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.t24 TTS g5904.t24 12703137 12703137
chr_2 g5904 g5904.t24 isoform g5904.t24 12703139 12704512
chr_2 g5904 g5904.t24 exon g5904.t24.exon1 12703139 12704029
chr_2 g5904 g5904.t24 cds g5904.t24.CDS1 12703263 12704029
chr_2 g5904 g5904.t24 exon g5904.t24.exon2 12704097 12704368
chr_2 g5904 g5904.t24 cds g5904.t24.CDS2 12704097 12704334
chr_2 g5904 g5904.t24 exon g5904.t24.exon3 12704497 12704512
chr_2 g5904 g5904.t24 TSS g5904.t24 12704596 12704596

Sequences

>g5904.t24 Gene=g5904 Length=1179
CAGTGTAAAGGCTTCTGAAGAGATAAAAGTCACATTAAATAAAAATAAAGATGTTGTCAC
GCTTAGCTTGCACAAGAGCTGTCATTAACCCAGTGTTGCTTAAAAGCGCAATTCAAAATG
TCCCGAAACAGCGACAAGTCTTCAGACAATTTGCCGAAGATGTCAAGTTCAGAACTAGAT
CAGAACGAATTAATGAGCGAATGTCTTTAAAAGAACGAGCAATGGCACCAGCTGGTCCAA
ATGCTTATGCTATAGGAAAAGGAGCACTCGCAGGAGGTAGTTTATTAGGTCTCGGTGCAT
TATGTTATTATGGATTAGGCTTAGGATCAGGAACAAATGCTTTACAAAACTCAATGTTAT
GGCCACAATATGTTAGAGATCGCATTCATGACACATACTTATACTTTGGTGGCTCCATTC
TGATTTCAGCAGCATCAGCAGCTGCCGTATTTCGCACACCGGCCTTGCTTCGACTTGTTT
CTGGAGGTGGTTGGTTATCAATAATCGGTACTTTTGCTGTAATGATTGGTTCAGGTATGG
TGGCACAATCGATTCCCTATTCACCTGGCTTCGGAGCAAAACAATTAGCTTGGATGGCGC
ATTCAGCAATCCTCGGAGGAGTTGTCGCTCCTCTTTGCTTTGTGGGCGGTCCTATAATGA
TCAGAGCAGCATGGTACACTGCAGGCATTGTTGCTGGTTTGTCAACTGTTGCAGTTTGTG
CACCAAGCGAAAAGTTCCTTAATATGGCCGGACCATTATCTATCGGTCTTGGTGTAGTGT
TTGCTTCATCTATTGGCTCAATGTTCCTTTCCCCAGCAACAGCTCTCGGTGCATCACTCT
ACTCAATGAGTTTGTACGGTGGTCTATTGTTATTCTCTGGATTTTTACTCTACGATACAC
AAAAGATTATTAGACGTGCAGAAACACATCCACCATTCGGATTTGCACCATATGATCCAA
TCAACAATAGCATTTCAATTTACTTGGACACATTAAACATTTTCATTCGTATTGTCACAC
TTTTGGCTGGTGGTGGTGGCAATCGACGCAAGTAAAAAGCCAAAATGTGAGAGTTTTGAT
TTATTTTTCTGTAAATTATATTTTTGTTTTAAGTCATTATACTATTATATGTGAACATGC
AAGAGCTCTAATGAAATAAAAATTATAGCGAAAGAAAAA

>g5904.t24 Gene=g5904 Length=334
MLSRLACTRAVINPVLLKSAIQNVPKQRQVFRQFAEDVKFRTRSERINERMSLKERAMAP
AGPNAYAIGKGALAGGSLLGLGALCYYGLGLGSGTNALQNSMLWPQYVRDRIHDTYLYFG
GSILISAASAAAVFRTPALLRLVSGGGWLSIIGTFAVMIGSGMVAQSIPYSPGFGAKQLA
WMAHSAILGGVVAPLCFVGGPIMIRAAWYTAGIVAGLSTVAVCAPSEKFLNMAGPLSIGL
GVVFASSIGSMFLSPATALGASLYSMSLYGGLLLFSGFLLYDTQKIIRRAETHPPFGFAP
YDPINNSISIYLDTLNIFIRIVTLLAGGGGNRRK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
23 g5904.t24 CDD cd10431 GHITM 85 332 1.29826E-119
2 g5904.t24 PANTHER PTHR23291:SF32 GROWTH HORMONE-INDUCIBLE TRANSMEMBRANE PROTEIN 78 329 5.8E-75
3 g5904.t24 PANTHER PTHR23291 BAX INHIBITOR-RELATED 78 329 5.8E-75
1 g5904.t24 Pfam PF01027 Inhibitor of apoptosis-promoting Bax1 109 325 2.9E-42
11 g5904.t24 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 115 -
22 g5904.t24 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 116 134 -
15 g5904.t24 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 135 145 -
20 g5904.t24 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 146 167 -
13 g5904.t24 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 168 178 -
21 g5904.t24 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 179 200 -
16 g5904.t24 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 201 205 -
17 g5904.t24 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 206 224 -
10 g5904.t24 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 225 235 -
19 g5904.t24 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 236 255 -
14 g5904.t24 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 256 260 -
18 g5904.t24 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 261 281 -
12 g5904.t24 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 282 334 -
9 g5904.t24 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 73 95 -
8 g5904.t24 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 115 134 -
7 g5904.t24 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 143 165 -
5 g5904.t24 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 180 202 -
6 g5904.t24 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 229 248 -
4 g5904.t24 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.t24; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5904.t24.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