General information for g5687.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Transitional endoplasmic reticulum ATPase.
Parent gene
- The parent gene g5687 is located on chr_2: 11257043..11259984 (+ 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 | g5687 | g5687.t3 | TSS | g5687.t3 | 11254621 | 11254621 |
| chr_2 | g5687 | g5687.t3 | isoform | g5687.t3 | 11255404 | 11256073 |
| chr_2 | g5687 | g5687.t3 | exon | g5687.t3.exon1 | 11255404 | 11256073 |
| chr_2 | g5687 | g5687.t3 | cds | g5687.t3.CDS1 | 11255550 | 11256071 |
| chr_2 | g5687 | g5687.t3 | TTS | g5687.t3 | NA | NA |
Sequences
>g5687.t3 Gene=g5687 Length=670
GTGGATTCTTTTTTATTCAATCTGACACAATAATCACAATTTCATCATTGTATAAAAGTG
AGCAAGCAGAAAGTAAACAGCAGAAAATTTATACACTTGATAGAGTTGGTGGTCTCGATG
AAATTATTAATGATATTAAAACAATTATGGAAATAGCACTGAATCCTATCAATCAAATGT
CATTATCGAAAATATCGAGAGGAGCTTTAATTTATGGATTGTCAGGATGTGGCAAGACTT
TGCTTTCAGAAGCAATATGTGAGAGTTTTGTTGCTCATAAGATTCATATTGAATCGTGGA
AAATTTTTAGTAAATTTTATGGAGAATCAGAGAATAATCTAAGAAAACTTTTTGATGAAG
CAAATCAAATTTATCCAACACCTTGTATAATTTTAATTGATGAGCTGTCTAATATATGTC
CAAAAAACGACTCTTCTGATGTCGTGAAAAAAGTATCTTCTCTTTTAGTTTCACTTATAG
ATGGGTTACATACAAAACGAAATGGAAGCAAAACATTTATAATAGCTACAACAAACAACT
TGGACAATATTGATCCAGCAATACGTAGAAGTGGAAGATTAGATTATGAAATTGAAATTC
CTGTTCCAAATACCCAAATGCGAGAAGCTATTTTGAAGAAATTGTTGAAAAACTTTGAAA
TTTCTTCTTT
>g5687.t3 Gene=g5687 Length=174
MEIALNPINQMSLSKISRGALIYGLSGCGKTLLSEAICESFVAHKIHIESWKIFSKFYGE
SENNLRKLFDEANQIYPTPCIILIDELSNICPKNDSSDVVKKVSSLLVSLIDGLHTKRNG
SKTFIIATTNNLDNIDPAIRRSGRLDYEIEIPVPNTQMREAILKKLLKNFEISS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g5687.t3 | CDD | cd00009 | AAA | 1 | 152 | 5.40994E-13 |
| 7 | g5687.t3 | Gene3D | G3DSA:3.40.50.300 | - | 14 | 153 | 4.8E-43 |
| 8 | g5687.t3 | Gene3D | G3DSA:1.10.8.60 | - | 154 | 171 | 4.8E-43 |
| 2 | g5687.t3 | PANTHER | PTHR23077:SF27 | ATPASE FAMILY PROTEIN 2 HOMOLOG | 14 | 170 | 5.3E-41 |
| 3 | g5687.t3 | PANTHER | PTHR23077 | AAA-FAMILY ATPASE | 14 | 170 | 5.3E-41 |
| 1 | g5687.t3 | Pfam | PF00004 | ATPase family associated with various cellular activities (AAA) | 21 | 152 | 7.6E-31 |
| 6 | g5687.t3 | ProSitePatterns | PS00674 | AAA-protein family signature. | 123 | 141 | - |
| 5 | g5687.t3 | SMART | SM00382 | AAA_5 | 16 | 155 | 2.6E-11 |
| 4 | g5687.t3 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 15 | 173 | 8.47E-33 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5687/g5687.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5687.t3.fa.iupred3.txt does not exist
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.
