General information for g4858.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Voltage-dependent anion-selective channel.
Parent gene
- The parent gene g4858 is located on chr_2: 5442898..5451158 (+ 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 | g4858 | g4858.t6 | isoform | g4858.t6 | 5440459 | 5442613 |
| chr_2 | g4858 | g4858.t6 | exon | g4858.t6.exon1 | 5440459 | 5440594 |
| chr_2 | g4858 | g4858.t6 | TSS | g4858.t6 | 5440498 | 5440498 |
| chr_2 | g4858 | g4858.t6 | exon | g4858.t6.exon2 | 5441973 | 5442293 |
| chr_2 | g4858 | g4858.t6 | cds | g4858.t6.CDS1 | 5441974 | 5442293 |
| chr_2 | g4858 | g4858.t6 | exon | g4858.t6.exon3 | 5442533 | 5442613 |
| chr_2 | g4858 | g4858.t6 | cds | g4858.t6.CDS2 | 5442533 | 5442611 |
| chr_2 | g4858 | g4858.t6 | TTS | g4858.t6 | 5443364 | 5443364 |
Sequences
>g4858.t6 Gene=g4858 Length=538
GAAAGTGCGAAAACCCTGGTTTTCTCGCAAATCGAAATTTGTGAAAAGAGTTTGAAGTCG
GTCGCATTTAATTGAAATTTCATATCGTTTCCGTAATTCGCTCAGTCAGTAATTAATTAA
AACTAATCCAAAGTAAAATGTCTCCACCAGCATATTCAGATTTGGGCAAAAACGCTCGCG
ATGTTTTCGGCAAGGGTTACCACTTTGGTTTGTGGAAATTGGATGTTAAGACAAGAACAA
ACAGTGGCGTTGAATTCACCAGTGCAGGACATTCAAATCAAGATACTGGAAAAGTTTTTG
GTTCATTGGAGACCAAATACAAGTTGAAGGAATACGGACTTACTTTCTCAGAAAAGTGGA
ACACAGATAACACTTTAACATCAGAAGTTTCCGTTGAAGACCAACTCGTTAAGGGTCTCA
AATTGAGTTTTGATGGCTCATTTGCACCACAAACAGGAAGCAAAACAGGGCGCTTCAAGA
CTGCATACTCGCATGAGCGTGTTCGATTGGATGGCGATTTCAACCTCGATTTGGGTGG
>g4858.t6 Gene=g4858 Length=133
MSPPAYSDLGKNARDVFGKGYHFGLWKLDVKTRTNSGVEFTSAGHSNQDTGKVFGSLETK
YKLKEYGLTFSEKWNTDNTLTSEVSVEDQLVKGLKLSFDGSFAPQTGSKTGRFKTAYSHE
RVRLDGDFNLDLG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g4858.t6 | CDD | cd07306 | Porin3_VDAC | 3 | 133 | 0 |
| 6 | g4858.t6 | Gene3D | G3DSA:2.40.160.10 | Porin | 1 | 133 | 0 |
| 2 | g4858.t6 | PANTHER | PTHR11743:SF12 | VOLTAGE-DEPENDENT ANION-SELECTIVE CHANNEL PROTEIN 2 | 3 | 132 | 0 |
| 3 | g4858.t6 | PANTHER | PTHR11743 | VOLTAGE-DEPENDENT ANION-SELECTIVE CHANNEL | 3 | 132 | 0 |
| 5 | g4858.t6 | PRINTS | PR00185 | Eukaryotic porin signature | 4 | 19 | 0 |
| 4 | g4858.t6 | PRINTS | PR00185 | Eukaryotic porin signature | 67 | 82 | 0 |
| 1 | g4858.t6 | Pfam | PF01459 | Eukaryotic porin | 3 | 130 | 0 |
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:0055085 | transmembrane transport | BP |
| GO:0008308 | voltage-gated anion channel activity | MF |
| GO:0005741 | mitochondrial outer membrane | CC |
| GO:0098656 | anion transmembrane 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. There were no conditions that were differentially expressed