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Gene Card

Enter a TK1151 or OH-1004 gene ID to view sequences, annotations and analyses in the corresponding reference genome.
Flanking length, max 10000 bp
Examples TkA01G624900 LXL04_000258

Gene overview

TkA04G135690
Reference: TK1151 Chr: Chr04 Coordinates: 35276506-35279709 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

1920 bp · TkA04G135690|TK1151|cDNA

AAGAAACAAGAAATGTTGTTTTCTAGACGAAAACGAAAGCAGAAGTTGATACAGTTGCACCTCCTCTGCATTCAGGTTCACTCGTTCATCCTGGTTATCATCACCTATCTCTCTCTCTCTCTCTCACACACACACACACTCACTCACTCACCATTGCTAGAGCTCGGTACCGAAGAATTTTGAAGTAAGTGATTGCCAGTAAACCTGGAGACCTGTTCAACAATCTGTTGTATATGTTTAAGAGGAAGTATATCATGGTT...

CDS

Download CDS FASTA

696 bp · TkA04G135690|TK1151|CDS

ATGTCGATTGCACAACGATACGATAACATGGGAGCTCAAATGGCTGACCTAATTCAGGGAGGTCTAATTGGACTACTTCGAGGGATTGAAAAATACGATTCATCAAGGGGTTTCAAGATCTCTACGTACGTTTATTGGTGGATACGACAGGGTGTTTCAAGAGCTTTAATCGAGAATTCAAAAATCCTTCGATTGCCTACTCATTTGCATGAAAGACAGAGTGCAATCCGGAATGCTAAAGTCAAACTACAAGACCAAGG...

Protein

Download Protein FASTA

231 aa · TkA04G135690|TK1151|PROTEIN

MSIAQRYDNMGAQMADLIQGGLIGLLRGIEKYDSSRGFKISTYVYWWIRQGVSRALIENSKILRLPTHLHERQSAIRNAKVKLQDQGITPSIDRIAESLNISRKKVMNATQAMTKVFSVDNGTLYSVSPESLVTLMQDIADNSMENDPWHGVDETALKKEVNKLITLTLGEREREIIRLYYGLDKECLYWEDIGKRIGLSRERVRQIGLVAVEKLKNAAKKNGLEAMLVKH

Flanking Sequence Download

Sequence orientation and download details

Upstream/downstream are capped at 10000 bp per side. Negative-strand genes are reverse-complemented so the final FASTA follows transcriptional 5′→3′ orientation.

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ID Mapping

Input IDTkA04G135690
TK1151 IDTkA04G135690
OH-1004 IDLXL04_035351
Relationship / confidenceNon Reciprocal Best Hit / Complex relationship
Protein identity (%)94.800
Protein coverage (%)TK1151 100.000 / OH-1004 47.619
Coverage and evidence

Coverage is the aligned span of the best-scoring HSP divided by representative protein length. A homolog match does not establish functional validation.

Source versionTK1151 / GWHBCHF00000000
Open Full ID Mapping
SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene IDTkA04G135690
LocationChr04:35276506-35279709 (-)
DescriptionSimilar to SIGA: RNA polymerase sigma factor sigA
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At1g64860 Essential protein. No verified direct reference in this release
At5g13730 Sigma factors are initiation factors that promote the attachment of plastid-encoded RNA polymerase (PEP) to specific initiation sites and are then released.
Specific function of a plastid sigma factor for ndhF gene transcription.2005 · DOI: 10.1093/nar/gki908

Rice

Reference gene IDPossible functionPapers / DOI
Os08g0163400 Sigma factors are initiation factors that promote the attachment of plastid-encoded RNA polymerase (PEP) to specific initiation sites and are then released (Probable).
The plastid sigma factor SIG1 maintains photosystem I activity via regulated expression of the psaA operon in rice chloroplasts.2007 · DOI: 10.1111/j.1365-313x.2007.03216.x
Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_035351 · GCA_047496595.1_OSU_TarKok_2.0. These OH1004 annotations are retrieved through ID mapping; the Arabidopsis/rice table below uses protein alignments from the query reference.

