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 g19 g19.t2 isoform g19.t2 313665 319629
chr_3 g19 g19.t2 exon g19.t2.exon1 313665 314165
chr_3 g19 g19.t2 exon g19.t2.exon2 315358 315600
chr_3 g19 g19.t2 exon g19.t2.exon3 316632 316736
chr_3 g19 g19.t2 exon g19.t2.exon4 316791 316878
chr_3 g19 g19.t2 exon g19.t2.exon5 317060 317106
chr_3 g19 g19.t2 exon g19.t2.exon6 317161 317524
chr_3 g19 g19.t2 cds g19.t2.CDS1 317229 317524
chr_3 g19 g19.t2 exon g19.t2.exon7 317607 317877
chr_3 g19 g19.t2 cds g19.t2.CDS2 317607 317877
chr_3 g19 g19.t2 exon g19.t2.exon8 318303 318362
chr_3 g19 g19.t2 cds g19.t2.CDS3 318303 318362
chr_3 g19 g19.t2 exon g19.t2.exon9 318426 318534
chr_3 g19 g19.t2 cds g19.t2.CDS4 318426 318534
chr_3 g19 g19.t2 exon g19.t2.exon10 318592 318679
chr_3 g19 g19.t2 cds g19.t2.CDS5 318592 318679
chr_3 g19 g19.t2 exon g19.t2.exon11 318753 318792
chr_3 g19 g19.t2 cds g19.t2.CDS6 318753 318792
chr_3 g19 g19.t2 exon g19.t2.exon12 318857 319058
chr_3 g19 g19.t2 cds g19.t2.CDS7 318857 319058
chr_3 g19 g19.t2 exon g19.t2.exon13 319118 319629
chr_3 g19 g19.t2 cds g19.t2.CDS8 319118 319629
chr_3 g19 g19.t2 TTS g19.t2 319710 319710
chr_3 g19 g19.t2 TSS g19.t2 NA NA

Sequences

>g19.t2 Gene=g19 Length=2630
AGATAATTGAAGTTATTATTGTTTATAATTAATAAATCTTTTATGAGTTCATTTTAGGAT
GTAACTTGCTTACTCTAGAAATTTTTATCAGAAATAATAAAAAGTTAAGACCACAATGAA
GTAATAAATTAATTCATCTATCACATTATTGTCGCACTTATAGCAGCAATTTGAAATAAT
TTTCATTCATCAATGTGATTAACTCAAATTGCTTTTTTTTTAATTTATCGTTTTCCTGCA
AAATCAAACTCTCAACACGGTAGAAATGACAGCTGTGTATGGTTTTTTTTAAATTTTTTT
AAACTCACTTTACTAACACCTTGCAATTATAATAGTATTATTTTATTCACTTGCTCAAAT
AGTACTGTTTAAACTTTTTTTATCTATACAATAACGCATTATGTGAAATGTTCACTTCAG
TTCATATTCTGAGCTCGAGTTGTTCACACATTTGGTATTTAAACTTAAAATATTTTACGA
ATTGTGGTGATATTTTATTAGCTCAAAACATTTTTTTGAATAAAATATAGTAAAAAGTAT
CTGTAATGTGGTATTTCTATGGAAACATCCTATTTTAATGAACAGTAACTATCAACTTAT
ACAAACATACAGACAAAGTGAAGTAAATAAAAGAGTGAAACAAAAATTTTATAGACATTC
ATCATAGAAAGGGAGCAAAATAAGTTTATTACAAAAATGGGTAAACAAGGTTCATATAAC
ATGGGATTTGACGCATCTAATGAGGACATAAAAACAGTCAATGGTATATCAAACGGTGTG
TCATCATCGCCAACCAATATGATGGCAATAAATGTCAGCGATAAAGCTTCTACAAATAAC
CATGATGAGATTAATCATGATTTGGAGCATGGACCTGAAAGAGCAACATGGGGACATGGA
TTAGAATTTTTGATGAGTTGCATTTCTCTTTCAGTTGATCTTATGTTTTTAGGCGGTTTC
CATTTACTTGTTATGAAAATGGAGGTGGAGCATTTTTAATTCCATACATCATTGTACTCA
TACTCATTGGAAAACCGATTTATTATTACGAGATGGTTCTCGGTCAATTTGTTTCTAAAG
CTTCAGTAAAAGCTACATCAGTAATTCCAGCTTTGAAAGGAATAGCAATTGGACAACAAC
TAGGAGTTTTATGCATCGTCACATATTATACTTCACTTATCGCTCTCACACTTTTTTATA
TGATTAAAAGTTTCTCTGAAACATTACCTTGGAGTTTCTGTTGGGATAAATGGACTGATG
TAATTTGTATTCCTGCTGATCCTAAATTTCAAACAAATGATGGTGAAAAAGTTGTCAATG
GAACAAGTTCAAGTGAACTTTATTTTATTCGAGAAGTGATAAAAGAGAAAAATGATATAA
GTGACGGTCTAGGTTTTCCTGATTGGCAGCTGACAATTTACTTGCTTTTAGCATGGATTG
TAATTTATCTGATTATTATAAAAGGTGTCAAAAGTAGTGGAAAAGTAAGCTATTTTCTCG
CTTGCTTCCCTTATGTTGTGTTGATAATTCTATTGATTCGAGCCTCAACTTTAAATGGAA
CTTGGGATGGCATTAGGTATTTCATCACACCAGACTTTAAGCGGCTTATCGAACCACAAG
TATGGTATGCTGCCACAACTCAGTTATTCTTCTCTCTTTCAGTGGGCCAAGGGACTATAA
TTATGTTTGCATCTTTTAATCGATTTGATCATAATATTCATAGAGATGCAATGATTGTCA
CAACTATGGATACTTTTACAAGTTTACTTGGAGGCTTTACGATTTTTGGTATTTTGGGAA
ATTTGGCATATAGCATTGGTGAAGAGGATATTGGAAACGTTATTAAAAGCGGGGGCAGTG
GGTTAGCGTTTATTTCATACCCTGAAGCAATTTCAAAGTTCAAATTTGTTCCACAGCTCT
TTGCCGTTCTCTTCTTCTTTATGCTTTTTACACTGGGAGTTGGTAGTGCTGTTGGATTAC
AAAGTGCCATAGTAGCAAATTTAATGGACTTTTTCCCAAAAATAAAGCAATGGATGATGG
CTTTAATCTGCTGCTTGATTGGATTTGTAATTGGCCTTTTATATGTCACGCCAGGAGGAC
AATGGATTCTAAATTTGGTTGACCATTTTGGAGGAACATTTTTGATTTTCACTCTTGCCA
TCTTTCAAATTGTAGGAATATTTTGGGTATATGGAATTGAAAACTTTTGCTGGGATGTTG
AATTTATGTTAAATAGAAAAGTTACAAAGTTTTGGCGATTTTCTTGGTTTATTGTCACTC
CTGTCTTGCTTATCATCATTTTCATATATTTTTTGATAAAAACCGAAAATCCTACTTATG
GTGCTCGAGAATATCCAGTCACAGTTTTAGCTACAGGTTGGATTATTTTTGGTGTTGGAA
TGTTCCAAATACTCTTGTGGATTTCATGGTCAATTATTAGAGATCCAAATAAATGTGAAG
CCTTTAAATCTCTCTTCAGACAAAATTCAGAATGGGGACCAAAATCTCCAAAAGTTTTCA
AAGAATGGAAAACATATAAAAGCGAAAGACTTGAAAAACGCAGAGCAAAAAGCAATGGAG
ATTCAAAGATTAAAAAATGTTTAAACATTTTACTCGATAAATATGAATAG

