General information for g5904.t29
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Growth hormone-inducible transmembrane protein.
Parent gene
- The parent gene g5904 is located on chr_2: 12703249..12704835 (- 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 | g5904 | g5904.t29 | TTS | g5904.t29 | 12703137 | 12703137 |
| chr_2 | g5904 | g5904.t29 | isoform | g5904.t29 | 12703195 | 12703822 |
| chr_2 | g5904 | g5904.t29 | exon | g5904.t29.exon1 | 12703195 | 12703648 |
| chr_2 | g5904 | g5904.t29 | cds | g5904.t29.CDS1 | 12703263 | 12703574 |
| chr_2 | g5904 | g5904.t29 | exon | g5904.t29.exon2 | 12703755 | 12703822 |
| chr_2 | g5904 | g5904.t29 | TSS | g5904.t29 | 12704596 | 12704596 |
Sequences
>g5904.t29 Gene=g5904 Length=522
TATCAATAATCGGTACTTTTGCTGTAATGATTGGTTCAGGTATGGTGGCACAATCGATTC
CCTATTCACATGGTACACTGCAGGCATTGTTGCTGGTTTGTCAACTGTTGCAGTTTGTGC
ACCAAGCGAAAAGTTCCTTAATATGGCCGGACCATTATCTATCGGTCTTGGTGTAGTGTT
TGCTTCATCTATTGGCTCAATGTTCCTTTCCCCAGCAACAGCTCTCGGTGCATCACTCTA
CTCAATGAGTTTGTACGGTGGTCTATTGTTATTCTCTGGATTTTTACTCTACGATACACA
AAAGATTATTAGACGTGCAGAAACACATCCACCATTCGGATTTGCACCATATGATCCAAT
CAACAATAGCATTTCAATTTACTTGGACACATTAAACATTTTCATTCGTATTGTCACACT
TTTGGCTGGTGGTGGTGGCAATCGACGCAAGTAAAAAGCCAAAATGTGAGAGTTTTGATT
TATTTTTCTGTAAATTATATTTTTGTTTTAAGTCATTATACT
>g5904.t29 Gene=g5904 Length=103
MAGPLSIGLGVVFASSIGSMFLSPATALGASLYSMSLYGGLLLFSGFLLYDTQKIIRRAE
THPPFGFAPYDPINNSISIYLDTLNIFIRIVTLLAGGGGNRRK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g5904.t29 | PANTHER | PTHR23291:SF32 | GROWTH HORMONE-INDUCIBLE TRANSMEMBRANE PROTEIN | 1 | 99 | 2.3E-27 |
| 3 | g5904.t29 | PANTHER | PTHR23291 | BAX INHIBITOR-RELATED | 1 | 99 | 2.3E-27 |
| 1 | g5904.t29 | Pfam | PF01027 | Inhibitor of apoptosis-promoting Bax1 | 1 | 94 | 8.7E-20 |
| 8 | g5904.t29 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 14 | - |
| 9 | g5904.t29 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 1 | - |
| 10 | g5904.t29 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 2 | 9 | - |
| 12 | g5904.t29 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 10 | 14 | - |
| 7 | g5904.t29 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 15 | 29 | - |
| 11 | g5904.t29 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 30 | 50 | - |
| 6 | g5904.t29 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 51 | 103 | - |
| 5 | g5904.t29 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 5 | 22 | - |
| 4 | g5904.t29 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 27 | 49 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5904/g5904.t29; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5904.t29.fa.iupred3.txt does not exist
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.
