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.t3 TSS g21.t3 321722 321722
chr_3 g21 g21.t3 isoform g21.t3 321870 324005
chr_3 g21 g21.t3 exon g21.t3.exon1 321870 322056
chr_3 g21 g21.t3 cds g21.t3.CDS1 321870 322056
chr_3 g21 g21.t3 exon g21.t3.exon2 322202 322273
chr_3 g21 g21.t3 cds g21.t3.CDS2 322202 322273
chr_3 g21 g21.t3 exon g21.t3.exon3 322378 322735
chr_3 g21 g21.t3 cds g21.t3.CDS3 322378 322735
chr_3 g21 g21.t3 exon g21.t3.exon4 322795 323303
chr_3 g21 g21.t3 cds g21.t3.CDS4 322795 323303
chr_3 g21 g21.t3 exon g21.t3.exon5 323359 323486
chr_3 g21 g21.t3 cds g21.t3.CDS5 323359 323486
chr_3 g21 g21.t3 exon g21.t3.exon6 323644 323794
chr_3 g21 g21.t3 cds g21.t3.CDS6 323644 323794
chr_3 g21 g21.t3 exon g21.t3.exon7 323853 324005
chr_3 g21 g21.t3 cds g21.t3.CDS7 323853 324004
chr_3 g21 g21.t3 TTS g21.t3 324375 324375

Sequences

>g21.t3 Gene=g21 Length=1558
ATGGCAAGAGGTCATGATAATCCATCCTTCTCAGATATTCCTGATAGTGAAAAATTCTCA
AATCATTACATCATAAACAATGAAAATGACAGCGAGCAAAGTAGTAGAAATGCAGAAGAT
GAAAACGACCGCGATCAATGGGGAAAAGGGATCCAATTTACATTGTCATGTATCGCGTGT
TGTGTTGAATCTGCAGTTGTAATTATTCAATCTTATGTTTTTAGGCGGTTTCCATTTATT
GCTTTGCAGAATGGAGGAGGTGCTTTTGTGATACCTTACATAATTATGCTTTTATTAGTT
GGTAGACCTGGATATTTCTTAGAGATGATCATGGGACAATTTTCATCACGTGGTACAATC
AAAGTGTATGATTGTGCACCAGCTATGAGAGGAGTTGGAATGGGTCAAATGGTTACAATT
CTTGCAGTTTCTACTTATTATTCAAGCATTTTAGCTATCGCTTTACGATATTTCTTTTAT
TCTTTTAATACTGTCTTACCATGGAGTGAATGCAAACCTGAATGGACAGAACCATGCTAT
TCAGCAAATGGAATTCAAACAAATGATGATGAATCTGGAAATATTACGAGAAAATCTTCT
ACTGAACTTTATTTCTTAAAAGAAGTTCTTCATGCAAGAGAAAATATAAATGATGGAATT
GGATCAATAAATTGGAACCTTTTTGGTTTTCTAGCTCTTACTTGGATTACCGTCTGTTTG
ATTTTAATGCGTGGAGTTCGAAGTTCTGGAAAAGCAGCTTATATTACAGGAATAGTGCCA
TTTATATTTCTTTTTATCTTTCTTATTCGTGCTCTCACTCTTCCTGGTGCTTTCAATGGC
ATTGCTTTCTTTTTTACTCCTAAATGGGAAGATATTTTAAAGCCAGGTGTTTGGTATGCT
GCTGTAACTCAACTATTTTTCTCTCTCAATGTTTTCTTTGCAAATATTATCATGTATGCT
TCTTATAACAAATTTTCACACAAAATTCATCGAGATTCAAATATTATTACTATAATTGAC
ACTGGAACTTCTTTACTTGCTGGTTGTATTAGTTTTGGTATTATTGGTCATTTAGCTCAT
GAATTAGGTGTCGATGATATTTCCAAAGTTTTTCAAGGTGGTCCTGGTTTGGTCTTTGTA
ACTTATGCCGAAACGATCTCAAAATTTAGAGTACTTCCACAAGTATTTTCAGTATTATTT
TTTCTTATGCTTTATATTCTTGGATTAGGAAGTTTAATAGCACAAACATCATGTGGGGGA
CAATCAGTTTTAAATTTAGTCGATCATTATGGAACAACATTTGTTAATTTTTTGTTAGCT
GTTTTTGAAATTATGGCATTTTGTCATATTTATGGAGTTAATAGAATATGCAAAGATGTA
AAATTCATGCTTGGATTTATACCAGGAATTTATTGGACTGTATGTTGGCGGGTAGTAACA
CCACTTATTATGATGGCAATTATTGTTTATCATTTCATTTACTATGAAAATCCAAAAGAT
AATGGAGCTGAATTTCCATTTATTGCTCATGTTGTTGGTTGGTGTATTACTGCTTCAG

