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 g21 g21.t2 TSS g21.t2 321722 321722
chr_3 g21 g21.t2 isoform g21.t2 321870 323996
chr_3 g21 g21.t2 exon g21.t2.exon1 321870 322076
chr_3 g21 g21.t2 exon g21.t2.exon2 322202 322273
chr_3 g21 g21.t2 exon g21.t2.exon3 322378 322735
chr_3 g21 g21.t2 cds g21.t2.CDS1 322443 322735
chr_3 g21 g21.t2 exon g21.t2.exon4 322795 323303
chr_3 g21 g21.t2 cds g21.t2.CDS2 322795 323303
chr_3 g21 g21.t2 exon g21.t2.exon5 323359 323591
chr_3 g21 g21.t2 cds g21.t2.CDS3 323359 323591
chr_3 g21 g21.t2 exon g21.t2.exon6 323644 323794
chr_3 g21 g21.t2 cds g21.t2.CDS4 323644 323794
chr_3 g21 g21.t2 exon g21.t2.exon7 323853 323996
chr_3 g21 g21.t2 cds g21.t2.CDS5 323853 323995
chr_3 g21 g21.t2 TTS g21.t2 324375 324375

Sequences

>g21.t2 Gene=g21 Length=1674
ATGGCAAGAGGTCATGATAATCCATCCTTCTCAGATATTCCTGATAGTGAAAAATTCTCA
AATCATTACATCATAAACAATGAAAATGACAGCGAGCAAAGTAGTAGAAATGCAGAAGAT
GAAAACGACCGCGATCAATGGGGAAAAGGGATCCAATTTACATTGTCATGTATCGCGTGT
TGTGTTGGTGAGGCCAAATAAAAAGCAAATCTGCAGTTGTAATTATTCAATCTTATGTTT
TTAGGCGGTTTCCATTTATTGCTTTGCAGAATGGAGGAGGTGCTTTTGTGATACCTTACA
TAATTATGCTTTTATTAGTTGGTAGACCTGGATATTTCTTAGAGATGATCATGGGACAAT
TTTCATCACGTGGTACAATCAAAGTGTATGATTGTGCACCAGCTATGAGAGGAGTTGGAA
TGGGTCAAATGGTTACAATTCTTGCAGTTTCTACTTATTATTCAAGCATTTTAGCTATCG
CTTTACGATATTTCTTTTATTCTTTTAATACTGTCTTACCATGGAGTGAATGCAAACCTG
AATGGACAGAACCATGCTATTCAGCAAATGGAATTCAAACAAATGATGATGAATCTGGAA
ATATTACGAGAAAATCTTCTACTGAACTTTATTTCTTAAAAGAAGTTCTTCATGCAAGAG
AAAATATAAATGATGGAATTGGATCAATAAATTGGAACCTTTTTGGTTTTCTAGCTCTTA
CTTGGATTACCGTCTGTTTGATTTTAATGCGTGGAGTTCGAAGTTCTGGAAAAGCAGCTT
ATATTACAGGAATAGTGCCATTTATATTTCTTTTTATCTTTCTTATTCGTGCTCTCACTC
TTCCTGGTGCTTTCAATGGCATTGCTTTCTTTTTTACTCCTAAATGGGAAGATATTTTAA
AGCCAGGTGTTTGGTATGCTGCTGTAACTCAACTATTTTTCTCTCTCAATGTTTTCTTTG
CAAATATTATCATGTATGCTTCTTATAACAAATTTTCACACAAAATTCATCGAGATTCAA
ATATTATTACTATAATTGACACTGGAACTTCTTTACTTGCTGGTTGTATTAGTTTTGGTA
TTATTGGTCATTTAGCTCATGAATTAGGTGTCGATGATATTTCCAAAGTTTTTCAAGGTG
GTCCTGGTTTGGTCTTTGTAACTTATGCCGAAACGATCTCAAAATTTAGAGTACTTCCAC
AAGTATTTTCAGTATTATTTTTTCTTATGCTTTATATTCTTGGATTAGGAAGTTTAATAG
CACAAACATCATGTGTGATAACAGTCATAAGAGATCAATTTAAAAATGTTAAAAATTGGC
ATGCAGCTGTTGGGTATTCAATTTTTGGTGCTCTTTGTGGAAGTTTATATACAACTGAAG
GGGGACAATCAGTTTTAAATTTAGTCGATCATTATGGAACAACATTTGTTAATTTTTTGT
TAGCTGTTTTTGAAATTATGGCATTTTGTCATATTTATGGAGTTAATAGAATATGCAAAG
ATGTAAAATTCATGCTTGGATTTATACCAGGAATTTATTGGACTGTATGTTGGCGGGTAG
TAACACCACTTATTATGATGGCAATTATTGTTTATCATTTCATTTACTATGAAAATCCAA
AAGATAATGGAGCTGAATTTCCATTTATTGCTCATGTTGTTGGTTGGTGTATTA

