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.t14 isoform g5904.t14 12703136 12704027
chr_2 g5904 g5904.t14 exon g5904.t14.exon1 12703136 12704027
chr_2 g5904 g5904.t14 TTS g5904.t14 12703137 12703137
chr_2 g5904 g5904.t14 cds g5904.t14.CDS1 12703263 12703964
chr_2 g5904 g5904.t14 TSS g5904.t14 12704596 12704596

Sequences

>g5904.t14 Gene=g5904 Length=892
CTCGGTGCATTATGTTATTATGGATTAGGCTTAGGATCAGGAACAAATGCTTTACAAAAC
TCAATGTTATGGCCACAATATGTTAGAGATCGCATTCATGACACATACTTATACTTTGGT
GGCTCCATTCTGATTTCAGCAGCATCAGCAGCTGCCGTATTTCGCACACCGGCCTTGCTT
CGACTTGTTTCTGGAGGTGGTTGGTTATCAATAATCGGTACTTTTGCTGTAATGATTGGT
TCAGGTATGGTGGCACAATCGATTCCCTATTCACCTGGCTTCGGAGCAAAACAATTAGCT
TGGATGGCGCATTCAGCAATCCTCGGAGGAGTTGTCGCTCCTCTTTGCTTTGTGGGCGGT
CCTATAATGATCAGAGCAGCATGGTACACTGCAGGCATTGTTGCTGGTTTGTCAACTGTT
GCAGTTTGTGCACCAAGCGAAAAGTTCCTTAATATGGCCGGACCATTATCTATCGGTCTT
GGTGTAGTGTTTGCTTCATCTATTGGCTCAATGTTCCTTTCCCCAGCAACAGCTCTCGGT
GCATCACTCTACTCAATGAGTTTGTACGGTGGTCTATTGTTATTCTCTGGATTTTTACTC
TACGATACACAAAAGATTATTAGACGTGCAGAAACACATCCACCATTCGGATTTGCACCA
TATGATCCAATCAACAATAGCATTTCAATTTACTTGGACACATTAAACATTTTCATTCGT
ATTGTCACACTTTTGGCTGGTGGTGGTGGCAATCGACGCAAGTAAAAAGCCAAAATGTGA
GAGTTTTGATTTATTTTTCTGTAAATTATATTTTTGTTTTAAGTCATTATACTATTATAT
GTGAACATGCAAGAGCTCTAATGAAATAAAAATTATAGCGAAAGAAAAACGA

>g5904.t14 Gene=g5904 Length=233
MLWPQYVRDRIHDTYLYFGGSILISAASAAAVFRTPALLRLVSGGGWLSIIGTFAVMIGS
GMVAQSIPYSPGFGAKQLAWMAHSAILGGVVAPLCFVGGPIMIRAAWYTAGIVAGLSTVA
VCAPSEKFLNMAGPLSIGLGVVFASSIGSMFLSPATALGASLYSMSLYGGLLLFSGFLLY
DTQKIIRRAETHPPFGFAPYDPINNSISIYLDTLNIFIRIVTLLAGGGGNRRK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g5904.t14 PANTHER PTHR23291:SF32 GROWTH HORMONE-INDUCIBLE TRANSMEMBRANE PROTEIN 2 228 6.0E-73
3 g5904.t14 PANTHER PTHR23291 BAX INHIBITOR-RELATED 2 228 6.0E-73
1 g5904.t14 Pfam PF01027 Inhibitor of apoptosis-promoting Bax1 8 224 8.6E-43
12 g5904.t14 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 14 -
20 g5904.t14 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 15 33 -
14 g5904.t14 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 34 44 -
18 g5904.t14 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 45 66 -
11 g5904.t14 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 67 77 -
16 g5904.t14 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 78 99 -
15 g5904.t14 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 100 104 -
19 g5904.t14 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 105 123 -
10 g5904.t14 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 124 134 -
21 g5904.t14 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 135 154 -
13 g5904.t14 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 155 159 -
17 g5904.t14 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 160 180 -
9 g5904.t14 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 181 233 -
5 g5904.t14 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 15 37 -
8 g5904.t14 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 44 66 -
7 g5904.t14 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 86 108 -
6 g5904.t14 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 128 147 -
4 g5904.t14 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 157 179 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5904/g5904.t14; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5904.t14.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