LXL04_034458 | RubberDandelionOmics

Gene overview

LXL04_034458

Reference: OH-1004 Chr: Chr07 Coordinates: 101562410-101566634 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2763 bp · LXL04_034458|LXL04_034458|OH1004|cDNA

ATGTCGATTCCAAGCGACTTGTATCCAAGCCAAGACGATCTTCTGTACGAGGAAGAACTCCTCAGAAACCCCTTTAGTCTCAAGCTATGGTGGCGTTACTTAATTGCACGAACCGAATCTCCCTTCAAGAAAAGAGCCGTAATCTACGAACGAGCGCTCAAAGCTCTTCCCGGAAGCTACAAACTATGGCATGCTTACCTCCGCGAACGCCTCGAATTGGTACGTAATTTACCCATTTCTCACTCACAATACCAAACCCT...

CDS

Download CDS FASTA

2763 bp · LXL04_034458|LXL04_034458|OH1004|CDS

ATGTCGATTCCAAGCGACTTGTATCCAAGCCAAGACGATCTTCTGTACGAGGAAGAACTCCTCAGAAACCCCTTTAGTCTCAAGCTATGGTGGCGTTACTTAATTGCACGAACCGAATCTCCCTTCAAGAAAAGAGCCGTAATCTACGAACGAGCGCTCAAAGCTCTTCCCGGAAGCTACAAACTATGGCATGCTTACCTCCGCGAACGCCTCGAATTGGTACGTAATTTACCCATTTCTCACTCACAATACCAAACCCT...

Protein

Download Protein FASTA

920 aa · LXL04_034458|LXL04_034458|OH1004|PROTEIN

MSIPSDLYPSQDDLLYEEELLRNPFSLKLWWRYLIARTESPFKKRAVIYERALKALPGSYKLWHAYLRERLELVRNLPISHSQYQTLNNTFERALVTMHKMPRIWFMYLTSLTEQKLVTRTRRTFDRALCALPVTQHERIWDPYLVFVSQRGVPIETSLRVYRRYLKYDPGHIENLIEFLLNSGLWQEAAERLAGVLNDDRFYSIKGKTKHRLWLELCDLLTQHATEISGLNVDAIIRGGIRKFTDEVGRLWTSLADYYI...

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.

ID Mapping

Input ID	`LXL04_034458`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID	`LXL04_034458`
Location	Chr07:101562410-101566634 (-)
Description	Similar to Xab2: Pre-mRNA-splicing factor SYF1
Arabidopsis / Rice Reference Genes and Papers	Download references for this gene Arabidopsis No hit for this species in the current source table. Rice No hit for this species in the current source table.
Functional annotation source	View annotation sources Functional annotation source: OH1004 · `LXL04_034458` · GCA_047496595.1_OSU_TarKok_2.0.
GO annotations (OH1004 source)	GO:0000349 generation of catalytic spliceosome for first transesterification step Biological Process GO:0000381 regulation of alternative mRNA splicing, via spliceosome Biological Process GO:0000398 mRNA splicing, via spliceosome Biological Process GO:0006281 DNA repair Biological Process GO:0006283 transcription-coupled nucleotide-excision repair Biological Process GO:0006351 DNA-templated transcription Biological Process GO:0008380 RNA splicing Biological Process GO:0000974 Prp19 complex Cellular Component GO:0005634 nucleus Cellular Component GO:0005654 nucleoplasm Cellular Component GO:0005681 spliceosomal complex Cellular Component GO:0016020 membrane Cellular Component
KEGG gene cross-reference	ddi:DDB_G0277977 dme:Dmel_CG6197 hsa:56949 mmu:67439 rno:245976 These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

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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.

Nucleus0.933

Rank 1 · LXL04_034458 · OH-1004

Cytoplasm0.130

Rank 2 · LXL04_034458 · OH-1004

Cell membrane0.019

Rank 3 · LXL04_034458 · OH-1004

Mitochondrion0.016

Rank 4 · LXL04_034458 · OH-1004

Endoplasmic reticulum0.011

Rank 5 · LXL04_034458 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

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

PF23233.2HAT_Syf1_CNRKL1_N12-170 aa

PF23240.2HAT_PRP39_N16-144 aa

PF23240.2HAT_PRP39_N80-169 aa

PF23241.2HAT_PRP39_C80-178 aa

PF23220.2HAT_Syf1_M173-320 aa

PF23220.2HAT_Syf1_M352-414 aa

PF29376.1PRP6_TPR379-493 aa

PF23240.2HAT_PRP39_N380-546 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_034458	`PF23233.2`	HAT_Syf1_CNRKL1_N	12	170	7.5e-73	244.3
LXL04_034458	`PF23240.2`	HAT_PRP39_N	16	144	2e-29	103.5
LXL04_034458	`PF23240.2`	HAT_PRP39_N	80	169	2e-29	103.5
LXL04_034458	`PF23241.2`	HAT_PRP39_C	80	178	2.8e-28	99.4
LXL04_034458	`PF23220.2`	HAT_Syf1_M	173	320	5e-86	288.7
LXL04_034458	`PF23220.2`	HAT_Syf1_M	352	414	5e-86	288.7
LXL04_034458	`PF29376.1`	PRP6_TPR	379	493	2.5e-17	63.4
LXL04_034458	`PF23240.2`	HAT_PRP39_N	380	546	2e-29	103.5
LXL04_034458	`PF23231.2`	HAT_Syf1_CNRKL1_C	416	809	7.3e-191	634.9
LXL04_034458	`PF23233.2`	HAT_Syf1_CNRKL1_N	512	654	7.5e-73	244.3
LXL04_034458	`PF23241.2`	HAT_PRP39_C	514	580	2.8e-28	99.4
LXL04_034458	`PF29376.1`	PRP6_TPR	518	776	2.5e-17	63.4
LXL04_034458	`PF05843.21`	Suf	518	662	1.5e-13	50.9
LXL04_034458	`PF23233.2`	HAT_Syf1_CNRKL1_N	555	687	7.5e-73	244.3
LXL04_034458	`PF23240.2`	HAT_PRP39_N	555	622	2e-29	103.5
LXL04_034458	`PF23241.2`	HAT_PRP39_C	585	670	2.8e-28	99.4

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.

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