GO annotations (OH1004 source)
GO:0006352 DNA-templated transcription initiation Biological Process
GO:0006355 regulation of DNA-templated transcription Biological Process
GO:0006399 tRNA metabolic process Biological Process
GO:0009658 chloroplast organization Biological Process
GO:0010114 response to red light Biological Process
GO:0071461 cellular response to redox state Biological Process
GO:0071482 cellular response to light stimulus Biological Process
GO:0080005 photosystem stoichiometry adjustment Biological Process
GO:2001141 regulation of RNA biosynthetic process Biological Process
GO:0005737 cytoplasm Cellular Component
GO:0009507 chloroplast Cellular Component
GO:1903865 sigma factor antagonist complex Cellular Component
KEGG gene cross-reference
ana:all5263
ath:AT1G08540
ath:AT1G64860
dosa:Os08g0163400
osa:4344738
syf:Synpcc7942_0672
These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.
Open Annotation Module

Gene expression

View expression in different studies, tissues and treatments. Results are presented separately by study and measurement unit.

View expression for this gene
Data sources and gene correspondence

Expression data come from public transcriptome studies. Reference genomes, sample metadata and measurement units are shown with the results. Ambiguous cross-reference correspondences do not select an expression record automatically; missing values do not mean zero expression.

Subcellular Localization Top 5

Computational predictions or homology annotations below do not replace localization experiments.

Nucleus0.411
Rank 1 · TkA04G135690 · TK1151
Cytoplasm0.272
Rank 2 · TkA04G135690 · TK1151
Mitochondrion0.188
Rank 3 · TkA04G135690 · TK1151
Plastid0.106
Rank 4 · TkA04G135690 · TK1151
Cell membrane0.022
Rank 5 · TkA04G135690 · TK1151

LocPro · Direct prediction · Computational prediction, not experimental localization

Open Subcellular Module

Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF04542Sigma70_r22-56 aa
PF04539Sigma70_r375-120 aa
PF13730HTH_3688-110 aa
PF08281Sigma70_r4_291-109 aa
PF13404HTH_AsnC-type91-108 aa
PF04545Sigma70_r493-106 aa
PF13730HTH_36151-167 aa
PF04545Sigma70_r4168-216 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
TkA04G135690PF04542Sigma70_r22565e-1452.5
TkA04G135690PF04539Sigma70_r3751201.3e-0629.1
TkA04G135690PF13730HTH_36881100.01415.9
TkA04G135690PF08281Sigma70_r4_2911090.04814.0
TkA04G135690PF13404HTH_AsnC-type911080.08413.5
TkA04G135690PF04545Sigma70_r4931064.7e-1246.0
TkA04G135690PF13730HTH_361511670.01415.9
TkA04G135690PF04545Sigma70_r41682164.7e-1246.0
TkA04G135690PF08281Sigma70_r4_21692040.04814.0
TkA04G135690PF13404HTH_AsnC-type1902050.08413.5
TkA04G135690PF04539Sigma70_r31912071.3e-0629.1
TkA04G135690PF13730HTH_361932050.01415.9

Arabidopsis / Rice Protein Homology

Only Arabidopsis and rice are shown. Swiss-Prot entries are reviewed; TrEMBL entries are supplementary sequence candidates. Similarity is not experimental validation.

Download current result

ProteinOrganismDescriptionIdentityDatabaseConfidence
O24629Arabidopsis thalianasp|O24629|SIGA_ARATH RNA polymerase sigma factor sigA71.900%Swiss-ProtHigh
Q9ZSL6Arabidopsis thalianasp|Q9ZSL6|SIGD_ARATH RNA polymerase sigma factor sigD, chloroplastic37.800%Swiss-ProtMedium
Q0J7T6Oryza sativa subsp. japonicasp|Q0J7T6|SIGA_ORYSJ RNA polymerase sigma factor sigA64.900%Swiss-ProtHigh

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