Gene loci information

Transcript annotation

  • This transcript has been annotated as Growth hormone-inducible transmembrane protein.

Parent gene

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.t27 TTS g5904.t27 12703137 12703137
chr_2 g5904 g5904.t27 isoform g5904.t27 12703139 12704571
chr_2 g5904 g5904.t27 exon g5904.t27.exon1 12703139 12703993
chr_2 g5904 g5904.t27 cds g5904.t27.CDS1 12703263 12703993
chr_2 g5904 g5904.t27 exon g5904.t27.exon2 12704198 12704368
chr_2 g5904 g5904.t27 cds g5904.t27.CDS2 12704198 12704225
chr_2 g5904 g5904.t27 exon g5904.t27.exon3 12704485 12704571
chr_2 g5904 g5904.t27 TSS g5904.t27 12704596 12704596

Sequences

>g5904.t27 Gene=g5904 Length=1113
GTAAAATTTTTATTTCATTCGATTTAAAATTCAAATCGTTCGTGAATAAATATAAATTGC
AGTGTAAAGGCTTCTGTTCGTCATAAAGAAGAGATAAAAGTCACATTAAATAAAAATAAA
GATGTTGTCACGCTTAGCTTGCACAAGAGCTGTCATTAACCCAGTGTTGCTTAAAAGCGC
AATTCAAAATGTCCCGAAACAGCGACAAGTCTTCAGACAATTTGCCGAAGATGTCAAGTT
CAGAACTAGATCAGAACGGATCAGGAACAAATGCTTTACAAAACTCAATGTTATGGCCAC
AATATGTTAGAGATCGCATTCATGACACATACTTATACTTTGGTGGCTCCATTCTGATTT
CAGCAGCATCAGCAGCTGCCGTATTTCGCACACCGGCCTTGCTTCGACTTGTTTCTGGAG
GTGGTTGGTTATCAATAATCGGTACTTTTGCTGTAATGATTGGTTCAGGTATGGTGGCAC
AATCGATTCCCTATTCACCTGGCTTCGGAGCAAAACAATTAGCTTGGATGGCGCATTCAG
CAATCCTCGGAGGAGTTGTCGCTCCTCTTTGCTTTGTGGGCGGTCCTATAATGATCAGAG
CAGCATGGTACACTGCAGGCATTGTTGCTGGTTTGTCAACTGTTGCAGTTTGTGCACCAA
GCGAAAAGTTCCTTAATATGGCCGGACCATTATCTATCGGTCTTGGTGTAGTGTTTGCTT
CATCTATTGGCTCAATGTTCCTTTCCCCAGCAACAGCTCTCGGTGCATCACTCTACTCAA
TGAGTTTGTACGGTGGTCTATTGTTATTCTCTGGATTTTTACTCTACGATACACAAAAGA
TTATTAGACGTGCAGAAACACATCCACCATTCGGATTTGCACCATATGATCCAATCAACA
ATAGCATTTCAATTTACTTGGACACATTAAACATTTTCATTCGTATTGTCACACTTTTGG
CTGGTGGTGGTGGCAATCGACGCAAGTAAAAAGCCAAAATGTGAGAGTTTTGATTTATTT
TTCTGTAAATTATATTTTTGTTTTAAGTCATTATACTATTATATGTGAACATGCAAGAGC
TCTAATGAAATAAAAATTATAGCGAAAGAAAAA

>g5904.t27 Gene=g5904 Length=252
MSSSELDQNGSGTNALQNSMLWPQYVRDRIHDTYLYFGGSILISAASAAAVFRTPALLRL
VSGGGWLSIIGTFAVMIGSGMVAQSIPYSPGFGAKQLAWMAHSAILGGVVAPLCFVGGPI
MIRAAWYTAGIVAGLSTVAVCAPSEKFLNMAGPLSIGLGVVFASSIGSMFLSPATALGAS
LYSMSLYGGLLLFSGFLLYDTQKIIRRAETHPPFGFAPYDPINNSISIYLDTLNIFIRIV
TLLAGGGGNRRK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g5904.t27 PANTHER PTHR23291:SF32 GROWTH HORMONE-INDUCIBLE TRANSMEMBRANE PROTEIN 14 247 2.7E-75
3 g5904.t27 PANTHER PTHR23291 BAX INHIBITOR-RELATED 14 247 2.7E-75
1 g5904.t27 Pfam PF01027 Inhibitor of apoptosis-promoting Bax1 27 243 1.2E-42
11 g5904.t27 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 33 -
16 g5904.t27 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 34 52 -
14 g5904.t27 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 53 63 -
18 g5904.t27 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 64 85 -
12 g5904.t27 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 86 96 -
17 g5904.t27 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 97 118 -
13 g5904.t27 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 119 123 -
21 g5904.t27 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 124 142 -
10 g5904.t27 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 143 153 -
19 g5904.t27 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 154 173 -
15 g5904.t27 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 174 178 -
20 g5904.t27 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 179 199 -
9 g5904.t27 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 200 252 -
8 g5904.t27 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 30 52 -
7 g5904.t27 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 61 83 -
5 g5904.t27 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 98 120 -
4 g5904.t27 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 147 166 -
6 g5904.t27 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 176 198 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5904/g5904.t27; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5904.t27.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.

Raw TPM values