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.t3 TSS g4155.t3 31020408 31020408
chr_3 g4155 g4155.t3 isoform g4155.t3 31020547 31026475
chr_3 g4155 g4155.t3 exon g4155.t3.exon1 31020547 31020612
chr_3 g4155 g4155.t3 cds g4155.t3.CDS1 31020547 31020612
chr_3 g4155 g4155.t3 exon g4155.t3.exon2 31025826 31025976
chr_3 g4155 g4155.t3 cds g4155.t3.CDS2 31025826 31025976
chr_3 g4155 g4155.t3 exon g4155.t3.exon3 31026100 31026475
chr_3 g4155 g4155.t3 cds g4155.t3.CDS3 31026100 31026473
chr_3 g4155 g4155.t3 TTS g4155.t3 31027208 31027208

Sequences

>g4155.t3 Gene=g4155 Length=593
ATGGGTTTAGATTGTGGAGCAAGTTTGATTAAATATGTTCTTTTTATATTCAATTTAATC
TGTGCGATTGGCGGTATTGCTTTGATGGTAGTAGGTGGAATAGCACTAAAGAAAATTGGA
GATGTAAAAGAAGTATTTGAGGACGGAAATCATCCTGGTATTTTTCCTGCATTCATTATA
GCAATTGGAGCATTGGTCTTTGTTATTGCATTTTTCGGTTGTTGTGGAGCTATTCGTGAA
TCGCAATGTCTTCTCAACCTCTATTCATTGTGTCTACTTTGCCTTGTCGTTTTGCAAGTA
GTGCTTGCAATTTTTGTCTTTGTCTATAATGAAGATGTTCAAAGAGGCGCCCTTAAGGGA
TGGGATAAAATCTGGAGTGGTCGCCAACAAGGACCTCTTAATGATCAAGCGATTAATCAA
ATTCAACGAGCTTTGCAATGCTGTGGAAGTACGACTTTTTTGGACTATGGTGTGACTTTA
CCTAGTAGCTGTTGTGATCCAGAAGCATCTTCTTGTAATCAACTAGTTGCATATAAAACA
GGATGTCGACCACAAATCAAATATGTCGTTCAAAATTCAGCTCAATGGATTGC

>g4155.t3 Gene=g4155 Length=197
MGLDCGASLIKYVLFIFNLICAIGGIALMVVGGIALKKIGDVKEVFEDGNHPGIFPAFII
AIGALVFVIAFFGCCGAIRESQCLLNLYSLCLLCLVVLQVVLAIFVFVYNEDVQRGALKG
WDKIWSGRQQGPLNDQAINQIQRALQCCGSTTFLDYGVTLPSSCCDPEASSCNQLVAYKT
GCRPQIKYVVQNSAQWI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g4155.t3 CDD cd03127 tetraspanin_LEL 107 187 1.0851E-13
8 g4155.t3 Gene3D G3DSA:1.10.1450.10 Tetraspanin 110 191 8.7E-9
2 g4155.t3 PANTHER PTHR19282:SF273 TETRASPANIN 4 177 3.2E-31
3 g4155.t3 PANTHER PTHR19282 TETRASPANIN 4 177 3.2E-31
16 g4155.t3 PIRSF PIRSF002419 Tetraspanin 1 197 3.4E-42
5 g4155.t3 PRINTS PR00259 Transmembrane four family signature 12 35 1.8E-21
4 g4155.t3 PRINTS PR00259 Transmembrane four family signature 52 78 1.8E-21
6 g4155.t3 PRINTS PR00259 Transmembrane four family signature 79 107 1.8E-21
1 g4155.t3 Pfam PF00335 Tetraspanin family 10 197 6.8E-40
9 g4155.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
15 g4155.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 34 -
12 g4155.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 35 53 -
14 g4155.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 54 78 -
10 g4155.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 79 84 -
13 g4155.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 85 109 -
11 g4155.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 110 197 -
21 g4155.t3 ProSitePatterns PS00421 Transmembrane 4 family signature. 63 85 -
7 g4155.t3 SUPERFAMILY SSF48652 Tetraspanin 107 190 8.76E-13
19 g4155.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 13 35 -
18 g4155.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 55 77 -
20 g4155.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 84 106 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

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