General information for g10846.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as O-phosphoseryl-tRNA(Sec) selenium transferase.
Parent gene
- The parent gene g10846 is located on chr_1: 12226784..12227877 (+ strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_1 | g10846 | g10846.t1 | isoform | g10846.t1 | 12225211 | 12226784 |
| chr_1 | g10846 | g10846.t1 | exon | g10846.t1.exon1 | 12225211 | 12225270 |
| chr_1 | g10846 | g10846.t1 | cds | g10846.t1.CDS1 | 12225211 | 12225270 |
| chr_1 | g10846 | g10846.t1 | exon | g10846.t1.exon2 | 12225329 | 12225388 |
| chr_1 | g10846 | g10846.t1 | cds | g10846.t1.CDS2 | 12225329 | 12225388 |
| chr_1 | g10846 | g10846.t1 | exon | g10846.t1.exon3 | 12225443 | 12225650 |
| chr_1 | g10846 | g10846.t1 | cds | g10846.t1.CDS3 | 12225443 | 12225650 |
| chr_1 | g10846 | g10846.t1 | exon | g10846.t1.exon4 | 12225709 | 12226784 |
| chr_1 | g10846 | g10846.t1 | cds | g10846.t1.CDS4 | 12225709 | 12226784 |
| chr_1 | g10846 | g10846.t1 | TTS | g10846.t1 | 12226965 | 12226965 |
| chr_1 | g10846 | g10846.t1 | TSS | g10846.t1 | NA | NA |
Sequences
>g10846.t1 Gene=g10846 Length=1404
ATGATGTCTGATGAATCAATTAAAGAATTGTGCTCAAAATTAGTTCCAATCAATTATTTA
AATATCTCAGCAGATGCAAAGAAACAACGTGATAAGAAAATTAAAGAATTATTAGAAAAG
AGAAAATTACTTCAAAAAGGACTTGATGAAAATTCAATTGAAATGTTTATAAGAGAAATC
TCATTGATGGATTCAAATAATTACACTAACAAATGTGGTGTAGGTGAAAGAGAGGGACGT
ATAGTATGTGATTTAGTTAGAAGAAGACATTTCAATTTTGCTCATGGTATAGGCAGATCT
GGAGATATTTCAGAAATACAACCAAAAGCAACTGGATCTAGTTTATTGAATCAACTTACA
AACGCTCTCTGTTTAGATTTAATAAAAATGATGGGTGTTCGGAGTGCTGAAAAATGCATA
ATTTTTCCAATGGCGACAGGAATGACTTTGACATTAGCTCTTCTCACTCTTAAATCAAAA
AGATTTGATGCAAATTTAGTGCTATGGTCAAGAATTGATCAAAAATCTTGTTTCAAGTGT
ATTTTAACGGCTAACTTAGTTCCTATAATAATCGATACAATCAAAAATGATAATGATGAG
CTTCATACAAATGTTGAAGAATTTGAGAAGCAAATAGAAATTTTTGGAGCTGGTCAAATT
CTTTGTATTATTTCTACAACATCATGCTTTGCACCTCGAGGTTGTGATGATATTGAAGCA
TTATCAAAATTATCAAAGAAATATGATATTCCTCATTTAGTGAATAATGCTTATGGTCTT
CAAAGTACTTATTTTACACATCAAATTGAACAGGCACAACGTGAAGGAAATATTGATTTT
GTTGTTCAGTCGACTGACAAGAATCTTCTTGTGCCAGTGGGTGGTTGCATTCTATTTGGA
TTTAATCAAGAATTAATCAATGATGTAGCTAAAATGTATGCTGGAAGAGGTTCTTCGTCT
TCAACTTTAGATGTACTTATGACACTTCTACATCTTGGTCGTGATGGTTATATGAAATTG
GTTCATGAAAGAAAAGAAATGTTTCAATATTTAAAAGAGAATCTTGAAAAACTTGCTTAT
CAGCATGATGAAAAAGTTATAGTAAATAAGAGAAATCCGATTTCAATGGCAATGACGTTA
AAGAGTTTTAATAAAAATAAAGTCACAATGATTGGATCGATGTTATTCACTCGAGGTATC
AGTGGAGCACGTGTAGTATCAACATTAGAGAATAAAACTATCGATGGCTATACTTTCAAT
CAATGGGGTTCACACATTTCAAATGAGAATAATGTTCCATATATCACTGTAGCCGCAAGT
ATTGGCATTACAAAAAACGAAATTGATGATTTTATTGAGAAATTTGACAAAGTTTTATTG
AAAGTAAAAAACAATGAGAGTTAA
>g10846.t1 Gene=g10846 Length=467
MMSDESIKELCSKLVPINYLNISADAKKQRDKKIKELLEKRKLLQKGLDENSIEMFIREI
SLMDSNNYTNKCGVGEREGRIVCDLVRRRHFNFAHGIGRSGDISEIQPKATGSSLLNQLT
NALCLDLIKMMGVRSAEKCIIFPMATGMTLTLALLTLKSKRFDANLVLWSRIDQKSCFKC
ILTANLVPIIIDTIKNDNDELHTNVEEFEKQIEIFGAGQILCIISTTSCFAPRGCDDIEA
LSKLSKKYDIPHLVNNAYGLQSTYFTHQIEQAQREGNIDFVVQSTDKNLLVPVGGCILFG
FNQELINDVAKMYAGRGSSSSTLDVLMTLLHLGRDGYMKLVHERKEMFQYLKENLEKLAY
QHDEKVIVNKRNPISMAMTLKSFNKNKVTMIGSMLFTRGISGARVVSTLENKTIDGYTFN
QWGSHISNENNVPYITVAASIGITKNEIDDFIEKFDKVLLKVKNNES
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g10846.t1 | Coils | Coil | Coil | 191 | 211 | - |
| 4 | g10846.t1 | Gene3D | G3DSA:3.40.640.10 | - | 2 | 464 | 3.9E-190 |
| 2 | g10846.t1 | PANTHER | PTHR12944 | SOLUBLE LIVER ANTIGEN/LIVER PANCREAS ANTIGEN | 5 | 465 | 4.9E-192 |
| 9 | g10846.t1 | PIRSF | PIRSF017689 | SepSecS | 4 | 467 | 8.3E-174 |
| 1 | g10846.t1 | Pfam | PF05889 | O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS | 63 | 459 | 5.3E-132 |
| 6 | g10846.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 138 | - |
| 8 | g10846.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 139 | 157 | - |
| 7 | g10846.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 158 | 467 | - |
| 3 | g10846.t1 | SUPERFAMILY | SSF53383 | PLP-dependent transferases | 30 | 464 | 7.78E-107 |
| 10 | g10846.t1 | TIGRFAM | TIGR03531 | selenium_SpcS: O-phosphoseryl-tRNA(Sec) selenium transferase | 15 | 459 | 5.8E-181 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016785 | selenotransferase activity | MF |
| GO:0097056 | selenocysteinyl-tRNA(Sec) biosynthetic process | BP |
| GO:0016740 | transferase activity | MF |
| GO:0003824 | catalytic activity | MF |
KEGG
Orthology
- This transcript has been annotated with K03341 (O-phospho-L-seryl-tRNASec:L-selenocysteinyl-tRNA synthase)
Pathway
- This transcript belongs to the following pathways
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.