>g19.t2 Gene=g19 Length=525
MVLGQFVSKASVKATSVIPALKGIAIGQQLGVLCIVTYYTSLIALTLFYMIKSFSETLPW
SFCWDKWTDVICIPADPKFQTNDGEKVVNGTSSSELYFIREVIKEKNDISDGLGFPDWQL
TIYLLLAWIVIYLIIIKGVKSSGKVSYFLACFPYVVLIILLIRASTLNGTWDGIRYFITP
DFKRLIEPQVWYAATTQLFFSLSVGQGTIIMFASFNRFDHNIHRDAMIVTTMDTFTSLLG
GFTIFGILGNLAYSIGEEDIGNVIKSGGSGLAFISYPEAISKFKFVPQLFAVLFFFMLFT
LGVGSAVGLQSAIVANLMDFFPKIKQWMMALICCLIGFVIGLLYVTPGGQWILNLVDHFG
GTFLIFTLAIFQIVGIFWVYGIENFCWDVEFMLNRKVTKFWRFSWFIVTPVLLIIIFIYF
LIKTENPTYGAREYPVTVLATGWIIFGVGMFQILLWISWSIIRDPNKCEAFKSLFRQNSE
WGPKSPKVFKEWKTYKSERLEKRRAKSNGDSKIKKCLNILLDKYE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
32 g19.t2 CDD cd10324 SLC6sbd 1 411 3.60777E-126
2 g19.t2 PANTHER PTHR11616 SODIUM/CHLORIDE DEPENDENT TRANSPORTER 1 496 8.9E-182
3 g19.t2 PANTHER PTHR11616:SF269 TRANSPORTER 1 496 8.9E-182
4 g19.t2 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 23 49 8.9E-33
5 g19.t2 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 145 162 8.9E-33
7 g19.t2 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 227 247 8.9E-33
9 g19.t2 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 284 303 8.9E-33
8 g19.t2 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 362 382 8.9E-33
6 g19.t2 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 402 422 8.9E-33
1 g19.t2 Pfam PF00209 Sodium:neurotransmitter symporter family 2 459 4.6E-119
16 g19.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 29 -
22 g19.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 30 51 -
18 g19.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 52 117 -
29 g19.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 118 135 -
12 g19.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 136 146 -
31 g19.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 147 171 -
17 g19.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 172 190 -
30 g19.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 191 215 -
11 g19.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 216 234 -
24 g19.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 235 255 -
20 g19.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 256 288 -
27 g19.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 289 315 -
14 g19.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 316 326 -
28 g19.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 327 346 -
21 g19.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 347 357 -
25 g19.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 358 382 -
15 g19.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 383 402 -
23 g19.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 403 422 -
19 g19.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 423 433 -
26 g19.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 434 457 -
13 g19.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 458 525 -
43 g19.t2 ProSitePatterns PS00754 Sodium:neurotransmitter symporter family signature 2. 49 68 -
44 g19.t2 ProSiteProfiles PS50267 Sodium:neurotransmitter symporter family profile. 1 466 62.707
10 g19.t2 SUPERFAMILY SSF161070 SNF-like 1 461 1.57E-115
37 g19.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 29 51 -
42 g19.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 118 136 -
33 g19.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 145 167 -
34 g19.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 191 213 -
40 g19.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 234 256 -
35 g19.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 292 314 -
39 g19.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 327 349 -
36 g19.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 359 381 -
41 g19.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 400 422 -
38 g19.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 437 459 -

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. There were no conditions that were differentially expressed