Gene loci information

Transcript annotation

  • This transcript has been annotated as hypothetical.

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 g4155 g4155.t17 isoform g4155.t17 31025824 31026313
chr_3 g4155 g4155.t17 exon g4155.t17.exon1 31025824 31025976
chr_3 g4155 g4155.t17 cds g4155.t17.CDS1 31025844 31025976
chr_3 g4155 g4155.t17 exon g4155.t17.exon2 31026100 31026313
chr_3 g4155 g4155.t17 cds g4155.t17.CDS2 31026100 31026311
chr_3 g4155 g4155.t17 TTS g4155.t17 31027208 31027208
chr_3 g4155 g4155.t17 TSS g4155.t17 NA NA

Sequences

>g4155.t17 Gene=g4155 Length=367
AGATTGGCGGTATTGCTTTGATGGTAGTAGGTGGAATAGCACTAAAGAAAATTGGAGATG
TAAAAGAAGTATTTGAGGACGGAAATCATCCTGGTATTTTTCCTGCATTCATTATAGCAA
TTGGAGCATTGGTCTTTGTTATTGCATTTTTCGGTTGTTGTGGAGCTATTCGTGAATCGC
AATGTCTTCTCAACCTCTATTCATTGTGTCTACTTTGCCTTGTCGTTTTGCAAGTAGTGC
TTGCAATTTTTGTCTTTGTCTATAATGAAGATGTTCAAAGAGGCGCCCTTAAGGGATGGG
ATAAAATCTGGAGTGGTCGCCAACAAGGACCTCTTAATGATCAAGCGATTAATCAAATTC
AACGAGC

>g4155.t17 Gene=g4155 Length=115
MVVGGIALKKIGDVKEVFEDGNHPGIFPAFIIAIGALVFVIAFFGCCGAIRESQCLLNLY
SLCLLCLVVLQVVLAIFVFVYNEDVQRGALKGWDKIWSGRQQGPLNDQAINQIQR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g4155.t17 PANTHER PTHR19282 TETRASPANIN 28 113 3.5E-14
4 g4155.t17 PRINTS PR00259 Transmembrane four family signature 24 50 8.7E-16
3 g4155.t17 PRINTS PR00259 Transmembrane four family signature 51 79 8.7E-16
1 g4155.t17 Pfam PF00335 Tetraspanin family 16 114 5.0E-22
9 g4155.t17 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 25 -
11 g4155.t17 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 26 50 -
8 g4155.t17 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 51 56 -
12 g4155.t17 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 57 81 -
10 g4155.t17 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 82 115 -
7 g4155.t17 ProSitePatterns PS00421 Transmembrane 4 family signature. 35 57 -
5 g4155.t17 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 25 47 -
6 g4155.t17 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 59 81 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

## Warning: Removed 1 row(s) containing missing values (geom_path).

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0016021 integral component of membrane CC

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