>g21.t3 Gene=g21 Length=519
MARGHDNPSFSDIPDSEKFSNHYIINNENDSEQSSRNAEDENDRDQWGKGIQFTLSCIAC
CVESAVVIIQSYVFRRFPFIALQNGGGAFVIPYIIMLLLVGRPGYFLEMIMGQFSSRGTI
KVYDCAPAMRGVGMGQMVTILAVSTYYSSILAIALRYFFYSFNTVLPWSECKPEWTEPCY
SANGIQTNDDESGNITRKSSTELYFLKEVLHARENINDGIGSINWNLFGFLALTWITVCL
ILMRGVRSSGKAAYITGIVPFIFLFIFLIRALTLPGAFNGIAFFFTPKWEDILKPGVWYA
AVTQLFFSLNVFFANIIMYASYNKFSHKIHRDSNIITIIDTGTSLLAGCISFGIIGHLAH
ELGVDDISKVFQGGPGLVFVTYAETISKFRVLPQVFSVLFFLMLYILGLGSLIAQTSCGG
QSVLNLVDHYGTTFVNFLLAVFEIMAFCHIYGVNRICKDVKFMLGFIPGIYWTVCWRVVT
PLIMMAIIVYHFIYYENPKDNGAEFPFIAHVVGWCITAS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
36 g21.t3 CDD cd10324 SLC6sbd 45 492 2.55077E-134
4 g21.t3 PANTHER PTHR11616 SODIUM/CHLORIDE DEPENDENT TRANSPORTER 22 418 2.1E-193
6 g21.t3 PANTHER PTHR11616:SF269 TRANSPORTER 22 418 2.1E-193
3 g21.t3 PANTHER PTHR11616 SODIUM/CHLORIDE DEPENDENT TRANSPORTER 416 518 2.1E-193
5 g21.t3 PANTHER PTHR11616:SF269 TRANSPORTER 416 518 2.1E-193
7 g21.t3 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 88 107 9.8E-27
11 g21.t3 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 131 157 9.8E-27
9 g21.t3 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 252 269 9.8E-27
8 g21.t3 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 334 354 9.8E-27
10 g21.t3 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 390 409 9.8E-27
2 g21.t3 Pfam PF00209 Sodium:neurotransmitter symporter family 44 415 7.1E-104
1 g21.t3 Pfam PF00209 Sodium:neurotransmitter symporter family 416 518 2.7E-19
16 g21.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 52 -
25 g21.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 53 74 -
22 g21.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 75 79 -
27 g21.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 80 101 -
15 g21.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 102 137 -
30 g21.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 138 159 -
24 g21.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 160 226 -
29 g21.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 227 246 -
17 g21.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 247 257 -
32 g21.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 258 285 -
20 g21.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 286 296 -
26 g21.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 297 322 -
14 g21.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 323 333 -
35 g21.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 334 355 -
21 g21.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 356 366 -
28 g21.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 367 383 -
18 g21.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 384 394 -
31 g21.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 395 414 -
23 g21.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 415 433 -
33 g21.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 434 453 -
13 g21.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 454 473 -
34 g21.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 474 493 -
19 g21.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 494 519 -
48 g21.t3 ProSiteProfiles PS50267 Sodium:neurotransmitter symporter family profile. 43 519 59.386
12 g21.t3 SUPERFAMILY SSF161070 SNF-like 44 518 2.22E-126
39 g21.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 52 74 -
44 g21.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 79 101 -
41 g21.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 138 160 -
45 g21.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 223 245 -
42 g21.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 252 274 -
37 g21.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 298 320 -
47 g21.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 333 355 -
40 g21.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 370 387 -
43 g21.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 394 416 -
38 g21.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 431 453 -
46 g21.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 473 495 -

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