General information for g5926.t9
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5926 is located on chr_2: 12880705..12881875 (- 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 | g5926 | g5926.t9 | isoform | g5926.t9 | 12879861 | 12881579 |
| chr_2 | g5926 | g5926.t9 | exon | g5926.t9.exon1 | 12879861 | 12880168 |
| chr_2 | g5926 | g5926.t9 | cds | g5926.t9.CDS1 | 12879863 | 12880168 |
| chr_2 | g5926 | g5926.t9 | exon | g5926.t9.exon2 | 12881454 | 12881579 |
| chr_2 | g5926 | g5926.t9 | cds | g5926.t9.CDS2 | 12881454 | 12881579 |
| chr_2 | g5926 | g5926.t9 | TSS | g5926.t9 | 12881780 | 12881780 |
| chr_2 | g5926 | g5926.t9 | TTS | g5926.t9 | NA | NA |
Sequences
>g5926.t9 Gene=g5926 Length=434
ATGGACTCAGAAATGATTTTAAATCTCGTAATAAAAGTCCAGCAATTTGAGGACAAACGA
ATTGAGGCGAAAGCATCATGGAATATAAGAGAATTAAAAGGAAAACTTAGTGAAATATAT
CCTACAAGCACTGAAGAACAGAAACTTATATATTCTGGAAAGCTCTTGAACGATACTGTT
ATATTAAAGGACGTTTTACGAGAATACGAAGGACAAGAGGCTCATACAGTTCATTTAGTT
TTCACACCCAAACAAAATTCGCGTATTCAAAATAAATTTCAGGAAAGCAAACAAAATTCA
TCTGTCAACTCCATTAATAACCAGACATCATCATCGTCATCAGATATGAGTACAAGCGAA
TTAAGACAGAGACATACAGCTACTGCCACTGTTGCTCCTAACAATACAACTGAACAACAA
CAGATGACTTCTAG
>g5926.t9 Gene=g5926 Length=144
MDSEMILNLVIKVQQFEDKRIEAKASWNIRELKGKLSEIYPTSTEEQKLIYSGKLLNDTV
ILKDVLREYEGQEAHTVHLVFTPKQNSRIQNKFQESKQNSSVNSINNQTSSSSSDMSTSE
LRQRHTATATVAPNNTTEQQQMTS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g5926.t9 | Gene3D | G3DSA:3.10.20.90 | - | 2 | 90 | 1.4E-17 |
| 6 | g5926.t9 | MobiDBLite | mobidb-lite | consensus disorder prediction | 90 | 144 | - |
| 2 | g5926.t9 | PANTHER | PTHR12943:SF27 | HOMOCYSTEINE-INDUCED ENDOPLASMIC RETICULUM PROTEIN, ISOFORM A | 8 | 142 | 1.7E-26 |
| 3 | g5926.t9 | PANTHER | PTHR12943 | HOMOCYSTEINE-RESPONSIVE ENDOPLASMIC RETICULUM-RESIDENT UNIQUITIN-LIKE DOMAIN HERPUD PROTEIN FAMILY MEMBER | 8 | 142 | 1.7E-26 |
| 1 | g5926.t9 | Pfam | PF00240 | Ubiquitin family | 11 | 83 | 9.6E-11 |
| 8 | g5926.t9 | ProSiteProfiles | PS50053 | Ubiquitin domain profile. | 7 | 86 | 14.164 |
| 5 | g5926.t9 | SMART | SM00213 | ubq_7 | 7 | 82 | 3.3E-8 |
| 4 | g5926.t9 | SUPERFAMILY | SSF54236 | Ubiquitin-like | 7 | 85 | 9.69E-15 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5926/g5926.t9; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5926.t9.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005515 | protein binding | 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.
