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.t18 isoform g4155.t18 31025825 31027215
chr_3 g4155 g4155.t18 exon g4155.t18.exon1 31025825 31025976
chr_3 g4155 g4155.t18 cds g4155.t18.CDS1 31025844 31025976
chr_3 g4155 g4155.t18 exon g4155.t18.exon2 31026100 31026506
chr_3 g4155 g4155.t18 cds g4155.t18.CDS2 31026100 31026506
chr_3 g4155 g4155.t18 exon g4155.t18.exon3 31026572 31027215
chr_3 g4155 g4155.t18 cds g4155.t18.CDS3 31026572 31026640
chr_3 g4155 g4155.t18 TTS g4155.t18 31027208 31027208
chr_3 g4155 g4155.t18 TSS g4155.t18 NA NA

Sequences

>g4155.t18 Gene=g4155 Length=1203
GATTGGCGGTATTGCTTTGATGGTAGTAGGTGGAATAGCACTAAAGAAAATTGGAGATGT
AAAAGAAGTATTTGAGGACGGAAATCATCCTGGTATTTTTCCTGCATTCATTATAGCAAT
TGGAGCATTGGTCTTTGTTATTGCATTTTTCGGTTGTTGTGGAGCTATTCGTGAATCGCA
ATGTCTTCTCAACCTCTATTCATTGTGTCTACTTTGCCTTGTCGTTTTGCAAGTAGTGCT
TGCAATTTTTGTCTTTGTCTATAATGAAGATGTTCAAAGAGGCGCCCTTAAGGGATGGGA
TAAAATCTGGAGTGGTCGCCAACAAGGACCTCTTAATGATCAAGCGATTAATCAAATTCA
ACGAGCTTTGCAATGCTGTGGAAGTACGACTTTTTTGGACTATGGTGTGACTTTACCTAG
TAGCTGTTGTGATCCAGAAGCATCTTCTTGTAATCAACTAGTTGCATATAAAACAGGATG
TCGACCACAAATCAAATATGTCGTTCAAAATTCAGCTCAATGGATTGCCTATTTATCGAT
CATTATGGCCCTTGTTGAGCTGGTTGGAGTAATTTTTGGTTGCTGTCTTAGCTCAAACAT
TCGAAATTCATCTAGGTTCTCATTTTAATCCAAAAAGATTTGTAATTTGATTCAATTTGT
AATTAACATGCATGCATACATGTTTCTAATATGACAAATTGAGTCAATTTCGCTTATATG
CATATTCATTCTGTGACTAACATTTTTAAATTGTATTTTTCCCGATTGTTTGCAGATATG
AGTAAAGAATCAACAATTATTCTCACACCATCAACATTTTGGGCGATAACTATTAAATAT
TTAATTAACAAACATTTTTCTCATATACACACATAAAAACACTCCTTTATATTTTTTTCA
TTAGTATTGAAATATATGAGAACCTTAACAAAAAAAATACATTAAAAAATCAACCTATAT
GCATATATCATCAGCCATAATTGCTTACTTTTATATTATTCATGCACGCTTAAATCATAT
CGTTTATGTAATCAATTAGAGATATTCGTCAAATTTAGCGTATTTGTGTATCTCTAAATA
TACACATGTATTTTTTTAACGAAATAAGAGTTTCTCATCATATACGCTTAAGTCATTTGA
TGTCAGTTTCCAAAAAATACGTTTTAGTTGAAATGTAAAAAAATAAAATATTTTTGTCAA
AAA

>g4155.t18 Gene=g4155 Length=202
MVVGGIALKKIGDVKEVFEDGNHPGIFPAFIIAIGALVFVIAFFGCCGAIRESQCLLNLY
SLCLLCLVVLQVVLAIFVFVYNEDVQRGALKGWDKIWSGRQQGPLNDQAINQIQRALQCC
GSTTFLDYGVTLPSSCCDPEASSCNQLVAYKTGCRPQIKYVVQNSAQWIAYLSIIMALVE
LVGVIFGCCLSSNIRNSSRFSF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g4155.t18 CDD cd03127 tetraspanin_LEL 79 159 1.3139E-13
8 g4155.t18 Gene3D G3DSA:1.10.1450.10 Tetraspanin 82 163 9.2E-9
2 g4155.t18 PANTHER PTHR19282 TETRASPANIN 26 197 2.5E-28
3 g4155.t18 PANTHER PTHR19282:SF471 CD63 ANTIGEN 26 197 2.5E-28
16 g4155.t18 PIRSF PIRSF002419 Tetraspanin 8 201 1.8E-43
5 g4155.t18 PRINTS PR00259 Transmembrane four family signature 24 50 4.3E-25
4 g4155.t18 PRINTS PR00259 Transmembrane four family signature 51 79 4.3E-25
6 g4155.t18 PRINTS PR00259 Transmembrane four family signature 168 194 4.3E-25
1 g4155.t18 Pfam PF00335 Tetraspanin family 16 191 2.6E-38
12 g4155.t18 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 25 -
13 g4155.t18 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 26 50 -
10 g4155.t18 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 51 56 -
14 g4155.t18 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 57 81 -
11 g4155.t18 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 82 167 -
15 g4155.t18 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 168 190 -
9 g4155.t18 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 191 202 -
21 g4155.t18 ProSitePatterns PS00421 Transmembrane 4 family signature. 35 57 -
7 g4155.t18 SUPERFAMILY SSF48652 Tetraspanin 79 162 9.29E-13
19 g4155.t18 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 25 47 -
20 g4155.t18 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 59 81 -
18 g4155.t18 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 168 190 -

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