LXL04_009226 | RubberDandelionOmics

Gene overview

LXL04_009226

Reference: OH-1004 Chr: Chr02 Coordinates: 120936583-120946388 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

4185 bp · LXL04_009226|LXL04_009226|OH1004|cDNA

ATGTATAGTTTCATGTATTTAAAAGAATGGAATAGCAATACAGAAGTTTATGGGAAATATTGGTTTCAACATGGTATCAGGCTATTCTCTAAAACCCTAGCCGATCCTAGACCTTCCTATCATCTTCACTCTTCTTCTTCACCTTACTGTCTTTCTCCTCTTCTTATTCATCTCATTGCCTTTGTTTCCATTCTTCTGTTCAAATGGCCAAACCCACTGATAGGATATATGGTATCACCAACATCAAATCCTACATACCG...

CDS

Download CDS FASTA

4185 bp · LXL04_009226|LXL04_009226|OH1004|CDS

ATGTATAGTTTCATGTATTTAAAAGAATGGAATAGCAATACAGAAGTTTATGGGAAATATTGGTTTCAACATGGTATCAGGCTATTCTCTAAAACCCTAGCCGATCCTAGACCTTCCTATCATCTTCACTCTTCTTCTTCACCTTACTGTCTTTCTCCTCTTCTTATTCATCTCATTGCCTTTGTTTCCATTCTTCTGTTCAAATGGCCAAACCCACTGATAGGATATATGGTATCACCAACATCAAATCCTACATACCG...

Protein

Download Protein FASTA

1394 aa · LXL04_009226|LXL04_009226|OH1004|PROTEIN

MYSFMYLKEWNSNTEVYGKYWFQHGIRLFSKTLADPRPSYHLHSSSSPYCLSPLLIHLIAFVSILLFKWPNPLIGYMVSPTSNPTYRLSVPCIFLGYPSNHKGFRCLNLHTNQIIISRHVTFDETIFPFGSMTPDRSPNYDFLHVEEHRNCFNDPSHPSQPLGSPSSDDAASDPQTTVATDGAVVSDTASPSAASFPPVSTPVSPSPNPSLTNPTDTNPSPTVSAPTHSMTTRARHGIYKPIHKLNLHTDSSPSSSPTPR...

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_009226`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_009226

Location Chr02:120936583-120946388 (+)

Description Similar to At1g80880: Pentatricopeptide repeat-containing protein At1g80880, mitochondrial

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g80880`	Pentatricopeptide repeat-containing protein At1g80880, mitochondrial.	No verified direct reference in this release
`UniProt: Q94HW2`	Retrovirus-related Pol polyprotein from transposon RE1.	No verified direct reference in this release
`At5g15010`	Pentatricopeptide repeat-containing protein At5g15010, mitochondrial.	No verified direct reference in this release
`At4g02960`	Retrovirus-related Pol polyprotein from transposon RE2.	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_009226 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006310 DNA recombination Biological Process

GO:0006508 proteolysis Biological Process

GO:0015074 DNA integration Biological Process

GO:0005739 mitochondrion Cellular Component

GO:0003676 nucleic acid binding Molecular Function

GO:0003964 RNA-directed DNA polymerase activity Molecular Function

GO:0004190 aspartic-type endopeptidase activity Molecular Function

GO:0004519 endonuclease activity Molecular Function

GO:0008270 zinc ion binding Molecular Function

KEGG gene cross-reference

ath:AT1G80880

ath:AT5G15010

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.

Nucleus0.327

Rank 1 · LXL04_009226 · OH-1004

Plastid0.264

Rank 2 · LXL04_009226 · OH-1004

Mitochondrion0.214

Rank 3 · LXL04_009226 · OH-1004

Cytoplasm0.190

Rank 4 · LXL04_009226 · OH-1004

Cell membrane0.022

Rank 5 · LXL04_009226 · OH-1004

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.

PF25597.2SH3_retrovirus89-131 aa

PF07727.20RVT_2285-444 aa

PF29070.1MSC6_N1017-1159 aa

PF13041.13PPR_21044-1086 aa

PF13041.13PPR_21110-1156 aa

PF17177.11PPR_long1119-1258 aa

PF13812.13PPR_31130-1188 aa

PF23276.3TPR_241143-1237 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009226	`PF25597.2`	SH3_retrovirus	89	131	1e-16	61.1
LXL04_009226	`PF07727.20`	RVT_2	285	444	7.3e-47	160.7
LXL04_009226	`PF29070.1`	MSC6_N	1017	1159	2e-11	44.4
LXL04_009226	`PF13041.13`	PPR_2	1044	1086	1.9e-38	131.0
LXL04_009226	`PF13041.13`	PPR_2	1110	1156	1.9e-38	131.0
LXL04_009226	`PF17177.11`	PPR_long	1119	1258	6.9e-12	45.9
LXL04_009226	`PF13812.13`	PPR_3	1130	1188	1.7e-20	73.6
LXL04_009226	`PF23276.3`	TPR_24	1143	1237	3.6e-15	56.8
LXL04_009226	`PF13041.13`	PPR_2	1146	1188	1.9e-38	131.0
LXL04_009226	`PF01535.27`	PPR	1146	1174	2.1e-27	94.1
LXL04_009226	`PF29070.1`	MSC6_N	1162	1237	2e-11	44.4
LXL04_009226	`PF13812.13`	PPR_3	1200	1260	1.7e-20	73.6
LXL04_009226	`PF13041.13`	PPR_2	1212	1255	1.9e-38	131.0

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9SAH2`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At1g80880, mitochondrial	46.457%	Swiss-Prot	weak database homology
`Q94HW2`	Arabidopsis thaliana	Retrovirus-related Pol polyprotein from transposon RE1	52.466%	Swiss-Prot	weak database homology
`Q9LFQ4`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At5g15010, mitochondrial	31.640%	Swiss-Prot	weak database homology
`Q9ZT94`	Arabidopsis thaliana	Retrovirus-related Pol polyprotein from transposon RE2	51.121%	Swiss-Prot	weak database homology

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