Gene loci information

Transcript annotation

  • This transcript has been annotated as 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 g23 g23.t10 isoform g23.t10 331261 332566
chr_3 g23 g23.t10 exon g23.t10.exon1 331261 331983
chr_3 g23 g23.t10 cds g23.t10.CDS1 331291 331983
chr_3 g23 g23.t10 exon g23.t10.exon2 332040 332414
chr_3 g23 g23.t10 cds g23.t10.CDS2 332040 332414
chr_3 g23 g23.t10 exon g23.t10.exon3 332474 332566
chr_3 g23 g23.t10 cds g23.t10.CDS3 332474 332566
chr_3 g23 g23.t10 TTS g23.t10 332670 332670
chr_3 g23 g23.t10 TSS g23.t10 NA NA

Sequences

>g23.t10 Gene=g23 Length=1191
CATGAAAGAAAATTAGAAGATGGAATAGGAATGCCAAACTGGAATCTTGTTTTATTTCTG
TTCCTTTCATGGGCAATTGTTTTCTTCATTCTCTTCAAAGGAGTCAAAATGTCTGGCAAA
GCTTCATACATAACTGGAATTGCTCCATTCATCTTTCTTGCAATTTTCCTCGTCCGTGCG
CTTACACTTGAAGGAGCTTGGGATGGTATTGAATATCTTATTAAACCAAGATGGGGAGAA
TTACTCGATCCAAAAGTTTGGTACGAAGCGTGTACTCAAGTATTTTTTACACTCAATGTT
TTCTTCGTAAATGTCATCATGTATGCTTCATACAATAAATTTGAACATAACATTCATCGT
GATTCAAACATAGTCACGACATTAGACACTTTGACATCTATAGTTGTTGGTTCAATCACT
TTTGGTATTATTGGTCATTTATCACATGAACTTAATACTCCAATTGAGACAGTAATCAAA
TCTGGTCCTGGTTTAGTTTTCATAACATACCCCGAAACTATTTCAAAATTCAAATTCTGG
CCACAACTTTTTTCTATAATGTTTTTTTTGATGCTTTATATCATTGCTCTTGGTAGTCTA
TTTGCAATTACATCATCTGCTATCACCGTTATTCGTGATCAATTTAAGAAGGTCAAAGAT
TGGCAAGCAGCATTAGGAATCGCAATTTTCGGAACTATTTCTGGATCAATTTATACAACA
CCAGCTGGGTTAAGTATTCTTGATCTCGTCGATCATTATTGTGCTACTTTTGTGATTTTC
ATTCTGGCCTGTTTTGAAATATGTACATTCTGTTATATTTATGGTGTTGATCGTATTTGC
AATGATGTTAAATTCATGCTTGGATTTAGACCAAATATTTTCTGGAGAACTTGCTGGCGA
TATATTACACCTTCAATTTTGACAGCATTAGTTATTTATTTACTGATGAAAGCTAAATTT
ATCAAAGATGATGCAAGCACATTTCCTGCGTCAGCACATGCAGTTGGCGTGTGCATAGCT
GTTATGGGTATTATTTGGTTACCTATTGTATTTATTTGGAGAGTTTTAAAACAAACACAT
GAAAAGACTTTAATCGATAAAATCAAAAGCGCCTGCAAACCAACAAAAAATTGGGGACCA
ATGGATCCTGTTAAAAATGCTAGGTACAAAGAATATATGGCCACAAATTAA

>g23.t10 Gene=g23 Length=386
MPNWNLVLFLFLSWAIVFFILFKGVKMSGKASYITGIAPFIFLAIFLVRALTLEGAWDGI
EYLIKPRWGELLDPKVWYEACTQVFFTLNVFFVNVIMYASYNKFEHNIHRDSNIVTTLDT
LTSIVVGSITFGIIGHLSHELNTPIETVIKSGPGLVFITYPETISKFKFWPQLFSIMFFL
MLYIIALGSLFAITSSAITVIRDQFKKVKDWQAALGIAIFGTISGSIYTTPAGLSILDLV
DHYCATFVIFILACFEICTFCYIYGVDRICNDVKFMLGFRPNIFWRTCWRYITPSILTAL
VIYLLMKAKFIKDDASTFPASAHAVGVCIAVMGIIWLPIVFIWRVLKQTHEKTLIDKIKS
ACKPTKNWGPMDPVKNARYKEYMATN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
29 g23.t10 CDD cd10324 SLC6sbd 1 305 3.39933E-114
2 g23.t10 PANTHER PTHR11616 SODIUM/CHLORIDE DEPENDENT TRANSPORTER 2 378 7.9E-137
3 g23.t10 PANTHER PTHR11616:SF269 TRANSPORTER 2 378 7.9E-137
7 g23.t10 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 31 48 2.7E-17
8 g23.t10 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 113 133 2.7E-17
6 g23.t10 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 168 187 2.7E-17
4 g23.t10 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 246 266 2.7E-17
5 g23.t10 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 286 306 2.7E-17
1 g23.t10 Pfam PF00209 Sodium:neurotransmitter symporter family 2 347 3.3E-91
17 g23.t10 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 5 -
22 g23.t10 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 6 25 -
10 g23.t10 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 26 36 -
24 g23.t10 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 37 57 -
19 g23.t10 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 58 76 -
23 g23.t10 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 77 101 -
14 g23.t10 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 102 112 -
27 g23.t10 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 113 134 -
15 g23.t10 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 135 175 -
28 g23.t10 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 176 201 -
12 g23.t10 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 202 212 -
26 g23.t10 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 213 237 -
18 g23.t10 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 238 242 -
21 g23.t10 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 243 266 -
13 g23.t10 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 267 286 -
25 g23.t10 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 287 306 -
16 g23.t10 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 307 317 -
20 g23.t10 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 318 343 -
11 g23.t10 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 344 386 -
39 g23.t10 ProSiteProfiles PS50267 Sodium:neurotransmitter symporter family profile. 1 350 51.347
9 g23.t10 SUPERFAMILY SSF161070 SNF-like 2 346 1.44E-89
36 g23.t10 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 4 22 -
37 g23.t10 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 31 53 -
32 g23.t10 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 80 102 -
35 g23.t10 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 114 136 -
31 g23.t10 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 173 195 -
34 g23.t10 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 215 237 -
30 g23.t10 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 247 266 -
33 g23.t10 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 287 306 -
38 g23.t10 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 321 343 -

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