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.t15 TSS g4155.t15 31020408 31020408
chr_3 g4155 g4155.t15 isoform g4155.t15 31020547 31027215
chr_3 g4155 g4155.t15 exon g4155.t15.exon1 31020547 31020616
chr_3 g4155 g4155.t15 cds g4155.t15.CDS1 31020547 31020616
chr_3 g4155 g4155.t15 exon g4155.t15.exon2 31025851 31025976
chr_3 g4155 g4155.t15 cds g4155.t15.CDS2 31025851 31025976
chr_3 g4155 g4155.t15 exon g4155.t15.exon3 31026100 31026506
chr_3 g4155 g4155.t15 cds g4155.t15.CDS3 31026100 31026506
chr_3 g4155 g4155.t15 exon g4155.t15.exon4 31026572 31026627
chr_3 g4155 g4155.t15 cds g4155.t15.CDS4 31026572 31026627
chr_3 g4155 g4155.t15 exon g4155.t15.exon5 31026788 31027215
chr_3 g4155 g4155.t15 cds g4155.t15.CDS5 31026788 31026797
chr_3 g4155 g4155.t15 TTS g4155.t15 31027208 31027208

Sequences

>g4155.t15 Gene=g4155 Length=1087
ATGGGTTTAGATTGTGGAGCAAGTTTGATTAAATATGTTCTTTTTATATTCAATTTAATC
TGTGCGGTAATAGGTGGAATAGCACTAAAGAAAATTGGAGATGTAAAAGAAGTATTTGAG
GACGGAAATCATCCTGGTATTTTTCCTGCATTCATTATAGCAATTGGAGCATTGGTCTTT
GTTATTGCATTTTTCGGTTGTTGTGGAGCTATTCGTGAATCGCAATGTCTTCTCAACCTC
TATTCATTGTGTCTACTTTGCCTTGTCGTTTTGCAAGTAGTGCTTGCAATTTTTGTCTTT
GTCTATAATGAAGATGTTCAAAGAGGCGCCCTTAAGGGATGGGATAAAATCTGGAGTGGT
CGCCAACAAGGACCTCTTAATGATCAAGCGATTAATCAAATTCAACGAGCTTTGCAATGC
TGTGGAAGTACGACTTTTTTGGACTATGGTGTGACTTTACCTAGTAGCTGTTGTGATCCA
GAAGCATCTTCTTGTAATCAACTAGTTGCATATAAAACAGGATGTCGACCACAAATCAAA
TATGTCGTTCAAAATTCAGCTCAATGGATTGCCTATTTATCGATCATTATGGCCCTTGTT
GAGCTGGTTGGAGTAATTTTTGGTTGCTGTCTTAGCTCAAACATTCGAAATTCATCTAGA
TATGAGTAAAGAATCAACAATTATTCTCACACCATCAACATTTTGGGCGATAACTATTAA
ATATTTAATTAACAAACATTTTTCTCATATACACACATAAAAACACTCCTTTATATTTTT
TTCATTAGTATTGAAATATATGAGAACCTTAACAAAAAAAATACATTAAAAAATCAACCT
ATATGCATATATCATCAGCCATAATTGCTTACTTTTATATTATTCATGCACGCTTAAATC
ATATCGTTTATGTAATCAATTAGAGATATTCGTCAAATTTAGCGTATTTGTGTATCTCTA
AATATACACATGTATTTTTTTAACGAAATAAGAGTTTCTCATCATATACGCTTAAGTCAT
TTGATGTCAGTTTCCAAAAAATACGTTTTAGTTGAAATGTAAAAAAATAAAATATTTTTG
TCAAAAA

>g4155.t15 Gene=g4155 Length=222
MGLDCGASLIKYVLFIFNLICAVIGGIALKKIGDVKEVFEDGNHPGIFPAFIIAIGALVF
VIAFFGCCGAIRESQCLLNLYSLCLLCLVVLQVVLAIFVFVYNEDVQRGALKGWDKIWSG
RQQGPLNDQAINQIQRALQCCGSTTFLDYGVTLPSSCCDPEASSCNQLVAYKTGCRPQIK
YVVQNSAQWIAYLSIIMALVELVGVIFGCCLSSNIRNSSRYE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
20 g4155.t15 CDD cd03127 tetraspanin_LEL 100 180 3.05035E-13
9 g4155.t15 Gene3D G3DSA:1.10.1450.10 Tetraspanin 103 184 1.0E-8
2 g4155.t15 PANTHER PTHR19282 TETRASPANIN 5 218 2.6E-30
3 g4155.t15 PANTHER PTHR19282:SF471 CD63 ANTIGEN 5 218 2.6E-30
19 g4155.t15 PIRSF PIRSF002419 Tetraspanin 1 222 1.9E-44
6 g4155.t15 PRINTS PR00259 Transmembrane four family signature 12 35 4.2E-27
4 g4155.t15 PRINTS PR00259 Transmembrane four family signature 45 71 4.2E-27
7 g4155.t15 PRINTS PR00259 Transmembrane four family signature 72 100 4.2E-27
5 g4155.t15 PRINTS PR00259 Transmembrane four family signature 189 215 4.2E-27
1 g4155.t15 Pfam PF00335 Tetraspanin family 10 212 2.9E-41
11 g4155.t15 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
16 g4155.t15 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 29 -
13 g4155.t15 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 30 48 -
15 g4155.t15 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 49 71 -
10 g4155.t15 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 72 77 -
18 g4155.t15 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 78 102 -
14 g4155.t15 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 103 188 -
17 g4155.t15 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 189 211 -
12 g4155.t15 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 212 222 -
25 g4155.t15 ProSitePatterns PS00421 Transmembrane 4 family signature. 56 78 -
8 g4155.t15 SUPERFAMILY SSF48652 Tetraspanin 100 183 1.15E-12
22 g4155.t15 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 7 29 -
21 g4155.t15 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 49 71 -
24 g4155.t15 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 78 100 -
23 g4155.t15 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 189 211 -

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. There were no conditions that were differentially expressed