GenBank
Analysis Date: 2019-07-11 (BLASTP analysis of N. oceanica IMET1 genes)
Total hits: 20
Match NameE-valueIdentityDescription
EWM21793.11.600e-43100.00u6 snrna-associated sm-like protein lsm4 [Nannochl... [more]
ETI45030.11.000e-3781.40U6 snRNA-associated Sm-like protein LSm4 [Phytopht... [more]
XP_008893374.11.000e-3781.40hypothetical protein PPTG_01744 [Phytophthora para... [more]
XP_024584582.12.300e-3780.23u6 snrna-associated sm-like protein lsm4 [Plasmopa... [more]
XP_009531179.12.900e-3781.18hypothetical protein PHYSODRAFT_347058 [Phytophtho... [more]
GAQ92019.13.300e-3682.56U6 snRNA-associated Sm-like protein LSm4 [Klebsorm... [more]
XP_024394039.15.500e-3681.40sm-like protein LSM4 [Physcomitrella patens] >PNR4... [more]
OIV91290.11.200e-3581.40hypothetical protein TanjilG_01821 [Lupinus angust... [more]
XP_019426976.11.200e-3581.40PREDICTED: sm-like protein LSM4 [Lupinus angustifo... [more]
ACU14927.11.600e-3581.40unknown [Glycine max][more]

Pages

back to top
Relationships

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

Feature NameUnique NameSpeciesType
nonsL134nonsL134Nannochloropsis oceanica (N. oceanica IMET1)syntenic_region
ncniR026ncniR026Nannochloropsis oceanica (N. oceanica IMET1)syntenic_region
ngnoR070ngnoR070Nannochloropsis oceanica (N. oceanica IMET1)syntenic_region


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

Feature NameUnique NameSpeciesType
NO13G01170.2NO13G01170.2-proteinNannochloropsis oceanica (N. oceanica IMET1)polypeptide
NO13G01170.1NO13G01170.1-proteinNannochloropsis oceanica (N. oceanica IMET1)polypeptide


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

Feature NameUnique NameSpeciesType
jgi.p|Nanoce1779_2|596686gene_6892Nannochloropsis oceanica (N. oceanica CCMP1779)gene
Naga_100065g3gene8646Nannochloropsis gaditana (N. gaditana B-31)gene


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

Feature NameUnique NameSpeciesType
NO13G01170.2NO13G01170.2Nannochloropsis oceanica (N. oceanica IMET1)mRNA
NO13G01170.1NO13G01170.1Nannochloropsis oceanica (N. oceanica IMET1)mRNA


Sequences
The following sequences are available for this feature:

gene sequence

>NO13G01170 ID=NO13G01170|Name=NO13G01170|organism=Nannochloropsis oceanica|type=gene|length=1533bp
ACAGGCAAGGGCACAAAGCAAGCTATCAGACGCCTGCATTCTTTGCCTCC
TCCGTCGCGTTTTTTCTCCACTATTACGTTATCAATTAGACCCCAGCGCA
CTCCATTACTTCTACTACATCATTAAACACAATGgtaagatcattgggat
aacatgccagcgtttccttggactcttagaacttcgtgcccgagcctgaa
ccaacctgcccctccttcctacccaccgtctacttagTTGCCCTTGTCCC
TCCTCAAGACGGCGCAAGGCCACCCAATGTTGGTGGAGCTTAAAAATGGC
GACACTTACAATGGCCGGCTAGTATCGTGTGATACCTGGATGAACATCAC
GTTGAGGGACGTCATCTGCACGTCACGGGTAGGAGAGGGTTAGAGAGGGG
TGGGAAAGATGGGAGAAAAGGTCCGAAGGGTGAGAGAGAGGTTGCAATAA
TATGATCTGAATTCTGATTGAGAAGTGGGCGGATAACCTGAGGCAGAAAG
TATGTATCATCGTTTAGAGCGCTGCAGAGGGGGTAACGAGGGCGTTGGCG
TGACATGCTTTCTGTTTTGTCAAAACGCGTAAAGGAGATGGGGAGCAGAC
AATTACTTACAACATCTCCTCCACTCCTTCCCCATTGGTCTTCGTCCACC
ATGATTGCGCAGGATGGTGACCGCTTCTGGAAGATCCCCGAGTGCTACGT
GCGTGGGAACAGCATCAAGTACCTGCGGGTGCCGGAGGAAGTGATCGACA
TGGTCAACGAGGAGGACTTGGAAAGGGAACgtgcgtatgccatggggtgg
gggctgtcgaacacttcgtttgctttattttcaattgtggttcatactgc
ttccaaggagagatgatgggggtatctctttgtgcatgtgtgtttgtgtg
tgtttgttatcgtgtggtagcaccagggggcggttgagtttttgtgtgca
tgtgtcttctatttcctttcccttgtcacggtgaagcaatcttttccatc
acattctgttcctttgtcaaaccatgtacagGCAGGGGAGGTGCCGGGCG
AGGACGCGGGCGATTGGGTGGGGGCCGGGGAGGACGAGgtaagggaaccg
aacggaagggagcaaaatggatgtagggacagagaacgtgatagagacag
acacaacccagatcgcaatttcacttaaacccgcgatcacacacactgct
ttgcttataccaacgaatcccaaacagGGTATGGTCGAGGTGGCGGGGAG
GGTCGTGGTGGCGCCCGGGGAGATTTTCGCGGCGGGCGTGGCGGGGGTGA
CCGAGGGGGACGAGGGGGAGGGAGGGGGGAGTATCGTGGGGGAGGAAGGG
GAGATTACAGGGGAGGACGCGGAGGGGGAGGTGGACGAGGAGGGGAGGGC
CCGAGTGGAAGACAATAGGGGCCTCTGCTGTGTGTTGGTGGGTGAGGGAA
AGGAGGAGAATGAAGGAAGAGGAGAAGAAGGCAACGATAGGGGAAAAAAG
ATGAGAAGAAAGAAAGAAGTATAGGACTGGAAA
back to top

protein sequence of NO13G01170.2

>NO13G01170.2-protein ID=NO13G01170.2-protein|Name=NO13G01170.2|organism=Nannochloropsis oceanica|type=polypeptide|length=158bp
MLSVLSKRVKEMGSRQLLTTSPPLLPHWSSSTMIAQDGDRFWKIPECYVR
GNSIKYLRVPEEVIDMVNEEDLERERRGGAGRGRGRLGGGRGGRGYGRGG
GEGRGGARGDFRGGRGGGDRGGRGGGRGEYRGGGRGDYRGGRGGGGGRGG
EGPSGRQ*
back to top

protein sequence of NO13G01170.1

>NO13G01170.1-protein ID=NO13G01170.1-protein|Name=NO13G01170.1|organism=Nannochloropsis oceanica|type=polypeptide|length=170bp
MLPLSLLKTAQGHPMLVELKNGDTYNGRLVSCDTWMNITLRDVICTSRDG
DRFWKIPECYVRGNSIKYLRVPEEVIDMVNEEDLERERRGGAGRGRGRLG
GGRGGRGYGRGGGEGRGGARGDFRGGRGGGDRGGRGGGRGEYRGGGRGDY
RGGRGGGGGRGGEGPSGRQ*
back to top
Synonyms
Publications