General information for g9940.t17
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Transitional endoplasmic reticulum ATPase.
Parent gene
- The parent gene g9940 is located on chr_1: 6119674..6120493 (+ 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 | g9940 | g9940.t17 | TSS | g9940.t17 | 6117534 | 6117534 |
| chr_1 | g9940 | g9940.t17 | isoform | g9940.t17 | 6118235 | 6118893 |
| chr_1 | g9940 | g9940.t17 | exon | g9940.t17.exon1 | 6118235 | 6118401 |
| chr_1 | g9940 | g9940.t17 | cds | g9940.t17.CDS1 | 6118297 | 6118401 |
| chr_1 | g9940 | g9940.t17 | exon | g9940.t17.exon2 | 6118480 | 6118645 |
| chr_1 | g9940 | g9940.t17 | cds | g9940.t17.CDS2 | 6118480 | 6118645 |
| chr_1 | g9940 | g9940.t17 | exon | g9940.t17.exon3 | 6118705 | 6118893 |
| chr_1 | g9940 | g9940.t17 | cds | g9940.t17.CDS3 | 6118705 | 6118892 |
| chr_1 | g9940 | g9940.t17 | TTS | g9940.t17 | NA | NA |
Sequences
>g9940.t17 Gene=g9940 Length=522
CATACTTCCTCGAAGCTTATCGTCCTATTCATAAAGACGATACTTTTATTGTTCGTGGTG
GCATGAGAGCTGTTGAATTTAAAGTTGTTGGAACAGATCCTGAACCATATTGTATAGTTG
CTCCCGATACTGTAATTCATTGTGAAGGAGATCCGATTAAACGTGAAGAAGAAGAAGAAG
CGTTGAATGCTGTCGGTTATGATGATATTGGTGGTTGTCGAAAGCAATTGGCTCAAATTA
AAGAAATGGTCGAGTTACCATTGCGTCATCCATCACTTTTCAAAGCAATTGGTGTTAAAC
CTCCACGAGGTATTTTGTTGTATGGACCACCAGGTACTGGAAAAACTTTAATTGCAAGAG
CTGTAGCAAATGAGACTGGCGCTTTCTTCTTCTTAATTAATGGTCCTGAGATTATGTCTA
AATTAGCTGGTGAATCAGAATCAAATTTGCGTAAAGCATTCGAAGAAGCAGATAAGAATT
CACCTGCAATTATATTTATTGATGAATTGGATGCAATTGCTC
>g9940.t17 Gene=g9940 Length=153
MRAVEFKVVGTDPEPYCIVAPDTVIHCEGDPIKREEEEEALNAVGYDDIGGCRKQLAQIK
EMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSK
LAGESESNLRKAFEEADKNSPAIIFIDELDAIA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g9940.t17 | CDD | cd00009 | AAA | 72 | 153 | 0 |
| 7 | g9940.t17 | Gene3D | G3DSA:3.10.330.10 | - | 1 | 46 | 0 |
| 6 | g9940.t17 | Gene3D | G3DSA:3.40.50.300 | - | 47 | 153 | 0 |
| 2 | g9940.t17 | PANTHER | PTHR23077:SF69 | TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE | 2 | 153 | 0 |
| 3 | g9940.t17 | PANTHER | PTHR23077 | AAA-FAMILY ATPASE | 2 | 153 | 0 |
| 1 | g9940.t17 | Pfam | PF00004 | ATPase family associated with various cellular activities (AAA) | 84 | 153 | 0 |
| 5 | g9940.t17 | SUPERFAMILY | SSF54585 | Cdc48 domain 2-like | 1 | 40 | 0 |
| 4 | g9940.t17 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 41 | 152 | 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:0005524 | ATP binding | MF |
| GO:0016887 | ATP hydrolysis activity | MF |
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.
