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.t9 isoform g23.t9 330950 332566
chr_3 g23 g23.t9 exon g23.t9.exon1 330950 330962
chr_3 g23 g23.t9 cds g23.t9.CDS1 330956 330962
chr_3 g23 g23.t9 exon g23.t9.exon2 331025 331983
chr_3 g23 g23.t9 cds g23.t9.CDS2 331025 331983
chr_3 g23 g23.t9 exon g23.t9.exon3 332040 332414
chr_3 g23 g23.t9 cds g23.t9.CDS3 332040 332414
chr_3 g23 g23.t9 exon g23.t9.exon4 332474 332566
chr_3 g23 g23.t9 cds g23.t9.CDS4 332474 332566
chr_3 g23 g23.t9 TTS g23.t9 332670 332670
chr_3 g23 g23.t9 TSS g23.t9 NA NA

Sequences

>g23.t9 Gene=g23 Length=1440
CCTGCTATGAGAGGAATTGGCATCGGTCAAACGTTATGCATCATGGTAGTTGCTACTTAT
TACAGTTTTATTATCGGCGTCATTTCGCGTTATCTTTTTGACTCATTTAGTTTCACTCTA
CCTTGGAGTGAATGTAATCCTAATTGGAATGTCTCATGTTATTCTTCAAATGGAAATAAT
GGGTCAAATGTTGTTATGAATGGTACAACCAAATCATCAGCTGAACTTTATTTTTTCAAA
GAAGTTCTTCATGAAAGAAAATTAGAAGATGGAATAGGAATGCCAAACTGGAATCTTGTT
TTATTTCTGTTCCTTTCATGGGCAATTGTTTTCTTCATTCTCTTCAAAGGAGTCAAAATG
TCTGGCAAAGCTTCATACATAACTGGAATTGCTCCATTCATCTTTCTTGCAATTTTCCTC
GTCCGTGCGCTTACACTTGAAGGAGCTTGGGATGGTATTGAATATCTTATTAAACCAAGA
TGGGGAGAATTACTCGATCCAAAAGTTTGGTACGAAGCGTGTACTCAAGTATTTTTTACA
CTCAATGTTTTCTTCGTAAATGTCATCATGTATGCTTCATACAATAAATTTGAACATAAC
ATTCATCGTGATTCAAACATAGTCACGACATTAGACACTTTGACATCTATAGTTGTTGGT
TCAATCACTTTTGGTATTATTGGTCATTTATCACATGAACTTAATACTCCAATTGAGACA
GTAATCAAATCTGGTCCTGGTTTAGTTTTCATAACATACCCCGAAACTATTTCAAAATTC
AAATTCTGGCCACAACTTTTTTCTATAATGTTTTTTTTGATGCTTTATATCATTGCTCTT
GGTAGTCTATTTGCAATTACATCATCTGCTATCACCGTTATTCGTGATCAATTTAAGAAG
GTCAAAGATTGGCAAGCAGCATTAGGAATCGCAATTTTCGGAACTATTTCTGGATCAATT
TATACAACACCAGCTGGGTTAAGTATTCTTGATCTCGTCGATCATTATTGTGCTACTTTT
GTGATTTTCATTCTGGCCTGTTTTGAAATATGTACATTCTGTTATATTTATGGTGTTGAT
CGTATTTGCAATGATGTTAAATTCATGCTTGGATTTAGACCAAATATTTTCTGGAGAACT
TGCTGGCGATATATTACACCTTCAATTTTGACAGCATTAGTTATTTATTTACTGATGAAA
GCTAAATTTATCAAAGATGATGCAAGCACATTTCCTGCGTCAGCACATGCAGTTGGCGTG
TGCATAGCTGTTATGGGTATTATTTGGTTACCTATTGTATTTATTTGGAGAGTTTTAAAA
CAAACACATGAAAAGACTTTAATCGATAAAATCAAAAGCGCCTGCAAACCAACAAAAAAT
TGGGGACCAATGGATCCTGTTAAAAATGCTAGGTACAAAGAATATATGGCCACAAATTAA

>g23.t9 Gene=g23 Length=477
MRGIGIGQTLCIMVVATYYSFIIGVISRYLFDSFSFTLPWSECNPNWNVSCYSSNGNNGS
NVVMNGTTKSSAELYFFKEVLHERKLEDGIGMPNWNLVLFLFLSWAIVFFILFKGVKMSG
KASYITGIAPFIFLAIFLVRALTLEGAWDGIEYLIKPRWGELLDPKVWYEACTQVFFTLN
VFFVNVIMYASYNKFEHNIHRDSNIVTTLDTLTSIVVGSITFGIIGHLSHELNTPIETVI
KSGPGLVFITYPETISKFKFWPQLFSIMFFLMLYIIALGSLFAITSSAITVIRDQFKKVK
DWQAALGIAIFGTISGSIYTTPAGLSILDLVDHYCATFVIFILACFEICTFCYIYGVDRI
CNDVKFMLGFRPNIFWRTCWRYITPSILTALVIYLLMKAKFIKDDASTFPASAHAVGVCI
AVMGIIWLPIVFIWRVLKQTHEKTLIDKIKSACKPTKNWGPMDPVKNARYKEYMATN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
32 g23.t9 CDD cd10324 SLC6sbd 1 396 1.51562E-118
2 g23.t9 PANTHER PTHR11616 SODIUM/CHLORIDE DEPENDENT TRANSPORTER 1 469 2.6E-170
3 g23.t9 PANTHER PTHR11616:SF269 TRANSPORTER 1 469 2.6E-170
5 g23.t9 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 3 29 2.5E-21
4 g23.t9 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 122 139 2.5E-21
6 g23.t9 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 204 224 2.5E-21
9 g23.t9 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 259 278 2.5E-21
8 g23.t9 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 337 357 2.5E-21
7 g23.t9 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 377 397 2.5E-21
1 g23.t9 Pfam PF00209 Sodium:neurotransmitter symporter family 2 438 5.6E-110
12 g23.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
27 g23.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 31 -
19 g23.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 32 94 -
29 g23.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 95 113 -
14 g23.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 114 124 -
26 g23.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 125 148 -
21 g23.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 149 167 -
24 g23.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 168 192 -
16 g23.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 193 203 -
30 g23.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 204 225 -
18 g23.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 226 266 -
28 g23.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 267 292 -
15 g23.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 293 303 -
31 g23.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 304 328 -
17 g23.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 329 333 -
23 g23.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 334 357 -
11 g23.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 358 377 -
22 g23.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 378 397 -
20 g23.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 398 408 -
25 g23.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 409 434 -
13 g23.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 435 477 -
43 g23.t9 ProSiteProfiles PS50267 Sodium:neurotransmitter symporter family profile. 1 441 56.029
10 g23.t9 SUPERFAMILY SSF161070 SNF-like 2 437 2.75E-108
40 g23.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 9 31 -
36 g23.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 91 113 -
34 g23.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 122 144 -
37 g23.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 171 193 -
38 g23.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 205 227 -
35 g23.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 264 286 -
42 g23.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 306 328 -
41 g23.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 338 357 -
33 g23.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 378 397 -
39 g23.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 412 434 -

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