Gene loci information

Transcript annotation

  • This transcript has been annotated as High-affinity choline transporter 1.

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 g1791 g1791.t2 isoform g1791.t2 13033606 13034301
chr_3 g1791 g1791.t2 exon g1791.t2.exon1 13033606 13033830
chr_3 g1791 g1791.t2 cds g1791.t2.CDS1 13033606 13033830
chr_3 g1791 g1791.t2 exon g1791.t2.exon2 13033896 13034010
chr_3 g1791 g1791.t2 cds g1791.t2.CDS2 13033896 13034010
chr_3 g1791 g1791.t2 exon g1791.t2.exon3 13034072 13034301
chr_3 g1791 g1791.t2 cds g1791.t2.CDS3 13034072 13034295
chr_3 g1791 g1791.t2 TSS g1791.t2 NA NA
chr_3 g1791 g1791.t2 TTS g1791.t2 NA NA

Sequences

>g1791.t2 Gene=g1791 Length=570
CTACTTATGGTCGTTCATTTCAAGCATCATTGTAATACATATGGCAGCTTGTCAGCATAT
ATTGTGGCTTTCTTCGTTCGTCTATCAGGAGGCGAACCGATTCTTGGTTTACCAGCAGCA
ATTCATTTTCCTGGTTATGATGAGGAAACACAAGAGCAACTTTTTCCATTCCGCACAATG
GCTATGTTGCTTAGTCTAATAACATTGGCTGGAGTTTCTTGGTTAACAAAATTCCTTTTC
TTAACTGGAAGACTTGCGCCACAATATGATTACTTTAGATGTGTTGTGAATATACCAGAA
GATGCTGTGCGTGTCGGAGATCCATCAGAAGTTGACGGCGAACAGATGAGTGTGATGGCT
GGCGCTATGAACAAAATGTATGGCGCAGCAACAATGGTGGGCAAGGATGAAAGAAATGGA
AGAATAAATCCAGCACTTGAGCCAGATGATGATCTACCAGCTGTTGAAGCACAAAGGCAA
ATGCAACAAATGGCACTTAGCAATGCTGCTGCTGCCATAAGTAATGTAGCCCAAACCGTC
CCTGGTGGACAAGGCACTACGGCATTTTAA

>g1791.t2 Gene=g1791 Length=187
MVVHFKHHCNTYGSLSAYIVAFFVRLSGGEPILGLPAAIHFPGYDEETQEQLFPFRTMAM
LLSLITLAGVSWLTKFLFLTGRLAPQYDYFRCVVNIPEDAVRVGDPSEVDGEQMSVMAGA
MNKMYGAATMVGKDERNGRINPALEPDDDLPAVEAQRQMQQMALSNAAAAISNVAQTVPG
GQGTTAF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
1 g1791.t2 PANTHER PTHR45897 HIGH-AFFINITY CHOLINE TRANSPORTER 1 1 112 3.8E-30
2 g1791.t2 PANTHER PTHR45897:SF4 HIGH-AFFINITY CHOLINE TRANSPORTER 1 1 112 3.8E-30
5 g1791.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
8 g1791.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 33 -
7 g1791.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 34 52 -
9 g1791.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 53 73 -
6 g1791.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 74 187 -
3 g1791.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 12 34 -
4 g1791.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 57 79 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

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