Gene loci information

Transcript annotation

  • This transcript has been annotated as Tumor suppressor candidate 3.

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_3 g442 g442.t4 TSS g442.t4 3371808 3371808
chr_3 g442 g442.t4 isoform g442.t4 3371890 3372948
chr_3 g442 g442.t4 exon g442.t4.exon1 3371890 3371959
chr_3 g442 g442.t4 exon g442.t4.exon2 3372156 3372948
chr_3 g442 g442.t4 cds g442.t4.CDS1 3372175 3372948
chr_3 g442 g442.t4 TTS g442.t4 3373100 3373100

Sequences

>g442.t4 Gene=g442 Length=863
ATGAAAATAGTGAATAGTATTGTATTTGCAATAGTAGCATTTATTCTTATCACTGCTGAT
GTAGAAGGACAAATTATTCTATAATTGTAATGTTTACTGCTTTACAACCGGCTCGACAAT
GTATTATTTGCAGACCAGCATCAGACGAATATACAATCTTAGCAAATTCTTATCGCTATT
CATCAGCATATTCTAATAAGCTTTTCTTCGCTATGGTTGATTTTGATGAAGGCTCAGACG
TATTTCAAATGCTTAGACTTAATACTGCTCCAGTTTTTATGCATTTCCCTGCTAAAGGCA
AAGCAAAAGGCAGTGACACTATGGACATTCAAAGAGTAGGCATTTCTGCGGAAGCAATTG
CAAAATGGGTACAAGAGCGCACAGATATACAAATTAGAATTTTTAGACCACCAAATTATT
CTGGAACTGTAGCAGTTATTATGTTAGTTGCATTCGTTGGAGGCTTTTTGTATTTAAAGA
GAAATAACTTAGAATTTCTACAAAACAAGCAACTTTGGGCATTGCTGGCAGTTTTGTTTA
CTTTTGCAATGGTCTCAGGTCAAATGTGGAATCACATTCGATCACCACCTTTCGTTCACA
AGAGTCAAAATGGAGGTATCTCATATTTCCATGGATCATCTCAAGGTCAACTTGTATTTG
AGACTTATATTGTAATGGTTCTTAATGGCCTTGTTGTAATTGGAATGATTCTATTAACTG
AATCTGGAAGTCAAAGTGATACAAGAAAAGGAAAATTGATGGCAATTGTTGGTCTCGTTT
TTGTAGCTGTTTTCTTCTCTCTACTTCTATCAGCATTCAGATCAAAAGCACACGGTTATC
CATATTCATTCCTTTTCAAGTAA

>g442.t4 Gene=g442 Length=257
MFTALQPARQCIICRPASDEYTILANSYRYSSAYSNKLFFAMVDFDEGSDVFQMLRLNTA
PVFMHFPAKGKAKGSDTMDIQRVGISAEAIAKWVQERTDIQIRIFRPPNYSGTVAVIMLV
AFVGGFLYLKRNNLEFLQNKQLWALLAVLFTFAMVSGQMWNHIRSPPFVHKSQNGGISYF
HGSSQGQLVFETYIVMVLNGLVVIGMILLTESGSQSDTRKGKLMAIVGLVFVAVFFSLLL
SAFRSKAHGYPYSFLFK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g442.t4 Gene3D G3DSA:3.40.30.10 Glutaredoxin 1 116 1.9E-28
2 g442.t4 PANTHER PTHR12692 DOLICHYL-DIPHOSPHOOLIGOSACCHARIDE–PROTEIN GLYCOSYLTRANSFERASE-RELATED 1 256 6.9E-114
3 g442.t4 PANTHER PTHR12692:SF1 TUMOR SUPPRESSOR CANDIDATE 3 1 256 6.9E-114
1 g442.t4 Pfam PF04756 OST3 / OST6 family, transporter family 1 252 2.2E-92
13 g442.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 109 -
16 g442.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 110 129 -
10 g442.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 130 140 -
15 g442.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 141 160 -
14 g442.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 161 192 -
18 g442.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 193 211 -
11 g442.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 212 222 -
17 g442.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 223 243 -
12 g442.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 244 257 -
8 g442.t4 SUPERFAMILY SSF52833 Thioredoxin-like 9 101 1.61E-6
5 g442.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 110 129 -
4 g442.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 142 160 -
7 g442.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 188 210 -
6 g442.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 223 245 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

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