General information for g9940.t3
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.t3 | isoform | g9940.t3 | 6117230 | 6118395 |
| chr_1 | g9940 | g9940.t3 | exon | g9940.t3.exon1 | 6117230 | 6117407 |
| chr_1 | g9940 | g9940.t3 | exon | g9940.t3.exon2 | 6117605 | 6117665 |
| chr_1 | g9940 | g9940.t3 | cds | g9940.t3.CDS1 | 6117649 | 6117665 |
| chr_1 | g9940 | g9940.t3 | exon | g9940.t3.exon3 | 6117775 | 6118134 |
| chr_1 | g9940 | g9940.t3 | cds | g9940.t3.CDS2 | 6117775 | 6118134 |
| chr_1 | g9940 | g9940.t3 | exon | g9940.t3.exon4 | 6118209 | 6118395 |
| chr_1 | g9940 | g9940.t3 | cds | g9940.t3.CDS3 | 6118209 | 6118395 |
| chr_1 | g9940 | g9940.t3 | TSS | g9940.t3 | NA | NA |
| chr_1 | g9940 | g9940.t3 | TTS | g9940.t3 | NA | NA |
Sequences
>g9940.t3 Gene=g9940 Length=786
AATTTATCGGTTAAAAAAATTCAAAAATTCGCAGTCCCCTATTTTCGCATCTTCTATAAG
TTTTTTGTGCCGCTGCTTCATAAAGAAATTTACGATTCTACAATCGATAAAAATTTTTAA
ATAAAAAGTGCTTGAGTTGTTTGCTAATCATTAAAACAAGATAAATCTGTGAAGAAACAA
GGTTTTTGAATACATATATTACTGATTGATTCAACTAACAATATGGCTGATCCAAAACAA
GGAGATGATTTAGCTACAGCAATTTTAAAGCAAAAGTCTAAACCTAATCGTTTGATGGTC
GATGATGCTACAAATGATGATAACTCAATTGTTTGTCTATCGCAAGCAAAAATGGACGAG
TTGCAATTGTTTCGCGGAGATACAGTTTTGTTAAAGGGGAAAAGAAGAAAGGAGACTGTT
TGTATTGTTTTATCTGACGATACATGTCCTAATGAGAAAATTCGTATGAATCGTGTTGTT
CGTAACAATTTGCGTGTTCGACTCTCGGATATTGTCGCCATTCAATCATGTCCTGATGTT
AAATATGGCAAACGTGTTCATATTTTGCCAATTGATGACACTGTCGAAGGTCTGACTGGC
AATATCTTTGATGTTTATTTGAAACCATACTTCCTCGAAGCTTATCGTCCTATTCATAAA
GACGATACTTTTATTGTTCGTGGTGGCATGAGAGCTGTTGAATTTAAAGTTGTTGGAACA
GATCCTGAACCATATTGTATAGTTGCTCCCGATACTGTAATTCATTGTGAAGGAGATCCG
ATTAAA
>g9940.t3 Gene=g9940 Length=188
MADPKQGDDLATAILKQKSKPNRLMVDDATNDDNSIVCLSQAKMDELQLFRGDTVLLKGK
RRKETVCIVLSDDTCPNEKIRMNRVVRNNLRVRLSDIVAIQSCPDVKYGKRVHILPIDDT
VEGLTGNIFDVYLKPYFLEAYRPIHKDDTFIVRGGMRAVEFKVVGTDPEPYCIVAPDTVI
HCEGDPIK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g9940.t3 | Gene3D | G3DSA:2.40.40.20 | - | 1 | 105 | 0 |
| 9 | g9940.t3 | Gene3D | G3DSA:3.10.330.10 | - | 106 | 187 | 0 |
| 3 | g9940.t3 | PANTHER | PTHR23077:SF69 | TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE | 5 | 188 | 0 |
| 4 | g9940.t3 | PANTHER | PTHR23077 | AAA-FAMILY ATPASE | 5 | 188 | 0 |
| 2 | g9940.t3 | Pfam | PF02359 | Cell division protein 48 (CDC48), N-terminal domain | 23 | 104 | 0 |
| 1 | g9940.t3 | Pfam | PF02933 | Cell division protein 48 (CDC48), domain 2 | 124 | 187 | 0 |
| 7 | g9940.t3 | SMART | SM01073 | CDC48_N_2 | 23 | 106 | 0 |
| 8 | g9940.t3 | SMART | SM01072 | CDC48_2_2 | 123 | 187 | 0 |
| 5 | g9940.t3 | SUPERFAMILY | SSF50692 | ADC-like | 20 | 103 | 0 |
| 6 | g9940.t3 | SUPERFAMILY | SSF54585 | Cdc48 domain 2-like | 105 | 188 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
