Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Organic cation transporter protein.

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 g2336 g2336.t12 isoform g2336.t12 16895470 16896052
chr_3 g2336 g2336.t12 exon g2336.t12.exon1 16895470 16896052
chr_3 g2336 g2336.t12 cds g2336.t12.CDS1 16895471 16896052
chr_3 g2336 g2336.t12 TSS g2336.t12 16896234 16896234
chr_3 g2336 g2336.t12 TTS g2336.t12 NA NA

Sequences

>g2336.t12 Gene=g2336 Length=583
ATGGTCTCAAAGTTGAATTATGACGACTTGCTCTCTCATATTGGTACATTCGGCGGGTAT
CAATTACGGAATTTTATTTTACTTTGCGTGCCAATAATTTTGTGTGCCTTCCATAAACTC
TCAAGTGTCTTTATACTTGCAAAAATTGATCATAGGTGTCAACTAAACTCAAATGATACA
GAATTTTTGCTCTCTAATAATCAAGATGTTTTATATACTATTCTCACTGCCTCATTTCCA
TATGATGAAAAGAAAGGCTTCTCGAAATGTCAGTACTATTTAGATAATTATTTTAACAGA
GGCGTCGAAAATACTACACATACAGCTGTCGCATGTGACGAGTATGTTTGGGACTATGAA
AAATTTCAATCGTCAGCAATTAAAACATTTAAATTGATTTGTGACCGAGATCACTTTAAG
GCAACAAGCGATTCAGTTTTTATGATTGGAGTTTTCATCGGAAGTTTTGCCTTTGGCCAT
TTATCGGACAAATATGGACGCCGCAAAGTGTTTGTGCTTTCACTAATATTTCAATTGATC
TTTGGCTTGCTGACTGCTCTTGCTACAAATTTTTATACATTTA

>g2336.t12 Gene=g2336 Length=194
MVSKLNYDDLLSHIGTFGGYQLRNFILLCVPIILCAFHKLSSVFILAKIDHRCQLNSNDT
EFLLSNNQDVLYTILTASFPYDEKKGFSKCQYYLDNYFNRGVENTTHTAVACDEYVWDYE
KFQSSAIKTFKLICDRDHFKATSDSVFMIGVFIGSFAFGHLSDKYGRRKVFVLSLIFQLI
FGLLTALATNFYTF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g2336.t12 Gene3D G3DSA:1.20.1250.20 MFS general substrate transporter like domains 125 194 6.4E-14
2 g2336.t12 PANTHER PTHR24064 SOLUTE CARRIER FAMILY 22 MEMBER 6 193 8.0E-33
3 g2336.t12 PANTHER PTHR24064:SF198 SOLUTE CARRIER FAMILY 22 MEMBER 13 6 193 8.0E-33
1 g2336.t12 Pfam PF07690 Major Facilitator Superfamily 144 192 3.5E-9
11 g2336.t12 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 24 -
12 g2336.t12 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 25 47 -
9 g2336.t12 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 48 169 -
13 g2336.t12 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 170 192 -
10 g2336.t12 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 193 194 -
8 g2336.t12 ProSiteProfiles PS50850 Major facilitator superfamily (MFS) profile. 70 194 10.888
6 g2336.t12 SUPERFAMILY SSF103473 MFS general substrate transporter 145 194 9.94E-13
4 g2336.t12 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 25 47 -
5 g2336.t12 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 170 192 -

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:0055085 transmembrane transport BP
GO:0022857 transmembrane transporter activity MF

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