General information for g5904.t25
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.t25 | TTS | g5904.t25 | 12703137 | 12703137 |
| chr_2 | g5904 | g5904.t25 | isoform | g5904.t25 | 12703139 | 12704571 |
| chr_2 | g5904 | g5904.t25 | exon | g5904.t25.exon1 | 12703139 | 12704029 |
| chr_2 | g5904 | g5904.t25 | cds | g5904.t25.CDS1 | 12703263 | 12704029 |
| chr_2 | g5904 | g5904.t25 | exon | g5904.t25.exon2 | 12704109 | 12704368 |
| chr_2 | g5904 | g5904.t25 | cds | g5904.t25.CDS2 | 12704109 | 12704334 |
| chr_2 | g5904 | g5904.t25 | exon | g5904.t25.exon3 | 12704485 | 12704571 |
| chr_2 | g5904 | g5904.t25 | TSS | g5904.t25 | 12704596 | 12704596 |
Sequences
>g5904.t25 Gene=g5904 Length=1238
GTAAAATTTTTATTTCATTCGATTTAAAATTCAAATCGTTCGTGAATAAATATAAATTGC
AGTGTAAAGGCTTCTGTTCGTCATAAAGAAGAGATAAAAGTCACATTAAATAAAAATAAA
GATGTTGTCACGCTTAGCTTGCACAAGAGCTGTCATTAACCCAGTGTTGCTTAAAAGCGC
AATTCAAAATGTCCCGAAACAGCGACAAGTCTTCAGACAATTTGCCGAAGATGTCAAGTT
CAGAACTAGATCAGAACGAATTAATGAGCGAATGTCTTTAAAAGAACGAGCAATGGCACC
AGCTGGTCCAAATGCTTATGCTATAGGAAAAGGAGCACTCGCAGGAGGTCTCGGTGCATT
ATGTTATTATGGATTAGGCTTAGGATCAGGAACAAATGCTTTACAAAACTCAATGTTATG
GCCACAATATGTTAGAGATCGCATTCATGACACATACTTATACTTTGGTGGCTCCATTCT
GATTTCAGCAGCATCAGCAGCTGCCGTATTTCGCACACCGGCCTTGCTTCGACTTGTTTC
TGGAGGTGGTTGGTTATCAATAATCGGTACTTTTGCTGTAATGATTGGTTCAGGTATGGT
GGCACAATCGATTCCCTATTCACCTGGCTTCGGAGCAAAACAATTAGCTTGGATGGCGCA
TTCAGCAATCCTCGGAGGAGTTGTCGCTCCTCTTTGCTTTGTGGGCGGTCCTATAATGAT
CAGAGCAGCATGGTACACTGCAGGCATTGTTGCTGGTTTGTCAACTGTTGCAGTTTGTGC
ACCAAGCGAAAAGTTCCTTAATATGGCCGGACCATTATCTATCGGTCTTGGTGTAGTGTT
TGCTTCATCTATTGGCTCAATGTTCCTTTCCCCAGCAACAGCTCTCGGTGCATCACTCTA
CTCAATGAGTTTGTACGGTGGTCTATTGTTATTCTCTGGATTTTTACTCTACGATACACA
AAAGATTATTAGACGTGCAGAAACACATCCACCATTCGGATTTGCACCATATGATCCAAT
CAACAATAGCATTTCAATTTACTTGGACACATTAAACATTTTCATTCGTATTGTCACACT
TTTGGCTGGTGGTGGTGGCAATCGACGCAAGTAAAAAGCCAAAATGTGAGAGTTTTGATT
TATTTTTCTGTAAATTATATTTTTGTTTTAAGTCATTATACTATTATATGTGAACATGCA
AGAGCTCTAATGAAATAAAAATTATAGCGAAAGAAAAA
>g5904.t25 Gene=g5904 Length=330
MLSRLACTRAVINPVLLKSAIQNVPKQRQVFRQFAEDVKFRTRSERINERMSLKERAMAP
AGPNAYAIGKGALAGGLGALCYYGLGLGSGTNALQNSMLWPQYVRDRIHDTYLYFGGSIL
ISAASAAAVFRTPALLRLVSGGGWLSIIGTFAVMIGSGMVAQSIPYSPGFGAKQLAWMAH
SAILGGVVAPLCFVGGPIMIRAAWYTAGIVAGLSTVAVCAPSEKFLNMAGPLSIGLGVVF
ASSIGSMFLSPATALGASLYSMSLYGGLLLFSGFLLYDTQKIIRRAETHPPFGFAPYDPI
NNSISIYLDTLNIFIRIVTLLAGGGGNRRK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 23 | g5904.t25 | CDD | cd10431 | GHITM | 81 | 328 | 1.12119E-119 |
| 2 | g5904.t25 | PANTHER | PTHR23291:SF32 | GROWTH HORMONE-INDUCIBLE TRANSMEMBRANE PROTEIN | 79 | 325 | 6.6E-75 |
| 3 | g5904.t25 | PANTHER | PTHR23291 | BAX INHIBITOR-RELATED | 79 | 325 | 6.6E-75 |
| 1 | g5904.t25 | Pfam | PF01027 | Inhibitor of apoptosis-promoting Bax1 | 105 | 321 | 2.8E-42 |
| 11 | g5904.t25 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 111 | - |
| 20 | g5904.t25 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 112 | 130 | - |
| 16 | g5904.t25 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 131 | 141 | - |
| 18 | g5904.t25 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 142 | 163 | - |
| 13 | g5904.t25 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 164 | 174 | - |
| 17 | g5904.t25 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 175 | 196 | - |
| 15 | g5904.t25 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 197 | 201 | - |
| 22 | g5904.t25 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 202 | 220 | - |
| 12 | g5904.t25 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 221 | 231 | - |
| 19 | g5904.t25 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 232 | 251 | - |
| 14 | g5904.t25 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 252 | 256 | - |
| 21 | g5904.t25 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 257 | 277 | - |
| 10 | g5904.t25 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 278 | 330 | - |
| 5 | g5904.t25 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 66 | 88 | - |
| 9 | g5904.t25 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 108 | 130 | - |
| 8 | g5904.t25 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 139 | 161 | - |
| 7 | g5904.t25 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 176 | 198 | - |
| 4 | g5904.t25 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 225 | 244 | - |
| 6 | g5904.t25 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 254 | 276 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5904/g5904.t25; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5904.t25.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.
