General information for g5904.t16
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t16 | isoform | g5904.t16 | 12703136 | 12704334 |
| chr_2 | g5904 | g5904.t16 | exon | g5904.t16.exon1 | 12703136 | 12703909 |
| chr_2 | g5904 | g5904.t16 | TTS | g5904.t16 | 12703137 | 12703137 |
| chr_2 | g5904 | g5904.t16 | cds | g5904.t16.CDS1 | 12703263 | 12703909 |
| chr_2 | g5904 | g5904.t16 | exon | g5904.t16.exon2 | 12703972 | 12704029 |
| chr_2 | g5904 | g5904.t16 | cds | g5904.t16.CDS2 | 12703972 | 12703981 |
| chr_2 | g5904 | g5904.t16 | exon | g5904.t16.exon3 | 12704097 | 12704334 |
| chr_2 | g5904 | g5904.t16 | TSS | g5904.t16 | 12704596 | 12704596 |
Sequences
>g5904.t16 Gene=g5904 Length=1070
ATGTTGTCACGCTTAGCTTGCACAAGAGCTGTCATTAACCCAGTGTTGCTTAAAAGCGCA
ATTCAAAATGTCCCGAAACAGCGACAAGTCTTCAGACAATTTGCCGAAGATGTCAAGTTC
AGAACTAGATCAGAACGAATTAATGAGCGAATGTCTTTAAAAGAACGAGCAATGGCACCA
GCTGGTCCAAATGCTTATGCTATAGGAAAAGGAGCACTCGCAGGAGGTAGTTTATTAGGT
CTCGGTGCATTATGTTATTATGGATTAGGCTTAGGATCAGGAACAAATGCTTTACAGTGG
CTCCATTCTGATTTCAGCAGCATCAGCAGCTGCCGTATTTCGCACACCGGCCTTGCTTCG
ACTTGTTTCTGGAGGTGGTTGGTTATCAATAATCGGTACTTTTGCTGTAATGATTGGTTC
AGGTATGGTGGCACAATCGATTCCCTATTCACCTGGCTTCGGAGCAAAACAATTAGCTTG
GATGGCGCATTCAGCAATCCTCGGAGGAGTTGTCGCTCCTCTTTGCTTTGTGGGCGGTCC
TATAATGATCAGAGCAGCATGGTACACTGCAGGCATTGTTGCTGGTTTGTCAACTGTTGC
AGTTTGTGCACCAAGCGAAAAGTTCCTTAATATGGCCGGACCATTATCTATCGGTCTTGG
TGTAGTGTTTGCTTCATCTATTGGCTCAATGTTCCTTTCCCCAGCAACAGCTCTCGGTGC
ATCACTCTACTCAATGAGTTTGTACGGTGGTCTATTGTTATTCTCTGGATTTTTACTCTA
CGATACACAAAAGATTATTAGACGTGCAGAAACACATCCACCATTCGGATTTGCACCATA
TGATCCAATCAACAATAGCATTTCAATTTACTTGGACACATTAAACATTTTCATTCGTAT
TGTCACACTTTTGGCTGGTGGTGGTGGCAATCGACGCAAGTAAAAAGCCAAAATGTGAGA
GTTTTGATTTATTTTTCTGTAAATTATATTTTTGTTTTAAGTCATTATACTATTATATGT
GAACATGCAAGAGCTCTAATGAAATAAAAATTATAGCGAAAGAAAAACGA
>g5904.t16 Gene=g5904 Length=218
MLYSGSILISAASAAAVFRTPALLRLVSGGGWLSIIGTFAVMIGSGMVAQSIPYSPGFGA
KQLAWMAHSAILGGVVAPLCFVGGPIMIRAAWYTAGIVAGLSTVAVCAPSEKFLNMAGPL
SIGLGVVFASSIGSMFLSPATALGASLYSMSLYGGLLLFSGFLLYDTQKIIRRAETHPPF
GFAPYDPINNSISIYLDTLNIFIRIVTLLAGGGGNRRK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g5904.t16 | PANTHER | PTHR23291:SF32 | GROWTH HORMONE-INDUCIBLE TRANSMEMBRANE PROTEIN | 4 | 213 | 4.4E-64 |
| 3 | g5904.t16 | PANTHER | PTHR23291 | BAX INHIBITOR-RELATED | 4 | 213 | 4.4E-64 |
| 1 | g5904.t16 | Pfam | PF01027 | Inhibitor of apoptosis-promoting Bax1 | 4 | 209 | 3.7E-38 |
| 14 | g5904.t16 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 14 | - |
| 15 | g5904.t16 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 1 | - |
| 16 | g5904.t16 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 2 | 9 | - |
| 22 | g5904.t16 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 10 | 14 | - |
| 13 | g5904.t16 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 15 | 29 | - |
| 17 | g5904.t16 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 30 | 51 | - |
| 9 | g5904.t16 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 52 | 62 | - |
| 19 | g5904.t16 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 63 | 84 | - |
| 12 | g5904.t16 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 85 | 89 | - |
| 21 | g5904.t16 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 90 | 108 | - |
| 8 | g5904.t16 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 109 | 119 | - |
| 20 | g5904.t16 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 120 | 139 | - |
| 11 | g5904.t16 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 140 | 144 | - |
| 18 | g5904.t16 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 145 | 165 | - |
| 10 | g5904.t16 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 166 | 218 | - |
| 6 | g5904.t16 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 21 | 43 | - |
| 7 | g5904.t16 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 63 | 85 | - |
| 5 | g5904.t16 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 113 | 132 | - |
| 4 | g5904.t16 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 142 | 164 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5904/g5904.t16; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5904.t16.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. There were no conditions that were differentially expressed