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 g23 g23.t11 isoform g23.t11 331854 332566
chr_3 g23 g23.t11 exon g23.t11.exon1 331854 331983
chr_3 g23 g23.t11 exon g23.t11.exon2 332040 332418
chr_3 g23 g23.t11 cds g23.t11.CDS1 332172 332418
chr_3 g23 g23.t11 exon g23.t11.exon3 332474 332566
chr_3 g23 g23.t11 cds g23.t11.CDS2 332474 332529
chr_3 g23 g23.t11 TTS g23.t11 332670 332670
chr_3 g23 g23.t11 TSS g23.t11 NA NA

Sequences

>g23.t11 Gene=g23 Length=602
TAGTCTATTTGCAATTACATCATCTGCTATCACCGTTATTCGTGATCAATTTAAGAAGGT
CAAAGATTGGCAAGCAGCATTAGGAATCGCAATTTTCGGAACTATTTCTGGATCAATTTA
TACAACACCAGCTGGGTTAAGTATTCTTGATCTCGTCGATCATTATTGTGCTACTTTTGT
GATTTTCATTCTGGCCTGTTTTGAAATATGTACATTCTGTTATATTTATGGTGTTGATCG
TATTTGCAATGATGTTAAATTCATGCTTGGATTTAGACCAAATATTTTCTGGAGAACTTG
CTGGCGATATATTACACCTTCAATTTTGACAGCATTAGTTATTTATTTACTGATGAAAGC
TAAATTTATCAAAGATGATGCAAGCACATTTCCTGCGTCAGCACATGCAGTTGGCGTGTG
CATAGCTGTTATGGGTATTATTTGGTTACCTATTGTATTTATTTGGAGAGTTTTAAAACA
AACACATGAAAAGACTTTAATCGATGTAAAAAATCAAAAGCGCCTGCAAACCAACAAAAA
ATTGGGGACCAATGGATCCTGTTAAAAATGCTAGGTACAAAGAATATATGGCCACAAATT
AA

>g23.t11 Gene=g23 Length=100
MLGFRPNIFWRTCWRYITPSILTALVIYLLMKAKFIKDDASTFPASAHAVGVCIAVMGII
WLPIVFIWRVLKQTHEKTLIDVKNQKRLQTNKKLGTNGSC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g23.t11 PANTHER PTHR11616:SF268 TRANSPORTER 1 74 4.6E-12
3 g23.t11 PANTHER PTHR11616 SODIUM/CHLORIDE DEPENDENT TRANSPORTER 1 74 4.6E-12
1 g23.t11 Pfam PF00209 Sodium:neurotransmitter symporter family 1 72 1.4E-11
8 g23.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
12 g23.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 31 -
10 g23.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 32 42 -
11 g23.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 43 68 -
9 g23.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 69 100 -
7 g23.t11 ProSiteProfiles PS50267 Sodium:neurotransmitter symporter family profile. 1 75 10.236
6 g23.t11 SUPERFAMILY SSF161070 SNF-like 1 71 4.05E-9
5 g23.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 12 31 -
4 g23.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 46 68 -

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