>g21.t2 Gene=g21 Length=443
MIMGQFSSRGTIKVYDCAPAMRGVGMGQMVTILAVSTYYSSILAIALRYFFYSFNTVLPW
SECKPEWTEPCYSANGIQTNDDESGNITRKSSTELYFLKEVLHARENINDGIGSINWNLF
GFLALTWITVCLILMRGVRSSGKAAYITGIVPFIFLFIFLIRALTLPGAFNGIAFFFTPK
WEDILKPGVWYAAVTQLFFSLNVFFANIIMYASYNKFSHKIHRDSNIITIIDTGTSLLAG
CISFGIIGHLAHELGVDDISKVFQGGPGLVFVTYAETISKFRVLPQVFSVLFFLMLYILG
LGSLIAQTSCVITVIRDQFKNVKNWHAAVGYSIFGALCGSLYTTEGGQSVLNLVDHYGTT
FVNFLLAVFEIMAFCHIYGVNRICKDVKFMLGFIPGIYWTVCWRVVTPLIMMAIIVYHFI
YYENPKDNGAEFPFIAHVVGWCI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
30 g21.t2 CDD cd10324 SLC6sbd 1 419 1.07441E-120
2 g21.t2 PANTHER PTHR11616 SODIUM/CHLORIDE DEPENDENT TRANSPORTER 1 443 2.1E-180
3 g21.t2 PANTHER PTHR11616:SF269 TRANSPORTER 1 443 2.1E-180
6 g21.t2 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 23 49 1.4E-26
9 g21.t2 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 144 161 1.4E-26
4 g21.t2 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 226 246 1.4E-26
8 g21.t2 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 282 301 1.4E-26
5 g21.t2 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 360 380 1.4E-26
7 g21.t2 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 400 420 1.4E-26
1 g21.t2 Pfam PF00209 Sodium:neurotransmitter symporter family 2 443 7.2E-114
15 g21.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 29 -
21 g21.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 30 51 -
18 g21.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 52 118 -
29 g21.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 119 138 -
14 g21.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 139 149 -
23 g21.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 150 177 -
20 g21.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 178 188 -
26 g21.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 189 214 -
13 g21.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 215 225 -
27 g21.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 226 247 -
17 g21.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 248 289 -
25 g21.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 290 315 -
12 g21.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 316 326 -
28 g21.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 327 344 -
19 g21.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 345 363 -
22 g21.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 364 384 -
11 g21.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 385 395 -
24 g21.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 396 420 -
16 g21.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 421 443 -
40 g21.t2 ProSiteProfiles PS50267 Sodium:neurotransmitter symporter family profile. 1 443 57.118
10 g21.t2 SUPERFAMILY SSF161070 SNF-like 1 443 1.23E-112
34 g21.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 30 52 -
31 g21.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 112 134 -
37 g21.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 155 177 -
38 g21.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 192 214 -
36 g21.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 226 248 -
33 g21.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 283 305 -
32 g21.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 325 343 -
35 g21.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 358 380 -
39 g21.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 400 422 -

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