General information for g5904.t17
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.t17 | isoform | g5904.t17 | 12703136 | 12704499 |
| chr_2 | g5904 | g5904.t17 | exon | g5904.t17.exon1 | 12703136 | 12704029 |
| chr_2 | g5904 | g5904.t17 | TTS | g5904.t17 | 12703137 | 12703137 |
| chr_2 | g5904 | g5904.t17 | cds | g5904.t17.CDS1 | 12703263 | 12704029 |
| chr_2 | g5904 | g5904.t17 | exon | g5904.t17.exon2 | 12704097 | 12704368 |
| chr_2 | g5904 | g5904.t17 | cds | g5904.t17.CDS2 | 12704097 | 12704334 |
| chr_2 | g5904 | g5904.t17 | exon | g5904.t17.exon3 | 12704467 | 12704499 |
| chr_2 | g5904 | g5904.t17 | TSS | g5904.t17 | 12704596 | 12704596 |
Sequences
>g5904.t17 Gene=g5904 Length=1199
TCTGTTCGTCATAAAGTAAGATAAACTAATCAAGAAGAGATAAAAGTCACATTAAATAAA
AATAAAGATGTTGTCACGCTTAGCTTGCACAAGAGCTGTCATTAACCCAGTGTTGCTTAA
AAGCGCAATTCAAAATGTCCCGAAACAGCGACAAGTCTTCAGACAATTTGCCGAAGATGT
CAAGTTCAGAACTAGATCAGAACGAATTAATGAGCGAATGTCTTTAAAAGAACGAGCAAT
GGCACCAGCTGGTCCAAATGCTTATGCTATAGGAAAAGGAGCACTCGCAGGAGGTAGTTT
ATTAGGTCTCGGTGCATTATGTTATTATGGATTAGGCTTAGGATCAGGAACAAATGCTTT
ACAAAACTCAATGTTATGGCCACAATATGTTAGAGATCGCATTCATGACACATACTTATA
CTTTGGTGGCTCCATTCTGATTTCAGCAGCATCAGCAGCTGCCGTATTTCGCACACCGGC
CTTGCTTCGACTTGTTTCTGGAGGTGGTTGGTTATCAATAATCGGTACTTTTGCTGTAAT
GATTGGTTCAGGTATGGTGGCACAATCGATTCCCTATTCACCTGGCTTCGGAGCAAAACA
ATTAGCTTGGATGGCGCATTCAGCAATCCTCGGAGGAGTTGTCGCTCCTCTTTGCTTTGT
GGGCGGTCCTATAATGATCAGAGCAGCATGGTACACTGCAGGCATTGTTGCTGGTTTGTC
AACTGTTGCAGTTTGTGCACCAAGCGAAAAGTTCCTTAATATGGCCGGACCATTATCTAT
CGGTCTTGGTGTAGTGTTTGCTTCATCTATTGGCTCAATGTTCCTTTCCCCAGCAACAGC
TCTCGGTGCATCACTCTACTCAATGAGTTTGTACGGTGGTCTATTGTTATTCTCTGGATT
TTTACTCTACGATACACAAAAGATTATTAGACGTGCAGAAACACATCCACCATTCGGATT
TGCACCATATGATCCAATCAACAATAGCATTTCAATTTACTTGGACACATTAAACATTTT
CATTCGTATTGTCACACTTTTGGCTGGTGGTGGTGGCAATCGACGCAAGTAAAAAGCCAA
AATGTGAGAGTTTTGATTTATTTTTCTGTAAATTATATTTTTGTTTTAAGTCATTATACT
ATTATATGTGAACATGCAAGAGCTCTAATGAAATAAAAATTATAGCGAAAGAAAAACGA
>g5904.t17 Gene=g5904 Length=334
MLSRLACTRAVINPVLLKSAIQNVPKQRQVFRQFAEDVKFRTRSERINERMSLKERAMAP
AGPNAYAIGKGALAGGSLLGLGALCYYGLGLGSGTNALQNSMLWPQYVRDRIHDTYLYFG
GSILISAASAAAVFRTPALLRLVSGGGWLSIIGTFAVMIGSGMVAQSIPYSPGFGAKQLA
WMAHSAILGGVVAPLCFVGGPIMIRAAWYTAGIVAGLSTVAVCAPSEKFLNMAGPLSIGL
GVVFASSIGSMFLSPATALGASLYSMSLYGGLLLFSGFLLYDTQKIIRRAETHPPFGFAP
YDPINNSISIYLDTLNIFIRIVTLLAGGGGNRRK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 23 | g5904.t17 | CDD | cd10431 | GHITM | 85 | 332 | 1.29826E-119 |
| 2 | g5904.t17 | PANTHER | PTHR23291:SF32 | GROWTH HORMONE-INDUCIBLE TRANSMEMBRANE PROTEIN | 78 | 329 | 5.8E-75 |
| 3 | g5904.t17 | PANTHER | PTHR23291 | BAX INHIBITOR-RELATED | 78 | 329 | 5.8E-75 |
| 1 | g5904.t17 | Pfam | PF01027 | Inhibitor of apoptosis-promoting Bax1 | 109 | 325 | 2.9E-42 |
| 11 | g5904.t17 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 115 | - |
| 22 | g5904.t17 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 116 | 134 | - |
| 15 | g5904.t17 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 135 | 145 | - |
| 20 | g5904.t17 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 146 | 167 | - |
| 13 | g5904.t17 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 168 | 178 | - |
| 21 | g5904.t17 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 179 | 200 | - |
| 16 | g5904.t17 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 201 | 205 | - |
| 17 | g5904.t17 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 206 | 224 | - |
| 10 | g5904.t17 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 225 | 235 | - |
| 19 | g5904.t17 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 236 | 255 | - |
| 14 | g5904.t17 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 256 | 260 | - |
| 18 | g5904.t17 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 261 | 281 | - |
| 12 | g5904.t17 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 282 | 334 | - |
| 9 | g5904.t17 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 73 | 95 | - |
| 8 | g5904.t17 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 115 | 134 | - |
| 7 | g5904.t17 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 143 | 165 | - |
| 5 | g5904.t17 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 180 | 202 | - |
| 6 | g5904.t17 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 229 | 248 | - |
| 4 | g5904.t17 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 258 | 280 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5904/g5904.t17; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5904.t17.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K21890 (growth hormone-inducible transmembrane protein)
Pathway
This gene does not belong to any pathways.
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.
