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.t19 isoform g4155.t19 31025825 31027215
chr_3 g4155 g4155.t19 exon g4155.t19.exon1 31025825 31025976
chr_3 g4155 g4155.t19 cds g4155.t19.CDS1 31025844 31025976
chr_3 g4155 g4155.t19 exon g4155.t19.exon2 31026100 31026506
chr_3 g4155 g4155.t19 cds g4155.t19.CDS2 31026100 31026506
chr_3 g4155 g4155.t19 exon g4155.t19.exon3 31026788 31027215
chr_3 g4155 g4155.t19 cds g4155.t19.CDS3 31026788 31026793
chr_3 g4155 g4155.t19 TTS g4155.t19 31027208 31027208
chr_3 g4155 g4155.t19 TSS g4155.t19 NA NA

Sequences

>g4155.t19 Gene=g4155 Length=987
GATTGGCGGTATTGCTTTGATGGTAGTAGGTGGAATAGCACTAAAGAAAATTGGAGATGT
AAAAGAAGTATTTGAGGACGGAAATCATCCTGGTATTTTTCCTGCATTCATTATAGCAAT
TGGAGCATTGGTCTTTGTTATTGCATTTTTCGGTTGTTGTGGAGCTATTCGTGAATCGCA
ATGTCTTCTCAACCTCTATTCATTGTGTCTACTTTGCCTTGTCGTTTTGCAAGTAGTGCT
TGCAATTTTTGTCTTTGTCTATAATGAAGATGTTCAAAGAGGCGCCCTTAAGGGATGGGA
TAAAATCTGGAGTGGTCGCCAACAAGGACCTCTTAATGATCAAGCGATTAATCAAATTCA
ACGAGCTTTGCAATGCTGTGGAAGTACGACTTTTTTGGACTATGGTGTGACTTTACCTAG
TAGCTGTTGTGATCCAGAAGCATCTTCTTGTAATCAACTAGTTGCATATAAAACAGGATG
TCGACCACAAATCAAATATGTCGTTCAAAATTCAGCTCAATGGATTGCCTATTTATCGAT
CATTATGGCCCTTGTTGAGATATGAGTAAAGAATCAACAATTATTCTCACACCATCAACA
TTTTGGGCGATAACTATTAAATATTTAATTAACAAACATTTTTCTCATATACACACATAA
AAACACTCCTTTATATTTTTTTCATTAGTATTGAAATATATGAGAACCTTAACAAAAAAA
ATACATTAAAAAATCAACCTATATGCATATATCATCAGCCATAATTGCTTACTTTTATAT
TATTCATGCACGCTTAAATCATATCGTTTATGTAATCAATTAGAGATATTCGTCAAATTT
AGCGTATTTGTGTATCTCTAAATATACACATGTATTTTTTTAACGAAATAAGAGTTTCTC
ATCATATACGCTTAAGTCATTTGATGTCAGTTTCCAAAAAATACGTTTTAGTTGAAATGT
AAAAAAATAAAATATTTTTGTCAAAAA

>g4155.t19 Gene=g4155 Length=181
MVVGGIALKKIGDVKEVFEDGNHPGIFPAFIIAIGALVFVIAFFGCCGAIRESQCLLNLY
SLCLLCLVVLQVVLAIFVFVYNEDVQRGALKGWDKIWSGRQQGPLNDQAINQIQRALQCC
GSTTFLDYGVTLPSSCCDPEASSCNQLVAYKTGCRPQIKYVVQNSAQWIAYLSIIMALVE
I

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g4155.t19 CDD cd03127 tetraspanin_LEL 79 159 4.53072E-14
8 g4155.t19 Gene3D G3DSA:1.10.1450.10 Tetraspanin 82 163 7.7E-9
2 g4155.t19 PANTHER PTHR19282 TETRASPANIN 26 181 7.1E-23
3 g4155.t19 PANTHER PTHR19282:SF471 CD63 ANTIGEN 26 181 7.1E-23
14 g4155.t19 PIRSF PIRSF002419 Tetraspanin 7 181 8.5E-39
5 g4155.t19 PRINTS PR00259 Transmembrane four family signature 24 50 4.1E-18
4 g4155.t19 PRINTS PR00259 Transmembrane four family signature 51 79 4.1E-18
6 g4155.t19 PRINTS PR00259 Transmembrane four family signature 168 181 4.1E-18
1 g4155.t19 Pfam PF00335 Tetraspanin family 16 180 1.0E-34
11 g4155.t19 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 25 -
12 g4155.t19 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 26 50 -
9 g4155.t19 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 51 56 -
13 g4155.t19 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 57 81 -
10 g4155.t19 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 82 181 -
18 g4155.t19 ProSitePatterns PS00421 Transmembrane 4 family signature. 35 57 -
7 g4155.t19 SUPERFAMILY SSF48652 Tetraspanin 79 162 7.19E-13
16 g4155.t19 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 25 47 -
17 g4155.t19 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 59 81 -

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. There were no conditions that were differentially expressed