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.t18 isoform g5904.t18 12703136 12704571
chr_2 g5904 g5904.t18 exon g5904.t18.exon1 12703136 12703347
chr_2 g5904 g5904.t18 TTS g5904.t18 12703137 12703137
chr_2 g5904 g5904.t18 cds g5904.t18.CDS1 12703322 12703347
chr_2 g5904 g5904.t18 exon g5904.t18.exon2 12703430 12704029
chr_2 g5904 g5904.t18 cds g5904.t18.CDS2 12703430 12704029
chr_2 g5904 g5904.t18 exon g5904.t18.exon3 12704097 12704368
chr_2 g5904 g5904.t18 cds g5904.t18.CDS3 12704097 12704334
chr_2 g5904 g5904.t18 exon g5904.t18.exon4 12704485 12704571
chr_2 g5904 g5904.t18 TSS g5904.t18 12704596 12704596

Sequences

>g5904.t18 Gene=g5904 Length=1171
GTAAAATTTTTATTTCATTCGATTTAAAATTCAAATCGTTCGTGAATAAATATAAATTGC
AGTGTAAAGGCTTCTGTTCGTCATAAAGAAGAGATAAAAGTCACATTAAATAAAAATAAA
GATGTTGTCACGCTTAGCTTGCACAAGAGCTGTCATTAACCCAGTGTTGCTTAAAAGCGC
AATTCAAAATGTCCCGAAACAGCGACAAGTCTTCAGACAATTTGCCGAAGATGTCAAGTT
CAGAACTAGATCAGAACGAATTAATGAGCGAATGTCTTTAAAAGAACGAGCAATGGCACC
AGCTGGTCCAAATGCTTATGCTATAGGAAAAGGAGCACTCGCAGGAGGTAGTTTATTAGG
TCTCGGTGCATTATGTTATTATGGATTAGGCTTAGGATCAGGAACAAATGCTTTACAAAA
CTCAATGTTATGGCCACAATATGTTAGAGATCGCATTCATGACACATACTTATACTTTGG
TGGCTCCATTCTGATTTCAGCAGCATCAGCAGCTGCCGTATTTCGCACACCGGCCTTGCT
TCGACTTGTTTCTGGAGGTGGTTGGTTATCAATAATCGGTACTTTTGCTGTAATGATTGG
TTCAGGTATGGTGGCACAATCGATTCCCTATTCACCTGGCTTCGGAGCAAAACAATTAGC
TTGGATGGCGCATTCAGCAATCCTCGGAGGAGTTGTCGCTCCTCTTTGCTTTGTGGGCGG
TCCTATAATGATCAGAGCAGCATGGTACACTGCAGGCATTGTTGCTGGTTTGTCAACTGT
TGCAGTTTGTGCACCAAGCGAAAAGTTCCTTAATATGGCCGGACCATTATCTATCGGTCT
TGGTGTAGTGTTTGCTTCATCTATTGGCTCAATGTTCCTTTCCCCAGCAACAGCTCTCGG
TGCATCACTCTACTCAATGAGTTTGTACGGTGGTCTATTGTTATTCTCTGGATTTTTACC
ATTTCAATTTACTTGGACACATTAAACATTTTCATTCGTATTGTCACACTTTTGGCTGGT
GGTGGTGGCAATCGACGCAAGTAAAAAGCCAAAATGTGAGAGTTTTGATTTATTTTTCTG
TAAATTATATTTTTGTTTTAAGTCATTATACTATTATATGTGAACATGCAAGAGCTCTAA
TGAAATAAAAATTATAGCGAAAGAAAAACGA

>g5904.t18 Gene=g5904 Length=287
MLSRLACTRAVINPVLLKSAIQNVPKQRQVFRQFAEDVKFRTRSERINERMSLKERAMAP
AGPNAYAIGKGALAGGSLLGLGALCYYGLGLGSGTNALQNSMLWPQYVRDRIHDTYLYFG
GSILISAASAAAVFRTPALLRLVSGGGWLSIIGTFAVMIGSGMVAQSIPYSPGFGAKQLA
WMAHSAILGGVVAPLCFVGGPIMIRAAWYTAGIVAGLSTVAVCAPSEKFLNMAGPLSIGL
GVVFASSIGSMFLSPATALGASLYSMSLYGGLLLFSGFLPFQFTWTH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g5904.t18 PANTHER PTHR23291:SF32 GROWTH HORMONE-INDUCIBLE TRANSMEMBRANE PROTEIN 78 279 1.6E-52
3 g5904.t18 PANTHER PTHR23291 BAX INHIBITOR-RELATED 78 279 1.6E-52
1 g5904.t18 Pfam PF01027 Inhibitor of apoptosis-promoting Bax1 109 283 5.5E-26
12 g5904.t18 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 115 -
22 g5904.t18 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 116 134 -
15 g5904.t18 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 135 145 -
20 g5904.t18 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 146 167 -
14 g5904.t18 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 168 178 -
21 g5904.t18 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 179 200 -
17 g5904.t18 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 201 205 -
18 g5904.t18 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 206 224 -
11 g5904.t18 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 225 235 -
19 g5904.t18 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 236 254 -
16 g5904.t18 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 255 265 -
23 g5904.t18 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 266 285 -
13 g5904.t18 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 286 287 -
10 g5904.t18 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 73 95 -
7 g5904.t18 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 115 134 -
9 g5904.t18 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 146 168 -
8 g5904.t18 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 178 200 -
4 g5904.t18 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 207 224 -
6 g5904.t18 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 234 256 -
5 g5904.t18 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 263 285 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5904/g5904.t18; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5904.t18.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