RubberDandelionOmics Rubber Dandelion Multi-omics Website
More
Transcriptome Expression Annotation Rubber Pathway TF Prediction Targets Protein Network Resequencing Tools Downloads
ZH EN

How to use this page

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

TkA04G049940
Reference: TK1151 Chr: Chr04 Coordinates: 13382247-13383803 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

1158 bp · TkA04G049940|TK1151|cDNA

ATGGGATTTTGCTCGCATGTACATATCAGCACTGCTCTTGTGGACATGTATGGTAAATGTGGTGTGATATCCGATGCTCAGAACCTATTCGACGAAACGCCTCACAGAAACGTGATCACTTGGAACTCGCTAATTTCAGGTTACCTTCATACCCAATTCGTTGATGTTTCCATCGATTTGTTTGTCGCAATGCTTAGATTGGGAATACATCCAACTCAATTTACCGTTTCCACCATTCTCGTTGGGTGTTCAGAGTTAGA...

CDS

Download CDS FASTA

1158 bp · TkA04G049940|TK1151|CDS

ATGGGATTTTGCTCGCATGTACATATCAGCACTGCTCTTGTGGACATGTATGGTAAATGTGGTGTGATATCCGATGCTCAGAACCTATTCGACGAAACGCCTCACAGAAACGTGATCACTTGGAACTCGCTAATTTCAGGTTACCTTCATACCCAATTCGTTGATGTTTCCATCGATTTGTTTGTCGCAATGCTTAGATTGGGAATACATCCAACTCAATTTACCGTTTCCACCATTCTCGTTGGGTGTTCAGAGTTAGA...

Protein

Download Protein FASTA

385 aa · TkA04G049940|TK1151|PROTEIN

MGFCSHVHISTALVDMYGKCGVISDAQNLFDETPHRNVITWNSLISGYLHTQFVDVSIDLFVAMLRLGIHPTQFTVSTILVGCSELESLELGQQVHGLITKSGPDKNVVVWTSMITGYSQNQETEMAMDMITQMLVSDHKPDSITYNTLLSSFSGIKDMIHCQQIHCLIIKQGLHSDVYLANGLISMYSKCGQINKSIKIFTSMADHDTVSWNSLLSGYAQHGYCNKAIEVFEQMRESKVKPDLTTFLVLISACGHVGLV...

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.

Download Gene (CDS) Download Protein

ID Mapping

Input IDTkA04G049940
TK1151 IDTkA04G049940
OH-1004 IDLXL04_024214
Relationship / confidenceNon Reciprocal Best Hit / Complex relationship
Protein identity (%)30.800
Protein coverage (%)TK1151 98.961 / OH-1004 48.361
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 IDTkA04G049940
LocationChr04:13382247-13383803 (-)
DescriptionSimilar to PCMP-E90: Pentatricopeptide repeat-containing protein At3g02330, mitochondrial
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At2g33680 Pentatricopeptide repeat-containing protein At2g33680. No verified direct reference in this release
At1g11290 Involved in multiple sites RNA editing events in chloroplasts.
Pentatricopeptide repeat proteins with the DYW motif have distinct molecular functions in RNA editing and RNA cleavage in Arabidopsis chloroplasts.2009 · DOI: 10.1105/tpc.108.064667
At3g09040 Pentatricopeptide repeat-containing protein At3g09040, mitochondrial. No verified direct reference in this release
At2g03380 Pentatricopeptide repeat-containing protein At2g03380, mitochondrial. No verified direct reference in this release
At3g49170 May play a role in embryogenesis. No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_024214 · 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:0006397 mRNA processing Biological Process
GO:0009451 RNA modification Biological Process
GO:0016554 cytidine to uridine editing Biological Process
GO:0080156 mitochondrial mRNA modification Biological Process
GO:0005739 mitochondrion Cellular Component
GO:0003723 RNA binding Molecular Function
GO:0060090 molecular adaptor activity Molecular Function
KEGG gene cross-reference
ath:AT3G02330
ath:AT3G09040
ath:AT4G39530
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.

Mitochondrion0.623
Rank 1 · TkA04G049940 · TK1151
Plastid0.174
Rank 2 · TkA04G049940 · TK1151
Nucleus0.052
Rank 3 · TkA04G049940 · TK1151
Cytoplasm0.037
Rank 4 · TkA04G049940 · TK1151
Peroxisome0.007
Rank 5 · TkA04G049940 · 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.

PF13041PPR_211-32 aa
PF01535PPR11-32 aa
PF12854PPR_111-32 aa
PF10602RPN712-46 aa
PF18768RNPP_C35-61 aa
PF13041PPR_236-84 aa
PF12854PPR_136-48 aa
PF13812PPR_337-81 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
TkA04G049940PF13041PPR_211325.7e-47158.3
TkA04G049940PF01535PPR11329.7e-44145.3
TkA04G049940PF12854PPR_111327.5e-30103.1
TkA04G049940PF10602RPN712460.02914.8
TkA04G049940PF18768RNPP_C35610.001119.2
TkA04G049940PF13041PPR_236845.7e-47158.3
TkA04G049940PF12854PPR_136487.5e-30103.1
TkA04G049940PF13812PPR_337819.4e-2380.8
TkA04G049940PF01535PPR39699.7e-44145.3
TkA04G049940PF23276TPR_2440804e-0937.2
TkA04G049940PF29070MSC6_N431274.7e-1246.4
TkA04G049940PF10602RPN755700.02914.8
TkA04G049940PF12854PPR_168807.5e-30103.1
TkA04G049940PF01535PPR75989.7e-44145.3
TkA04G049940PF23276TPR_24782034e-0937.2
TkA04G049940PF17177PPR_long882001.8e-0938.0

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
P93005Arabidopsis thalianasp|P93005|PP181_ARATH Pentatricopeptide repeat-containing protein At2g3368030.800%Swiss-ProtMedium
Q3E6Q1Arabidopsis thalianasp|Q3E6Q1|PPR32_ARATH Pentatricopeptide repeat-containing protein At1g11290, chloroplastic30.500%Swiss-ProtMedium
Q9SS83Arabidopsis thalianasp|Q9SS83|PP220_ARATH Pentatricopeptide repeat-containing protein At3g09040, mitochondrial35.600%Swiss-ProtMedium
Q9ZQ74Arabidopsis thalianasp|Q9ZQ74|PP146_ARATH Pentatricopeptide repeat-containing protein At2g03380, mitochondrial29.200%Swiss-ProtLow
Q5G1T1Arabidopsis thalianasp|Q5G1T1|PP272_ARATH Pentatricopeptide repeat-containing protein At3g49170, chloroplastic29.200%Swiss-ProtLow

JBrowse

View in Genome Browser