General information for g5904.t28
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.t28 | TTS | g5904.t28 | 12703137 | 12703137 |
| chr_2 | g5904 | g5904.t28 | isoform | g5904.t28 | 12703139 | 12704571 |
| chr_2 | g5904 | g5904.t28 | exon | g5904.t28.exon1 | 12703139 | 12703563 |
| chr_2 | g5904 | g5904.t28 | cds | g5904.t28.CDS1 | 12703405 | 12703563 |
| chr_2 | g5904 | g5904.t28 | exon | g5904.t28.exon2 | 12703629 | 12704029 |
| chr_2 | g5904 | g5904.t28 | cds | g5904.t28.CDS2 | 12703629 | 12704029 |
| chr_2 | g5904 | g5904.t28 | exon | g5904.t28.exon3 | 12704097 | 12704368 |
| chr_2 | g5904 | g5904.t28 | cds | g5904.t28.CDS3 | 12704097 | 12704334 |
| chr_2 | g5904 | g5904.t28 | exon | g5904.t28.exon4 | 12704485 | 12704571 |
| chr_2 | g5904 | g5904.t28 | TSS | g5904.t28 | 12704596 | 12704596 |
Sequences
>g5904.t28 Gene=g5904 Length=1185
GTAAAATTTTTATTTCATTCGATTTAAAATTCAAATCGTTCGTGAATAAATATAAATTGC
AGTGTAAAGGCTTCTGTTCGTCATAAAGAAGAGATAAAAGTCACATTAAATAAAAATAAA
GATGTTGTCACGCTTAGCTTGCACAAGAGCTGTCATTAACCCAGTGTTGCTTAAAAGCGC
AATTCAAAATGTCCCGAAACAGCGACAAGTCTTCAGACAATTTGCCGAAGATGTCAAGTT
CAGAACTAGATCAGAACGAATTAATGAGCGAATGTCTTTAAAAGAACGAGCAATGGCACC
AGCTGGTCCAAATGCTTATGCTATAGGAAAAGGAGCACTCGCAGGAGGTAGTTTATTAGG
TCTCGGTGCATTATGTTATTATGGATTAGGCTTAGGATCAGGAACAAATGCTTTACAAAA
CTCAATGTTATGGCCACAATATGTTAGAGATCGCATTCATGACACATACTTATACTTTGG
TGGCTCCATTCTGATTTCAGCAGCATCAGCAGCTGCCGTATTTCGCACACCGGCCTTGCT
TCGACTTGTTTCTGGAGGTGGTTGGTTATCAATAATCGGTACTTTTGCTGTAATGATTGG
TTCAGGTATGGTGGCACAATCGATTCCCTATTCACCTGGCTTCGGAGCAAAACAATTAGC
TTGGATGGCGCATTCAGCAATCCTCGGAGGAGTTGTCGCTCCTCTTTGCTTTGTGGGCGG
TCCTATAATGATCAGAGCAGCATGGTACACTGCAGGCATTATTATCTATCGGTCTTGGTG
TAGTGTTTGCTTCATCTATTGGCTCAATGTTCCTTTCCCCAGCAACAGCTCTCGGTGCAT
CACTCTACTCAATGAGTTTGTACGGTGGTCTATTGTTATTCTCTGGATTTTTACTCTACG
ATACACAAAAGATTATTAGACGTGCAGAAACACATCCACCATTCGGATTTGCACCATATG
ATCCAATCAACAATAGCATTTCAATTTACTTGGACACATTAAACATTTTCATTCGTATTG
TCACACTTTTGGCTGGTGGTGGTGGCAATCGACGCAAGTAAAAAGCCAAAATGTGAGAGT
TTTGATTTATTTTTCTGTAAATTATATTTTTGTTTTAAGTCATTATACTATTATATGTGA
ACATGCAAGAGCTCTAATGAAATAAAAATTATAGCGAAAGAAAAA
>g5904.t28 Gene=g5904 Length=265
MLSRLACTRAVINPVLLKSAIQNVPKQRQVFRQFAEDVKFRTRSERINERMSLKERAMAP
AGPNAYAIGKGALAGGSLLGLGALCYYGLGLGSGTNALQNSMLWPQYVRDRIHDTYLYFG
GSILISAASAAAVFRTPALLRLVSGGGWLSIIGTFAVMIGSGMVAQSIPYSPGFGAKQLA
WMAHSAILGGVVAPLCFVGGPIMIRAAWYTAGIIIYRSWCSVCFIYWLNVPFPSNSSRCI
TLLNEFVRWSIVILWIFTLRYTKDY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g5904.t28 | PANTHER | PTHR23291:SF32 | GROWTH HORMONE-INDUCIBLE TRANSMEMBRANE PROTEIN | 78 | 216 | 1.4E-27 |
| 3 | g5904.t28 | PANTHER | PTHR23291 | BAX INHIBITOR-RELATED | 78 | 216 | 1.4E-27 |
| 1 | g5904.t28 | Pfam | PF01027 | Inhibitor of apoptosis-promoting Bax1 | 109 | 219 | 8.8E-13 |
| 11 | g5904.t28 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 71 | - |
| 18 | g5904.t28 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 72 | 95 | - |
| 15 | g5904.t28 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 96 | 114 | - |
| 20 | g5904.t28 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 115 | 134 | - |
| 12 | g5904.t28 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 135 | 145 | - |
| 22 | g5904.t28 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 146 | 168 | - |
| 16 | g5904.t28 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 169 | 179 | - |
| 21 | g5904.t28 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 180 | 199 | - |
| 13 | g5904.t28 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 200 | 205 | - |
| 17 | g5904.t28 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 206 | 228 | - |
| 14 | g5904.t28 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 229 | 239 | - |
| 19 | g5904.t28 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 240 | 259 | - |
| 10 | g5904.t28 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 260 | 265 | - |
| 9 | g5904.t28 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 73 | 95 | - |
| 8 | g5904.t28 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 115 | 134 | - |
| 7 | g5904.t28 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 147 | 169 | - |
| 5 | g5904.t28 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 179 | 201 | - |
| 4 | g5904.t28 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 208 | 230 | - |
| 6 | g5904.t28 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 240 | 259 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5904/g5904.t28; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5904.t28.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.
