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 g590 g590.t2 TSS g590.t2 4351266 4351266
chr_3 g590 g590.t2 isoform g590.t2 4351431 4355274
chr_3 g590 g590.t2 exon g590.t2.exon1 4351431 4351515
chr_3 g590 g590.t2 exon g590.t2.exon2 4352747 4352839
chr_3 g590 g590.t2 exon g590.t2.exon3 4352901 4352975
chr_3 g590 g590.t2 exon g590.t2.exon4 4353181 4353342
chr_3 g590 g590.t2 exon g590.t2.exon5 4353468 4353610
chr_3 g590 g590.t2 cds g590.t2.CDS1 4353562 4353610
chr_3 g590 g590.t2 exon g590.t2.exon6 4353663 4353849
chr_3 g590 g590.t2 cds g590.t2.CDS2 4353663 4353849
chr_3 g590 g590.t2 exon g590.t2.exon7 4353902 4354276
chr_3 g590 g590.t2 cds g590.t2.CDS3 4353902 4354276
chr_3 g590 g590.t2 exon g590.t2.exon8 4354331 4354974
chr_3 g590 g590.t2 cds g590.t2.CDS4 4354331 4354974
chr_3 g590 g590.t2 exon g590.t2.exon9 4355027 4355179
chr_3 g590 g590.t2 cds g590.t2.CDS5 4355027 4355179
chr_3 g590 g590.t2 exon g590.t2.exon10 4355236 4355274
chr_3 g590 g590.t2 cds g590.t2.CDS6 4355236 4355273
chr_3 g590 g590.t2 TTS g590.t2 4355494 4355494

Sequences

>g590.t2 Gene=g590 Length=1956
TGTGTTGATTTACTGAAAAAGAAGCATGAAACTTTAAAGCAATTTTTCAAAAGTCTGAGA
AAATAAATTTTATTAATTTTAAAATTCAATTGCCATGTTTGCCGGTGTTGAGTTGTTGAA
TGAGCATTACGGTACGAATAGACAGAATGGCCAAAATTTTTTACTTCTTGAGATACAAAT
GTCCTTGATTTGCAACGAGGAAAATAAAATTAAAAATAATTGTGAAAAGAAAATTGAAAT
TATTGGCATCGAGAACTCAAAAAACGAAAAGAATTTCATAGCAAAAGATAAATGGGGTAA
AGATATTGAGTTTTTACTCTCATGCATAGCACTTTCAGTAGGATTAGGAAACTTGTTGAG
GTTCCCTTTTACGGCTCTTGAAAATGGAGGAGGTATTGAAAAATTCTTATTCTTTTATCA
TAGTTCTGTTGCTTGTCGGCAAACCGCTTTATTATATGGAGTTATTATTGGGACAATTTT
CTTCACGTGGTTGCATCAAAGTATATGATATGGCGCCAGCAATGCGTGGAATTGGCATTG
GACAAGTTATGTCAACATGTTTCGTTACAACTTACTATGCATCACTAATGGGACTTACAA
TTCGGTATTTTTTGGCATCATTTAGCAACCCACTGCCATGGAGTGAATGCAAAGAAGAAT
GGAATGTTTCTTGCATTGATAGCAAAATAAAATCTGTCAATTTCTCAGATGAAATGCCAA
AATCATCAGCTGAACTTTATTTTATTAAAGAAATTTTAAAAGAAGCAACAACAATTGACA
ATGGAATTGGAACACCAAATTGGCAACTTGTTTTATGTCTTATTTTTGCATGGATTTGCA
TTGGTGGAATTCTCATAAAAGGAGTGAAAAGCTCAGGAAAGGCTTCTTACTTTCTTTCAG
CATTTCCGTACTTTGTTATGTTTATACTTCTCATACGATCAGCAACATTAGAAGGTGCAG
TCAATGGCATGATTTATTTTATAAAACCACAATGGGATAAAATCTTTGAAGCTCAAGTCT
GGTATGCTGCATGTACACAAGTTTTTTATTCACTTGCTGTCTGTTTTGGGTCAATTATCA
TGTACTCGTCCTACAATCGATTTGATCAAAATATTTACAAAGACGTAAATGTAATAACAC
TGCTTGATACTGGAACTTCTTTGCTATCTGGTTTAATTATATTTGGTATTATTGGTCATT
TAGCACATGTGATGGAAGTCGATGATATTCAAAAAGTGACCAAAAGTAATATAGCTCTCG
CATTCATGGCTTATCCTGATATTATTGTGAAAATCGGCTTCTTTCCACAATTTTTCTCAA
TGTTATTCTTCATTATGCTGTTTGTACTTGGAATTGGTAGTAATATCGGAATGACATCTT
GCATTATGACTGTCATCAAAGATAAATTTCCAAGAATTGAATGCTGGAAAATTGTTGCCG
GCATTGCAATTGTAGGAATTACTATTGGAAGCATTTACACAACTCCTGGTGGACAATTTT
TAATTAATTTTCTCGATTTTTATGGTGCTTCATTTGTTGCTTTAATTTTGGCCATTATTG
AACTTTTGACTGTCAGTTGGATTTATGGAGTTGATAGATTTTGCAAAGATATTGAATTCA
TGTTGAAGAGAAAAACTGGACTTTATTGGAGACTATGTTGGAAGTATATAACACCTTTTA
TTATGATTTCAATTTTTGTTTATTTTTTGGCAACTTGGAAACCAATTACATATCAAGGCT
ATGAATATCATCCAAATATGCATGTATTTGGCTGGTGTTTGTCATTATTTTGTTTACTTC
AACTGCCAATTTGGGCTGTCTATACAATAATGAAACAAGAGGAAAAAACATTATATGAAA
AGTTCATTAATGCATTCAAACCAAATTCTTATTGGGGTCCAAATGATCCCGAAAAAATGG
AACAATATAGAGAATTTCGAACACTTAAATCTCATT

