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.t20 isoform g4155.t20 31025827 31026797
chr_3 g4155 g4155.t20 exon g4155.t20.exon1 31025827 31025976
chr_3 g4155 g4155.t20 cds g4155.t20.CDS1 31025844 31025976
chr_3 g4155 g4155.t20 exon g4155.t20.exon2 31026184 31026506
chr_3 g4155 g4155.t20 cds g4155.t20.CDS2 31026184 31026506
chr_3 g4155 g4155.t20 exon g4155.t20.exon3 31026572 31026627
chr_3 g4155 g4155.t20 cds g4155.t20.CDS3 31026572 31026627
chr_3 g4155 g4155.t20 exon g4155.t20.exon4 31026788 31026797
chr_3 g4155 g4155.t20 cds g4155.t20.CDS4 31026788 31026797
chr_3 g4155 g4155.t20 TTS g4155.t20 31027208 31027208
chr_3 g4155 g4155.t20 TSS g4155.t20 NA NA

Sequences

>g4155.t20 Gene=g4155 Length=539
TTGGCGGTATTGCTTTGATGGTAGTAGGTGGAATAGCACTAAAGAAAATTGGAGATGTAA
AAGAAGTATTTGAGGACGGAAATCATCCTGGTATTTTTCCTGCATTCATTATAGCAATTG
GAGCATTGGTCTTTGTTATTGCATTTTTCGTGCTTGCAATTTTTGTCTTTGTCTATAATG
AAGATGTTCAAAGAGGCGCCCTTAAGGGATGGGATAAAATCTGGAGTGGTCGCCAACAAG
GACCTCTTAATGATCAAGCGATTAATCAAATTCAACGAGCTTTGCAATGCTGTGGAAGTA
CGACTTTTTTGGACTATGGTGTGACTTTACCTAGTAGCTGTTGTGATCCAGAAGCATCTT
CTTGTAATCAACTAGTTGCATATAAAACAGGATGTCGACCACAAATCAAATATGTCGTTC
AAAATTCAGCTCAATGGATTGCCTATTTATCGATCATTATGGCCCTTGTTGAGCTGGTTG
GAGTAATTTTTGGTTGCTGTCTTAGCTCAAACATTCGAAATTCATCTAGATATGAGTAA

>g4155.t20 Gene=g4155 Length=173
MVVGGIALKKIGDVKEVFEDGNHPGIFPAFIIAIGALVFVIAFFVLAIFVFVYNEDVQRG
ALKGWDKIWSGRQQGPLNDQAINQIQRALQCCGSTTFLDYGVTLPSSCCDPEASSCNQLV
AYKTGCRPQIKYVVQNSAQWIAYLSIIMALVELVGVIFGCCLSSNIRNSSRYE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g4155.t20 CDD cd03127 tetraspanin_LEL 51 131 3.32554E-14
7 g4155.t20 Gene3D G3DSA:1.10.1450.10 Tetraspanin 54 135 7.1E-9
2 g4155.t20 PANTHER PTHR19282 TETRASPANIN 37 169 1.0E-11
3 g4155.t20 PANTHER PTHR19282:SF169 TETRASPANIN-6 37 169 1.0E-11
1 g4155.t20 Pfam PF00335 Tetraspanin family 32 163 4.9E-21
10 g4155.t20 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 25 -
12 g4155.t20 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 26 53 -
8 g4155.t20 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 54 139 -
11 g4155.t20 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 140 166 -
9 g4155.t20 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 167 173 -
6 g4155.t20 SUPERFAMILY SSF48652 Tetraspanin 51 134 6.41E-13
4 g4155.t20 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 31 53 -
5 g4155.t20 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 140 162 -

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