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.t6 TSS g23.t6 329342 329342
chr_3 g23 g23.t6 isoform g23.t6 329745 332566
chr_3 g23 g23.t6 exon g23.t6.exon1 329745 329931
chr_3 g23 g23.t6 exon g23.t6.exon2 330009 330162
chr_3 g23 g23.t6 exon g23.t6.exon3 330853 330962
chr_3 g23 g23.t6 cds g23.t6.CDS1 330896 330962
chr_3 g23 g23.t6 exon g23.t6.exon4 331025 331983
chr_3 g23 g23.t6 cds g23.t6.CDS2 331025 331983
chr_3 g23 g23.t6 exon g23.t6.exon5 332040 332414
chr_3 g23 g23.t6 cds g23.t6.CDS3 332040 332414
chr_3 g23 g23.t6 exon g23.t6.exon6 332474 332566
chr_3 g23 g23.t6 cds g23.t6.CDS4 332474 332566
chr_3 g23 g23.t6 TTS g23.t6 332670 332670

Sequences

>g23.t6 Gene=g23 Length=1878
ATGACTCAAGCATACGATAACCCAACATTTGCAAACGATAAATCAGTTGTTGCCAATAGC
ACTTTGGCATTCACAATTGATCACAAAAGTGACGAATACAATGCACAGACAAAAAAACAT
GGAACAACTCGCGATACATGGGGAAAAGATGTAGAATTTCTTTTGTCATGCATTGCTATG
GCAGTAGGACTTGGGAACGTTTGGTAACTCTCTTTTATCAATTTTTTTGAGATTATTAAT
TATCACTCAATTATTATTATTTATATTAGAACCTGCAGTTGTAATTATTCAATCTTATGT
TTTTAGGCGATTCCCTTTCACTGCTTTAAGGAATGGAGGAGTATTGTTCTTGTATTGGTT
GGCAAGCCTGGATATTTCTTAGAGATGATCATGGGACAGTTTTCGTCACGTGGAACAGTA
AAAGTATATGACAGTGTTCCTGCTATGAGAGGAATTGGCATCGGTCAAACGTTATGCATC
ATGGTAGTTGCTACTTATTACAGTTTTATTATCGGCGTCATTTCGCGTTATCTTTTTGAC
TCATTTAGTTTCACTCTACCTTGGAGTGAATGTAATCCTAATTGGAATGTCTCATGTTAT
TCTTCAAATGGAAATAATGGGTCAAATGTTGTTATGAATGGTACAACCAAATCATCAGCT
GAACTTTATTTTTTCAAAGAAGTTCTTCATGAAAGAAAATTAGAAGATGGAATAGGAATG
CCAAACTGGAATCTTGTTTTATTTCTGTTCCTTTCATGGGCAATTGTTTTCTTCATTCTC
TTCAAAGGAGTCAAAATGTCTGGCAAAGCTTCATACATAACTGGAATTGCTCCATTCATC
TTTCTTGCAATTTTCCTCGTCCGTGCGCTTACACTTGAAGGAGCTTGGGATGGTATTGAA
TATCTTATTAAACCAAGATGGGGAGAATTACTCGATCCAAAAGTTTGGTACGAAGCGTGT
ACTCAAGTATTTTTTACACTCAATGTTTTCTTCGTAAATGTCATCATGTATGCTTCATAC
AATAAATTTGAACATAACATTCATCGTGATTCAAACATAGTCACGACATTAGACACTTTG
ACATCTATAGTTGTTGGTTCAATCACTTTTGGTATTATTGGTCATTTATCACATGAACTT
AATACTCCAATTGAGACAGTAATCAAATCTGGTCCTGGTTTAGTTTTCATAACATACCCC
GAAACTATTTCAAAATTCAAATTCTGGCCACAACTTTTTTCTATAATGTTTTTTTTGATG
CTTTATATCATTGCTCTTGGTAGTCTATTTGCAATTACATCATCTGCTATCACCGTTATT
CGTGATCAATTTAAGAAGGTCAAAGATTGGCAAGCAGCATTAGGAATCGCAATTTTCGGA
ACTATTTCTGGATCAATTTATACAACACCAGCTGGGTTAAGTATTCTTGATCTCGTCGAT
CATTATTGTGCTACTTTTGTGATTTTCATTCTGGCCTGTTTTGAAATATGTACATTCTGT
TATATTTATGGTGTTGATCGTATTTGCAATGATGTTAAATTCATGCTTGGATTTAGACCA
AATATTTTCTGGAGAACTTGCTGGCGATATATTACACCTTCAATTTTGACAGCATTAGTT
ATTTATTTACTGATGAAAGCTAAATTTATCAAAGATGATGCAAGCACATTTCCTGCGTCA
GCACATGCAGTTGGCGTGTGCATAGCTGTTATGGGTATTATTTGGTTACCTATTGTATTT
ATTTGGAGAGTTTTAAAACAAACACATGAAAAGACTTTAATCGATAAAATCAAAAGCGCC
TGCAAACCAACAAAAAATTGGGGACCAATGGATCCTGTTAAAAATGCTAGGTACAAAGAA
TATATGGCCACAAATTAA

