General information for g10846.t2
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.t2 | isoform | g10846.t2 | 12225211 | 12226784 |
| chr_1 | g10846 | g10846.t2 | exon | g10846.t2.exon1 | 12225211 | 12225388 |
| chr_1 | g10846 | g10846.t2 | exon | g10846.t2.exon2 | 12225443 | 12225650 |
| chr_1 | g10846 | g10846.t2 | cds | g10846.t2.CDS1 | 12225485 | 12225650 |
| chr_1 | g10846 | g10846.t2 | exon | g10846.t2.exon3 | 12225709 | 12226784 |
| chr_1 | g10846 | g10846.t2 | cds | g10846.t2.CDS2 | 12225709 | 12226784 |
| chr_1 | g10846 | g10846.t2 | TTS | g10846.t2 | 12226965 | 12226965 |
| chr_1 | g10846 | g10846.t2 | TSS | g10846.t2 | NA | NA |
Sequences
>g10846.t2 Gene=g10846 Length=1462
ATGATGTCTGATGAATCAATTAAAGAATTGTGCTCAAAATTAGTTCCAATCAATTATTTA
GTAAGTTGAAAATTATTCATAAGTTTTAATGCTAACTCATAAAATTCACACATTATAGAA
TATCTCAGCAGATGCAAAGAAACAACGTGATAAGAAAATTAAAGAATTATTAGAAAAGAG
AAAATTACTTCAAAAAGGACTTGATGAAAATTCAATTGAAATGTTTATAAGAGAAATCTC
ATTGATGGATTCAAATAATTACACTAACAAATGTGGTGTAGGTGAAAGAGAGGGACGTAT
AGTATGTGATTTAGTTAGAAGAAGACATTTCAATTTTGCTCATGGTATAGGCAGATCTGG
AGATATTTCAGAAATACAACCAAAAGCAACTGGATCTAGTTTATTGAATCAACTTACAAA
CGCTCTCTGTTTAGATTTAATAAAAATGATGGGTGTTCGGAGTGCTGAAAAATGCATAAT
TTTTCCAATGGCGACAGGAATGACTTTGACATTAGCTCTTCTCACTCTTAAATCAAAAAG
ATTTGATGCAAATTTAGTGCTATGGTCAAGAATTGATCAAAAATCTTGTTTCAAGTGTAT
TTTAACGGCTAACTTAGTTCCTATAATAATCGATACAATCAAAAATGATAATGATGAGCT
TCATACAAATGTTGAAGAATTTGAGAAGCAAATAGAAATTTTTGGAGCTGGTCAAATTCT
TTGTATTATTTCTACAACATCATGCTTTGCACCTCGAGGTTGTGATGATATTGAAGCATT
ATCAAAATTATCAAAGAAATATGATATTCCTCATTTAGTGAATAATGCTTATGGTCTTCA
AAGTACTTATTTTACACATCAAATTGAACAGGCACAACGTGAAGGAAATATTGATTTTGT
TGTTCAGTCGACTGACAAGAATCTTCTTGTGCCAGTGGGTGGTTGCATTCTATTTGGATT
TAATCAAGAATTAATCAATGATGTAGCTAAAATGTATGCTGGAAGAGGTTCTTCGTCTTC
AACTTTAGATGTACTTATGACACTTCTACATCTTGGTCGTGATGGTTATATGAAATTGGT
TCATGAAAGAAAAGAAATGTTTCAATATTTAAAAGAGAATCTTGAAAAACTTGCTTATCA
GCATGATGAAAAAGTTATAGTAAATAAGAGAAATCCGATTTCAATGGCAATGACGTTAAA
GAGTTTTAATAAAAATAAAGTCACAATGATTGGATCGATGTTATTCACTCGAGGTATCAG
TGGAGCACGTGTAGTATCAACATTAGAGAATAAAACTATCGATGGCTATACTTTCAATCA
ATGGGGTTCACACATTTCAAATGAGAATAATGTTCCATATATCACTGTAGCCGCAAGTAT
TGGCATTACAAAAAACGAAATTGATGATTTTATTGAGAAATTTGACAAAGTTTTATTGAA
AGTAAAAAACAATGAGAGTTAA
>g10846.t2 Gene=g10846 Length=413
MFIREISLMDSNNYTNKCGVGEREGRIVCDLVRRRHFNFAHGIGRSGDISEIQPKATGSS
LLNQLTNALCLDLIKMMGVRSAEKCIIFPMATGMTLTLALLTLKSKRFDANLVLWSRIDQ
KSCFKCILTANLVPIIIDTIKNDNDELHTNVEEFEKQIEIFGAGQILCIISTTSCFAPRG
CDDIEALSKLSKKYDIPHLVNNAYGLQSTYFTHQIEQAQREGNIDFVVQSTDKNLLVPVG
GCILFGFNQELINDVAKMYAGRGSSSSTLDVLMTLLHLGRDGYMKLVHERKEMFQYLKEN
LEKLAYQHDEKVIVNKRNPISMAMTLKSFNKNKVTMIGSMLFTRGISGARVVSTLENKTI
DGYTFNQWGSHISNENNVPYITVAASIGITKNEIDDFIEKFDKVLLKVKNNES
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g10846.t2 | Coils | Coil | Coil | 137 | 157 | - |
| 4 | g10846.t2 | Gene3D | G3DSA:3.40.640.10 | - | 1 | 410 | 5.4E-177 |
| 2 | g10846.t2 | PANTHER | PTHR12944 | SOLUBLE LIVER ANTIGEN/LIVER PANCREAS ANTIGEN | 1 | 411 | 3.9E-179 |
| 9 | g10846.t2 | PIRSF | PIRSF017689 | SepSecS | 1 | 413 | 8.2E-163 |
| 1 | g10846.t2 | Pfam | PF05889 | O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS | 9 | 405 | 3.4E-132 |
| 6 | g10846.t2 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 84 | - |
| 8 | g10846.t2 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 85 | 103 | - |
| 7 | g10846.t2 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 104 | 413 | - |
| 3 | g10846.t2 | SUPERFAMILY | SSF53383 | PLP-dependent transferases | 3 | 410 | 1.35E-102 |
| 10 | g10846.t2 | TIGRFAM | TIGR03531 | selenium_SpcS: O-phosphoseryl-tRNA(Sec) selenium transferase | 1 | 405 | 1.2E-168 |
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.
