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.t15 isoform g5904.t15 12703136 12704334
chr_2 g5904 g5904.t15 exon g5904.t15.exon1 12703136 12704029
chr_2 g5904 g5904.t15 TTS g5904.t15 12703137 12703137
chr_2 g5904 g5904.t15 cds g5904.t15.CDS1 12703263 12704029
chr_2 g5904 g5904.t15 exon g5904.t15.exon2 12704097 12704334
chr_2 g5904 g5904.t15 cds g5904.t15.CDS2 12704097 12704334
chr_2 g5904 g5904.t15 TSS g5904.t15 12704596 12704596

Sequences

>g5904.t15 Gene=g5904 Length=1132
ATGTTGTCACGCTTAGCTTGCACAAGAGCTGTCATTAACCCAGTGTTGCTTAAAAGCGCA
ATTCAAAATGTCCCGAAACAGCGACAAGTCTTCAGACAATTTGCCGAAGATGTCAAGTTC
AGAACTAGATCAGAACGAATTAATGAGCGAATGTCTTTAAAAGAACGAGCAATGGCACCA
GCTGGTCCAAATGCTTATGCTATAGGAAAAGGAGCACTCGCAGGAGGTAGTTTATTAGGT
CTCGGTGCATTATGTTATTATGGATTAGGCTTAGGATCAGGAACAAATGCTTTACAAAAC
TCAATGTTATGGCCACAATATGTTAGAGATCGCATTCATGACACATACTTATACTTTGGT
GGCTCCATTCTGATTTCAGCAGCATCAGCAGCTGCCGTATTTCGCACACCGGCCTTGCTT
CGACTTGTTTCTGGAGGTGGTTGGTTATCAATAATCGGTACTTTTGCTGTAATGATTGGT
TCAGGTATGGTGGCACAATCGATTCCCTATTCACCTGGCTTCGGAGCAAAACAATTAGCT
TGGATGGCGCATTCAGCAATCCTCGGAGGAGTTGTCGCTCCTCTTTGCTTTGTGGGCGGT
CCTATAATGATCAGAGCAGCATGGTACACTGCAGGCATTGTTGCTGGTTTGTCAACTGTT
GCAGTTTGTGCACCAAGCGAAAAGTTCCTTAATATGGCCGGACCATTATCTATCGGTCTT
GGTGTAGTGTTTGCTTCATCTATTGGCTCAATGTTCCTTTCCCCAGCAACAGCTCTCGGT
GCATCACTCTACTCAATGAGTTTGTACGGTGGTCTATTGTTATTCTCTGGATTTTTACTC
TACGATACACAAAAGATTATTAGACGTGCAGAAACACATCCACCATTCGGATTTGCACCA
TATGATCCAATCAACAATAGCATTTCAATTTACTTGGACACATTAAACATTTTCATTCGT
ATTGTCACACTTTTGGCTGGTGGTGGTGGCAATCGACGCAAGTAAAAAGCCAAAATGTGA
GAGTTTTGATTTATTTTTCTGTAAATTATATTTTTGTTTTAAGTCATTATACTATTATAT
GTGAACATGCAAGAGCTCTAATGAAATAAAAATTATAGCGAAAGAAAAACGA

>g5904.t15 Gene=g5904 Length=334
MLSRLACTRAVINPVLLKSAIQNVPKQRQVFRQFAEDVKFRTRSERINERMSLKERAMAP
AGPNAYAIGKGALAGGSLLGLGALCYYGLGLGSGTNALQNSMLWPQYVRDRIHDTYLYFG
GSILISAASAAAVFRTPALLRLVSGGGWLSIIGTFAVMIGSGMVAQSIPYSPGFGAKQLA
WMAHSAILGGVVAPLCFVGGPIMIRAAWYTAGIVAGLSTVAVCAPSEKFLNMAGPLSIGL
GVVFASSIGSMFLSPATALGASLYSMSLYGGLLLFSGFLLYDTQKIIRRAETHPPFGFAP
YDPINNSISIYLDTLNIFIRIVTLLAGGGGNRRK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
23 g5904.t15 CDD cd10431 GHITM 85 332 1.29826E-119
2 g5904.t15 PANTHER PTHR23291:SF32 GROWTH HORMONE-INDUCIBLE TRANSMEMBRANE PROTEIN 78 329 5.8E-75
3 g5904.t15 PANTHER PTHR23291 BAX INHIBITOR-RELATED 78 329 5.8E-75
1 g5904.t15 Pfam PF01027 Inhibitor of apoptosis-promoting Bax1 109 325 2.9E-42
11 g5904.t15 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 115 -
22 g5904.t15 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 116 134 -
15 g5904.t15 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 135 145 -
20 g5904.t15 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 146 167 -
13 g5904.t15 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 168 178 -
21 g5904.t15 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 179 200 -
16 g5904.t15 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 201 205 -
17 g5904.t15 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 206 224 -
10 g5904.t15 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 225 235 -
19 g5904.t15 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 236 255 -
14 g5904.t15 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 256 260 -
18 g5904.t15 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 261 281 -
12 g5904.t15 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 282 334 -
9 g5904.t15 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 73 95 -
8 g5904.t15 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 115 134 -
7 g5904.t15 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 143 165 -
5 g5904.t15 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 180 202 -
6 g5904.t15 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 229 248 -
4 g5904.t15 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 258 280 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5904/g5904.t15; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5904.t15.fa.iupred3.txt does not exist

GO terms from InterProScan

There are no GO annotations for this transcript.

KEGG

Orthology

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.

Raw TPM values