>g590.t2 Gene=g590 Length=482
MAPAMRGIGIGQVMSTCFVTTYYASLMGLTIRYFLASFSNPLPWSECKEEWNVSCIDSKI
KSVNFSDEMPKSSAELYFIKEILKEATTIDNGIGTPNWQLVLCLIFAWICIGGILIKGVK
SSGKASYFLSAFPYFVMFILLIRSATLEGAVNGMIYFIKPQWDKIFEAQVWYAACTQVFY
SLAVCFGSIIMYSSYNRFDQNIYKDVNVITLLDTGTSLLSGLIIFGIIGHLAHVMEVDDI
QKVTKSNIALAFMAYPDIIVKIGFFPQFFSMLFFIMLFVLGIGSNIGMTSCIMTVIKDKF
PRIECWKIVAGIAIVGITIGSIYTTPGGQFLINFLDFYGASFVALILAIIELLTVSWIYG
VDRFCKDIEFMLKRKTGLYWRLCWKYITPFIMISIFVYFLATWKPITYQGYEYHPNMHVF
GWCLSLFCLLQLPIWAVYTIMKQEEKTLYEKFINAFKPNSYWGPNDPEKMEQYREFRTLK
SH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
34 g590.t2 CDD cd10324 SLC6sbd 1 400 1.43431E-127
2 g590.t2 PANTHER PTHR11616 SODIUM/CHLORIDE DEPENDENT TRANSPORTER 1 474 1.0E-216
3 g590.t2 PANTHER PTHR11616:SF269 TRANSPORTER 1 474 1.0E-216
5 g590.t2 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 7 33 5.7E-32
8 g590.t2 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 125 142 5.7E-32
7 g590.t2 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 207 227 5.7E-32
6 g590.t2 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 263 282 5.7E-32
9 g590.t2 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 341 361 5.7E-32
4 g590.t2 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 381 401 5.7E-32
1 g590.t2 Pfam PF00209 Sodium:neurotransmitter symporter family 2 442 1.5E-115
18 g590.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 11 -
26 g590.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 35 -
16 g590.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 36 99 -
25 g590.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 100 119 -
17 g590.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 120 130 -
24 g590.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 131 158 -
12 g590.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 159 169 -
27 g590.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 170 195 -
19 g590.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 196 214 -
30 g590.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 215 235 -
11 g590.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 236 246 -
31 g590.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 247 265 -
21 g590.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 266 270 -
33 g590.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 271 296 -
15 g590.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 297 307 -
32 g590.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 308 325 -
22 g590.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 326 336 -
29 g590.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 337 361 -
14 g590.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 362 381 -
28 g590.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 382 399 -
20 g590.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 400 418 -
23 g590.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 419 441 -
13 g590.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 442 482 -
45 g590.t2 ProSiteProfiles PS50267 Sodium:neurotransmitter symporter family profile. 1 445 60.657
10 g590.t2 SUPERFAMILY SSF161070 SNF-like 2 441 2.75E-114
37 g590.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 13 35 -
41 g590.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 96 118 -
42 g590.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 125 147 -
43 g590.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 171 193 -
35 g590.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 206 228 -
38 g590.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 262 284 -
39 g590.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 305 327 -
36 g590.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 337 359 -
44 g590.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 380 402 -
40 g590.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 417 439 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g590/g590.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g590.t2.fa.iupred3.txt does not exist

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