Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Sodium-dependent nutrient amino acid 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 g19 g19.t5 isoform g19.t5 318575 319629
chr_3 g19 g19.t5 exon g19.t5.exon1 318575 318679
chr_3 g19 g19.t5 exon g19.t5.exon2 318753 318792
chr_3 g19 g19.t5 exon g19.t5.exon3 318857 319058
chr_3 g19 g19.t5 cds g19.t5.CDS1 318881 319058
chr_3 g19 g19.t5 exon g19.t5.exon4 319118 319629
chr_3 g19 g19.t5 cds g19.t5.CDS2 319118 319629
chr_3 g19 g19.t5 TTS g19.t5 319710 319710
chr_3 g19 g19.t5 TSS g19.t5 NA NA

Sequences

>g19.t5 Gene=g19 Length=859
ACTCAATATATAAACAGGTATTTTGGGAAATTTGGCATATAGCATTGGTGAAGAGGATAT
TGGAAACGTTATTAAAAGCGGGGGCAGTGGGTTAGCGTTTATTTCATACCCTGAAGCAAT
TTCAAAGTTCAAATTTGTTCCACAGCTCTTTGCCGTTCTCTTCTTCTTTATGCTTTTTAC
ACTGGGAGTTGGTAGTGCTGTTGGATTACAAAGTGCCATAGTAGCAAATTTAATGGACTT
TTTCCCAAAAATAAAGCAATGGATGATGGCTTTAATCTGCTGCTTGATTGGATTTGTAAT
TGGCCTTTTATATGTCACGCCAGGAGGACAATGGATTCTAAATTTGGTTGACCATTTTGG
AGGAACATTTTTGATTTTCACTCTTGCCATCTTTCAAATTGTAGGAATATTTTGGGTATA
TGGAATTGAAAACTTTTGCTGGGATGTTGAATTTATGTTAAATAGAAAAGTTACAAAGTT
TTGGCGATTTTCTTGGTTTATTGTCACTCCTGTCTTGCTTATCATCATTTTCATATATTT
TTTGATAAAAACCGAAAATCCTACTTATGGTGCTCGAGAATATCCAGTCACAGTTTTAGC
TACAGGTTGGATTATTTTTGGTGTTGGAATGTTCCAAATACTCTTGTGGATTTCATGGTC
AATTATTAGAGATCCAAATAAATGTGAAGCCTTTAAATCTCTCTTCAGACAAAATTCAGA
ATGGGGACCAAAATCTCCAAAAGTTTTCAAAGAATGGAAAACATATAAAAGCGAAAGACT
TGAAAAACGCAGAGCAAAAAGCAATGGAGATTCAAAGATTAAAAAATGTTTAAACATTTT
ACTCGATAAATATGAATAG

>g19.t5 Gene=g19 Length=229
MLFTLGVGSAVGLQSAIVANLMDFFPKIKQWMMALICCLIGFVIGLLYVTPGGQWILNLV
DHFGGTFLIFTLAIFQIVGIFWVYGIENFCWDVEFMLNRKVTKFWRFSWFIVTPVLLIII
FIYFLIKTENPTYGAREYPVTVLATGWIIFGVGMFQILLWISWSIIRDPNKCEAFKSLFR
QNSEWGPKSPKVFKEWKTYKSERLEKRRAKSNGDSKIKKCLNILLDKYE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g19.t5 PANTHER PTHR11616 SODIUM/CHLORIDE DEPENDENT TRANSPORTER 1 201 2.5E-50
3 g19.t5 PANTHER PTHR11616:SF269 TRANSPORTER 1 201 2.5E-50
5 g19.t5 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 66 86 2.2E-6
4 g19.t5 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 106 126 2.2E-6
1 g19.t5 Pfam PF00209 Sodium:neurotransmitter symporter family 1 163 8.8E-30
18 g19.t5 Phobius SIGNAL_PEPTIDE Signal peptide region 1 15 -
19 g19.t5 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 1 -
20 g19.t5 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 2 10 -
25 g19.t5 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 11 15 -
17 g19.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 16 30 -
23 g19.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 31 50 -
14 g19.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 51 61 -
21 g19.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 62 84 -
15 g19.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 85 103 -
24 g19.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 104 126 -
13 g19.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 127 137 -
22 g19.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 138 163 -
16 g19.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 164 229 -
12 g19.t5 ProSiteProfiles PS50267 Sodium:neurotransmitter symporter family profile. 1 170 21.641
11 g19.t5 SUPERFAMILY SSF161070 SNF-like 1 165 5.36E-32
10 g19.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 5 22 -
9 g19.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 35 57 -
7 g19.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 67 86 -
8 g19.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 107 126 -
6 g19.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 141 163 -

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. There were no conditions that were differentially expressed