>g23.t6 Gene=g23 Length=497
MIMGQFSSRGTVKVYDSVPAMRGIGIGQTLCIMVVATYYSFIIGVISRYLFDSFSFTLPW
SECNPNWNVSCYSSNGNNGSNVVMNGTTKSSAELYFFKEVLHERKLEDGIGMPNWNLVLF
LFLSWAIVFFILFKGVKMSGKASYITGIAPFIFLAIFLVRALTLEGAWDGIEYLIKPRWG
ELLDPKVWYEACTQVFFTLNVFFVNVIMYASYNKFEHNIHRDSNIVTTLDTLTSIVVGSI
TFGIIGHLSHELNTPIETVIKSGPGLVFITYPETISKFKFWPQLFSIMFFLMLYIIALGS
LFAITSSAITVIRDQFKKVKDWQAALGIAIFGTISGSIYTTPAGLSILDLVDHYCATFVI
FILACFEICTFCYIYGVDRICNDVKFMLGFRPNIFWRTCWRYITPSILTALVIYLLMKAK
FIKDDASTFPASAHAVGVCIAVMGIIWLPIVFIWRVLKQTHEKTLIDKIKSACKPTKNWG
PMDPVKNARYKEYMATN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
32 g23.t6 CDD cd10324 SLC6sbd 1 416 1.87699E-125
2 g23.t6 PANTHER PTHR11616 SODIUM/CHLORIDE DEPENDENT TRANSPORTER 1 489 7.5E-182
3 g23.t6 PANTHER PTHR11616:SF269 TRANSPORTER 1 489 7.5E-182
5 g23.t6 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 23 49 3.1E-21
4 g23.t6 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 142 159 3.1E-21
9 g23.t6 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 224 244 3.1E-21
8 g23.t6 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 279 298 3.1E-21
7 g23.t6 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 357 377 3.1E-21
6 g23.t6 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 397 417 3.1E-21
1 g23.t6 Pfam PF00209 Sodium:neurotransmitter symporter family 2 458 3.3E-115
14 g23.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 29 -
23 g23.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 30 51 -
19 g23.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 52 114 -
29 g23.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 115 133 -
15 g23.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 134 144 -
25 g23.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 145 168 -
17 g23.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 169 187 -
26 g23.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 188 212 -
13 g23.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 213 223 -
22 g23.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 224 245 -
20 g23.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 246 286 -
30 g23.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 287 312 -
11 g23.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 313 323 -
24 g23.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 324 348 -
21 g23.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 349 353 -
27 g23.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 354 377 -
12 g23.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 378 397 -
31 g23.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 398 417 -
18 g23.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 418 428 -
28 g23.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 429 454 -
16 g23.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 455 497 -
43 g23.t6 ProSiteProfiles PS50267 Sodium:neurotransmitter symporter family profile. 1 461 58.27
10 g23.t6 SUPERFAMILY SSF161070 SNF-like 1 457 3.01E-114
40 g23.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 24 46 -
33 g23.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 111 133 -
34 g23.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 142 164 -
36 g23.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 191 213 -
39 g23.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 225 247 -
37 g23.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 284 306 -
42 g23.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 326 348 -
38 g23.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 358 377 -
41 g23.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 398 417 -
35 g23.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 432 454 -

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