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.t7 TSS g4155.t7 31020408 31020408
chr_3 g4155 g4155.t7 isoform g4155.t7 31020547 31026797
chr_3 g4155 g4155.t7 exon g4155.t7.exon1 31020547 31020612
chr_3 g4155 g4155.t7 cds g4155.t7.CDS1 31020547 31020612
chr_3 g4155 g4155.t7 exon g4155.t7.exon2 31025826 31025976
chr_3 g4155 g4155.t7 cds g4155.t7.CDS2 31025826 31025976
chr_3 g4155 g4155.t7 exon g4155.t7.exon3 31026100 31026506
chr_3 g4155 g4155.t7 cds g4155.t7.CDS3 31026100 31026506
chr_3 g4155 g4155.t7 exon g4155.t7.exon4 31026572 31026653
chr_3 g4155 g4155.t7 cds g4155.t7.CDS4 31026572 31026640
chr_3 g4155 g4155.t7 exon g4155.t7.exon5 31026788 31026797
chr_3 g4155 g4155.t7 TTS g4155.t7 31027208 31027208

Sequences

>g4155.t7 Gene=g4155 Length=716
ATGGGTTTAGATTGTGGAGCAAGTTTGATTAAATATGTTCTTTTTATATTCAATTTAATC
TGTGCGATTGGCGGTATTGCTTTGATGGTAGTAGGTGGAATAGCACTAAAGAAAATTGGA
GATGTAAAAGAAGTATTTGAGGACGGAAATCATCCTGGTATTTTTCCTGCATTCATTATA
GCAATTGGAGCATTGGTCTTTGTTATTGCATTTTTCGGTTGTTGTGGAGCTATTCGTGAA
TCGCAATGTCTTCTCAACCTCTATTCATTGTGTCTACTTTGCCTTGTCGTTTTGCAAGTA
GTGCTTGCAATTTTTGTCTTTGTCTATAATGAAGATGTTCAAAGAGGCGCCCTTAAGGGA
TGGGATAAAATCTGGAGTGGTCGCCAACAAGGACCTCTTAATGATCAAGCGATTAATCAA
ATTCAACGAGCTTTGCAATGCTGTGGAAGTACGACTTTTTTGGACTATGGTGTGACTTTA
CCTAGTAGCTGTTGTGATCCAGAAGCATCTTCTTGTAATCAACTAGTTGCATATAAAACA
GGATGTCGACCACAAATCAAATATGTCGTTCAAAATTCAGCTCAATGGATTGCCTATTTA
TCGATCATTATGGCCCTTGTTGAGCTGGTTGGAGTAATTTTTGGTTGCTGTCTTAGCTCA
AACATTCGAAATTCATCTAGGTTCTCATTTTAATCCAAAAAGATTTATATGAGTAA

>g4155.t7 Gene=g4155 Length=230
MGLDCGASLIKYVLFIFNLICAIGGIALMVVGGIALKKIGDVKEVFEDGNHPGIFPAFII
AIGALVFVIAFFGCCGAIRESQCLLNLYSLCLLCLVVLQVVLAIFVFVYNEDVQRGALKG
WDKIWSGRQQGPLNDQAINQIQRALQCCGSTTFLDYGVTLPSSCCDPEASSCNQLVAYKT
GCRPQIKYVVQNSAQWIAYLSIIMALVELVGVIFGCCLSSNIRNSSRFSF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
20 g4155.t7 CDD cd03127 tetraspanin_LEL 107 187 2.03837E-13
9 g4155.t7 Gene3D G3DSA:1.10.1450.10 Tetraspanin 110 191 1.1E-8
2 g4155.t7 PANTHER PTHR19282:SF273 TETRASPANIN 4 225 5.4E-36
3 g4155.t7 PANTHER PTHR19282 TETRASPANIN 4 225 5.4E-36
19 g4155.t7 PIRSF PIRSF002419 Tetraspanin 1 229 1.1E-48
5 g4155.t7 PRINTS PR00259 Transmembrane four family signature 12 35 7.4E-31
4 g4155.t7 PRINTS PR00259 Transmembrane four family signature 52 78 7.4E-31
7 g4155.t7 PRINTS PR00259 Transmembrane four family signature 79 107 7.4E-31
6 g4155.t7 PRINTS PR00259 Transmembrane four family signature 196 222 7.4E-31
1 g4155.t7 Pfam PF00335 Tetraspanin family 10 219 1.3E-44
10 g4155.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
18 g4155.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 34 -
14 g4155.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 35 53 -
17 g4155.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 54 78 -
11 g4155.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 79 84 -
16 g4155.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 85 109 -
13 g4155.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 110 195 -
15 g4155.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 196 218 -
12 g4155.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 219 230 -
25 g4155.t7 ProSitePatterns PS00421 Transmembrane 4 family signature. 63 85 -
8 g4155.t7 SUPERFAMILY SSF48652 Tetraspanin 107 190 1.24E-12
23 g4155.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 13 35 -
21 g4155.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 55 77 -
24 g4155.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 84 106 -
22 g4155.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 196 218 -

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

Pathway

  • This transcript belongs to the following 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