General information for g9940.t11
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.t11 | TSS | g9940.t11 | 6117534 | 6117534 |
| chr_1 | g9940 | g9940.t11 | isoform | g9940.t11 | 6117649 | 6118641 |
| chr_1 | g9940 | g9940.t11 | exon | g9940.t11.exon1 | 6117649 | 6117669 |
| chr_1 | g9940 | g9940.t11 | exon | g9940.t11.exon2 | 6117775 | 6118102 |
| chr_1 | g9940 | g9940.t11 | cds | g9940.t11.CDS1 | 6118080 | 6118102 |
| chr_1 | g9940 | g9940.t11 | exon | g9940.t11.exon3 | 6118209 | 6118401 |
| chr_1 | g9940 | g9940.t11 | cds | g9940.t11.CDS2 | 6118209 | 6118401 |
| chr_1 | g9940 | g9940.t11 | exon | g9940.t11.exon4 | 6118480 | 6118641 |
| chr_1 | g9940 | g9940.t11 | cds | g9940.t11.CDS3 | 6118480 | 6118641 |
| chr_1 | g9940 | g9940.t11 | TTS | g9940.t11 | NA | NA |
Sequences
>g9940.t11 Gene=g9940 Length=704
ATGGCTGATCCAAAACAGTGAAGGAGATGATTTAGCTACAGCAATTTTAAAGCAAAAGTC
TAAACCTAATCGTTTGATGGTCGATGATGCTACAAATGATGATAACTCAATTGTTTGTCT
ATCGCAAGCAAAAATGGACGAGTTGCAATTGTTTCGCGGAGATACAGTTTTGTTAAAGGG
GAAAAGAAGAAAGGAGACTGTTTGTATTGTTTTATCTGACGATACATGTCCTAATGAGAA
AATTCGTATGAATCGTGTTGTTCGTAACAATTTGCGTGTTCGACTCTCGGATATTGTCGC
CATTCAATCATGTCCTGATGTTAAATATGGCAAACGTGTTCATATTTTGCAATATCTTTG
ATGTTTATTTGAAACCATACTTCCTCGAAGCTTATCGTCCTATTCATAAAGACGATACTT
TTATTGTTCGTGGTGGCATGAGAGCTGTTGAATTTAAAGTTGTTGGAACAGATCCTGAAC
CATATTGTATAGTTGCTCCCGATACTGTAATTCATTGTGAAGGAGATCCGATTAAACGTG
AAGAAGAAGAAGAAGCGTTGAATGCTGTCGGTTATGATGATATTGGTGGTTGTCGAAAGC
AATTGGCTCAAATTAAAGAAATGGTCGAGTTACCATTGCGTCATCCATCACTTTTCAAAG
CAATTGGTGTTAAACCTCCACGAGGTATTTTGTTGTATGGACCA
>g9940.t11 Gene=g9940 Length=126
MANVFIFCNIFDVYLKPYFLEAYRPIHKDDTFIVRGGMRAVEFKVVGTDPEPYCIVAPDT
VIHCEGDPIKREEEEEALNAVGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRG
ILLYGP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g9940.t11 | Gene3D | G3DSA:3.10.330.10 | - | 3 | 83 | 0 |
| 7 | g9940.t11 | Gene3D | G3DSA:3.40.50.300 | - | 84 | 126 | 0 |
| 2 | g9940.t11 | PANTHER | PTHR23077:SF63 | ZGC:136908 | 8 | 126 | 0 |
| 3 | g9940.t11 | PANTHER | PTHR23077 | AAA-FAMILY ATPASE | 8 | 126 | 0 |
| 1 | g9940.t11 | Pfam | PF02933 | Cell division protein 48 (CDC48), domain 2 | 11 | 70 | 0 |
| 6 | g9940.t11 | SMART | SM01072 | CDC48_2_2 | 6 | 71 | 0 |
| 5 | g9940.t11 | SUPERFAMILY | SSF54585 | Cdc48 domain 2-like | 6 | 77 | 0 |
| 4 | g9940.t11 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 68 | 126 | 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.
