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

TkA04G169740
Reference: TK1151 Chr: Chr04 Coordinates: 43836315-43838371 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

1254 bp · TkA04G169740|TK1151|cDNA

AAGAAACCAAAGATCGGACGGCTGTAGTTTCACCGAACCCGTAAAAAAGGTCAAAATTCCTTCGGATAGCCAGTTCTTCCCCCTTTCAGCCTCCCATCTTTTTTTCTCTCTCTTCTTGACGGGCAAATGCATCTGACAAACTGTGTGATCCCTTCCTACTGAAACCTTCAAATTCATCTATGGCGGAACAACATCAACCGTCGATTCTTCTCTGACTCTCTCTCCTCACTCGATCCGTCTCCAGTTTTTTAGATCTGAAA...

CDS

Download CDS FASTA

729 bp · TkA04G169740|TK1151|CDS

ATGGAAATGGCTGCAATTTCTTCAAGCCCCCGCACCGTCGAGGAGATCTTCAAGGATTACAGCGCTCGTCGCTCCGGCATCGTCCGAGCTCTCACTTACGACGTCGATGAATTCTATGCGACCTGTGATCCAGAAAAAGAGAATCTGTGTCTATACGGACATCCAAATGAAACATGGGAAGTAACACTTCCAGCAGAAGAAGTCCCTCCAGAACTCCCGGAACCAGCTCTCGGAATCAACTTTGCAAGAGACGGAATGCA...

Protein

Download Protein FASTA

242 aa · TkA04G169740|TK1151|PROTEIN

MEMAAISSSPRTVEEIFKDYSARRSGIVRALTYDVDEFYATCDPEKENLCLYGHPNETWEVTLPAEEVPPELPEPALGINFARDGMQRRDWLSLVAVHTDSWLLAVAFYFGARLNRNERKRLFSLINDLPTVFEVVTERKHVKDKPNVDNGNKSRSSTKRSSDGQAKITPRAYDESYAEDEDEHGETLCGSCGGNYSGDEFWIGCDICERWYHGKCVKITPAKAESIKQYKCPSCSTKKGRP

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 IDTkA04G169740
TK1151 IDTkA04G169740
OH-1004 IDLXL04_035092
Relationship / confidenceRbh High Identity Coverage Synteny / Strict
Protein identity (%)100.000
Protein coverage (%)TK1151 100.000 / OH-1004 100.000
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 IDTkA04G169740
LocationChr04:43836315-43838371 (+)
DescriptionSimilar to AL1: PHD finger protein ALFIN-LIKE 1
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At5g05610 Histone-binding component that specifically recognizes H3 tails trimethylated on 'Lys-4' (H3K4me3), which mark transcription start sites of virtually all active genes. No verified direct reference in this release
At3g11200 Histone-binding component that specifically recognizes H3 tails trimethylated on 'Lys-4' (H3K4me3), which mark transcription start sites of virtually all active genes. No verified direct reference in this release

Rice

Reference gene IDPossible functionPapers / DOI
UniProt: B8B8I3 Histone-binding component that specifically recognizes H3 tails trimethylated on 'Lys-4' (H3K4me3), which mark transcription start sites of virtually all active genes. No verified direct reference in this release
Os07g0233300 Histone-binding component that specifically recognizes H3 tails trimethylated on 'Lys-4' (H3K4me3), which mark transcription start sites of virtually all active genes. No verified direct reference in this release
UniProt: B8AMA8 Histone-binding component that specifically recognizes H3 tails trimethylated on 'Lys-4' (H3K4me3), which mark transcription start sites of virtually all active genes. No verified direct reference in this release
Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_035092 · 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:0006325 chromatin organization Biological Process
GO:0006351 DNA-templated transcription Biological Process
GO:0006355 regulation of DNA-templated transcription Biological Process
GO:0005634 nucleus Cellular Component
GO:0000976 transcription cis-regulatory region binding Molecular Function
GO:0003712 transcription coregulator activity Molecular Function
GO:0008270 zinc ion binding Molecular Function
GO:0042393 histone binding Molecular Function
KEGG gene cross-reference
ath:AT5G05610
dosa:Os05g0163100
dosa:Os07g0233300
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.

Nucleus0.860
Rank 1 · TkA04G169740 · TK1151
Cytoplasm0.212
Rank 2 · TkA04G169740 · TK1151
Cell membrane0.034
Rank 3 · TkA04G169740 · TK1151
Mitochondrion0.026
Rank 4 · TkA04G169740 · TK1151
Endoplasmic reticulum0.020
Rank 5 · TkA04G169740 · 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.

PF12165Alfin12-137 aa
PF30811PHD_UBR7-like178-192 aa
PF08271Zn_Ribbon_TF181-193 aa
PF03107C1_2181-217 aa
PF00130C1_1186-223 aa
PF14446Prok-RING_1187-218 aa
PF22908PHD_NSD188-233 aa
PF13639zf-RING_2188-235 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
TkA04G169740PF12165Alfin121372.4e-70235.0
TkA04G169740PF30811PHD_UBR7-like1781921.1e-0526.0
TkA04G169740PF08271Zn_Ribbon_TF1811933.77.9
TkA04G169740PF03107C1_21812177.17.8
TkA04G169740PF00130C1_11862231.29.8
TkA04G169740PF14446Prok-RING_11872182.19.3
TkA04G169740PF22908PHD_NSD1882330.05714.4
TkA04G169740PF13639zf-RING_21882350.9510.5
TkA04G169740PF00628PHD1892352e-0938.0
TkA04G169740PF31197PHD_JHD11892313.4e-0524.4
TkA04G169740PF27108PHD_Pygo1892350.002918.4
TkA04G169740PF16866PHD_42002350.3311.7
TkA04G169740PF30811PHD_UBR7-like2012381.1e-0526.0
TkA04G169740PF21257PHD_ash2p_like2042211.39.8
TkA04G169740PF00130C1_12272361.29.8
TkA04G169740PF03107C1_22282367.17.8

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
Q9FFF5Arabidopsis thalianasp|Q9FFF5|ALFL1_ARATH PHD finger protein ALFIN-LIKE 179.200%Swiss-ProtHigh
Q9SRM4Arabidopsis thalianasp|Q9SRM4|ALFL2_ARATH PHD finger protein ALFIN-LIKE 278.000%Swiss-ProtHigh
B8B8I3Oryza sativa subsp. indicasp|B8B8I3|ALFL2_ORYSI PHD finger protein ALFIN-LIKE 274.000%Swiss-ProtHigh
Q8H383Oryza sativa subsp. japonicasp|Q8H383|ALFL2_ORYSJ PHD finger protein ALFIN-LIKE 274.000%Swiss-ProtHigh
B8AMA8Oryza sativa subsp. indicasp|B8AMA8|ALFL3_ORYSI PHD finger protein ALFIN-LIKE 370.000%Swiss-ProtHigh

JBrowse

View in Genome Browser