General information for g5839.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Protein SAND.
Parent gene
- The parent gene g5839 is located on chr_2: 12221436..12223459 (+ 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_2 | g5839 | g5839.t2 | TSS | g5839.t2 | 12220079 | 12220079 |
| chr_2 | g5839 | g5839.t2 | isoform | g5839.t2 | 12220147 | 12220851 |
| chr_2 | g5839 | g5839.t2 | exon | g5839.t2.exon1 | 12220147 | 12220655 |
| chr_2 | g5839 | g5839.t2 | cds | g5839.t2.CDS1 | 12220147 | 12220655 |
| chr_2 | g5839 | g5839.t2 | exon | g5839.t2.exon2 | 12220714 | 12220851 |
| chr_2 | g5839 | g5839.t2 | cds | g5839.t2.CDS2 | 12220714 | 12220849 |
| chr_2 | g5839 | g5839.t2 | TTS | g5839.t2 | NA | NA |
Sequences
>g5839.t2 Gene=g5839 Length=647
ATGAGCGACATAAGCAATTTTTCAGATGATGACGATTCAAGGCAGGAAGATTGTGCATTA
GTTGATGCACTAAGTGAACTAAATTTTGAAGAAAATAATATTGAAAATATAAGAAAACGT
AAAAATAGCGATAATCAAGAGCAATCAGAGACAAATAGTGACCCATGTAGTTCTAATTCA
TTGAACTTTGTTGATGAGGAATATGACTATTTACATGATTCAGAATGGATAAATCAAAAA
TGTCAAGTTTTTATATTGAGCACAGCAGGAAAACCAATTTATACTTTACATGGCGATGAA
GATAAACTTAATCCACTTTTTGGCCTTTTACAAGCATTAGTTTCAGTAGTGAGTGTATCA
TCAAATGGAAATCCCGATGAAGATGATGATTGCATACGTTCAATAACAGCTAAAAATACT
AAATTTGTATTCCTTATCAAAAACCCATTAATACTAGTTGGTGTGAATAAATCAAAAAGA
AGCGAACAGCAGATTCTTAATCAATTAATGGATGTATATAATCAAATAATTTTTATAGTA
ACGTTGAAGCATATGAAGAATGTTTATGAGAAACGCAATAATTATGACTTACGAAAATTG
GTGGCGGGATCAGAAAGATGGATTGATCATTTGCTTAAAGATGAAAA
>g5839.t2 Gene=g5839 Length=215
MSDISNFSDDDDSRQEDCALVDALSELNFEENNIENIRKRKNSDNQEQSETNSDPCSSNS
LNFVDEEYDYLHDSEWINQKCQVFILSTAGKPIYTLHGDEDKLNPLFGLLQALVSVVSVS
SNGNPDEDDDCIRSITAKNTKFVFLIKNPLILVGVNKSKRSEQQILNQLMDVYNQIIFIV
TLKHMKNVYEKRNNYDLRKLVAGSERWIDHLLKDE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g5839.t2 | Coils | Coil | Coil | 20 | 47 | - |
| 8 | g5839.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 38 | 58 | - |
| 2 | g5839.t2 | PANTHER | PTHR13027:SF7 | FI21343P1 | 17 | 212 | 2.6E-41 |
| 3 | g5839.t2 | PANTHER | PTHR13027 | SAND PROTEIN-RELATED | 17 | 212 | 2.6E-41 |
| 4 | g5839.t2 | PRINTS | PR01546 | Saccharomyces cerevisiae 73.5kDa hypothetical protein signature | 81 | 98 | 2.8E-28 |
| 7 | g5839.t2 | PRINTS | PR01546 | Saccharomyces cerevisiae 73.5kDa hypothetical protein signature | 99 | 119 | 2.8E-28 |
| 5 | g5839.t2 | PRINTS | PR01546 | Saccharomyces cerevisiae 73.5kDa hypothetical protein signature | 164 | 192 | 2.8E-28 |
| 6 | g5839.t2 | PRINTS | PR01546 | Saccharomyces cerevisiae 73.5kDa hypothetical protein signature | 193 | 205 | 2.8E-28 |
| 1 | g5839.t2 | Pfam | PF19036 | First Longin domain of FUZ, MON1 and HPS1 | 83 | 211 | 3.5E-28 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5839/g5839.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5839.t2.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0006623 | protein targeting to vacuole | BP |
| GO:0016192 | vesicle-mediated transport | BP |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
