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.t5 isoform g590.t5 4355274 4357871
chr_3 g590 g590.t5 exon g590.t5.exon1 4355274 4355704
chr_3 g590 g590.t5 cds g590.t5.CDS1 4355547 4355704
chr_3 g590 g590.t5 exon g590.t5.exon2 4355758 4355921
chr_3 g590 g590.t5 cds g590.t5.CDS2 4355758 4355921
chr_3 g590 g590.t5 exon g590.t5.exon3 4356042 4356264
chr_3 g590 g590.t5 cds g590.t5.CDS3 4356042 4356264
chr_3 g590 g590.t5 exon g590.t5.exon4 4356323 4356528
chr_3 g590 g590.t5 cds g590.t5.CDS4 4356323 4356528
chr_3 g590 g590.t5 exon g590.t5.exon5 4356593 4356758
chr_3 g590 g590.t5 cds g590.t5.CDS5 4356593 4356758
chr_3 g590 g590.t5 exon g590.t5.exon6 4356850 4357493
chr_3 g590 g590.t5 cds g590.t5.CDS6 4356850 4357493
chr_3 g590 g590.t5 exon g590.t5.exon7 4357551 4357645
chr_3 g590 g590.t5 cds g590.t5.CDS7 4357551 4357645
chr_3 g590 g590.t5 exon g590.t5.exon8 4357703 4357760
chr_3 g590 g590.t5 cds g590.t5.CDS8 4357703 4357760
chr_3 g590 g590.t5 exon g590.t5.exon9 4357822 4357871
chr_3 g590 g590.t5 cds g590.t5.CDS9 4357822 4357871
chr_3 g590 g590.t5 TSS g590.t5 NA NA
chr_3 g590 g590.t5 TTS g590.t5 NA NA

Sequences

>g590.t5 Gene=g590 Length=2037
TGTAATGATGTAAGGAAAAATCAAATTAAAGCTTGAAATTTTGAATTTAATTATGAAGCT
TTATCAACTCAATGTCACATAAGTAAACGAAAAACATTGTTAAACATTCAACTATGATAC
ATAGGCATTTATCTAATATCACATGTTTTTATTACTAAAGTATTTTATAATGTACTCACA
TAGACAGGAGAAAATAAAGATAAAAATGAGATGAACATCACGAATCTTTTTAGTTTCTAT
CTATCACTTGAATTGTGCGGTTGAAAAATAAAAATGAGCGAGAATTTTGAAGAATTACAG
GAATTGAAAGTGAAAAAATCTAGTGAGAACGAGGAAGTGTCTAATAAAATTGAGAAACCA
AAATGGGGAAATGACATTGAATTTTTATGCTCGTGTATCACACTTTCTGTTGGGTTAGGA
AACATATATAGATTTCCTTTTACAGCTTTGCAGTATGGTGGCGGAACATTTGTTATACCT
TACACTTTTATCGTGATTTTAGTTGGAAAGCCACTTTACTATTTAGAAATACTTTTGGGT
CAATTTTCGTCTAAAGGATGTGTAAACGTTTATGATATGGCACCTGCAGTAAGAGGTGTT
GGTTACGGTCAATGTATATGTACAATAATTGTTTTATCAATTTATGCATCAGTCATGGCA
TTGACAATCCGCTTTTTTCTTGCTTCATTTGGTGATCCTTTACCTTGGAGTCAATGTAAA
GATAGTTGGAACGCAACATGTGTTGATAGTGGAATAAAAATTGGAAATTTATCTACAAAT
GTTACAAATGTAAAATCATCTGCTGAATTATTCTTTGTCAAAGATATTCTCAAAGAATCA
TCAACATTCGAAAGCTTAGGTTTTCCAAACATTCAACTAGTAATTTGTTTAATTATTGCT
TGGTGTGTGATTGGTATTGTACTTGTAAAAGGCATTCAAAGCTCAGGAAAAGCAGCTTAT
TTTCTTGCTGTTTTTCCTTATATTGTACTCATAATTCTACTGATAAGAGCTTCTACTTTA
GAAGGCGCAATCGACGGAATTCTTTATTTCATCATTCCTGACTTGAATAAAATTTTTGAT
GCTGAACTATGGTATGCAGCGGTCACTCAAGTGTTTTATGCTTTAGGAATTTGCTTTGGA
TCAATTATTATGTATTCTTCCTACAATCGTTTTGATCAAAATGTCTATCGAGATGTAAAC
ATCATAACAACAATGGATTATTTAACTTCACTACTTGCTGGTTTAATTATATTTGGAATT
CTTGGGCATTTAAAATTTGTGATGGGTATTGAAGATATTCAAGAAGTCACAACAAGTTTT
ATGGGTCTCACATTCATTGCATATCCTGAAGCTATTGCAAAATTTGACTATATTCCACAA
TTTTTTGCCATTGTATTTTTTCTTATGTTGTTTTTCTTCTGTGTTGGAAGCAATATGGGA
ATGGCTTCATGCATTCTTACTGTTATTCGTGATCGCTATCCTGAGATAAAATGCTGGAAA
ATTGTATTAGGAATTGTGATTTTTGGAATTACTATTGGAACTTTTTATACAACACCAAGT
GGTCAATATTTAATTAATTTTCTCGATTTTTATGGTGCTTCATTTGTTGCTTTAATTTTG
GCCATTATTGAACTTTTAACTGTTAGCTGGATTTATGGAGTTGATAGATTTTGCAAAGAC
ATTGAATTCATGTTGAAGAGAAAAACTGGACTTTATTGGAGACTGTGTTGGAAGTATATA
ACACCTTTTATTATGATTTCAATTTTTGTTTATTTTTTGGCAACTTGGAAACCAATTACG
TATGGAAAAATTGAATATTCTAACAAAATGCATGCATTCGGATCGTGTATTTCGCTTTTT
GGACTTTTACAACTTCCAATATGGATGATGTATGCTTTTTTAAAACAACCAGAAGGAAAT
TTTATTGAAAAATTCAAAACTATTTTCAAGCCAAACAAGAAATGGGGACCAGTTGATTCT
AGAATAAGAACACAATATAATAGATTTATGGAGATAAAGTTTAAAGAAACAAAATAA

>g590.t5 Gene=g590 Length=587
MSENFEELQELKVKKSSENEEVSNKIEKPKWGNDIEFLCSCITLSVGLGNIYRFPFTALQ
YGGGTFVIPYTFIVILVGKPLYYLEILLGQFSSKGCVNVYDMAPAVRGVGYGQCICTIIV
LSIYASVMALTIRFFLASFGDPLPWSQCKDSWNATCVDSGIKIGNLSTNVTNVKSSAELF
FVKDILKESSTFESLGFPNIQLVICLIIAWCVIGIVLVKGIQSSGKAAYFLAVFPYIVLI
ILLIRASTLEGAIDGILYFIIPDLNKIFDAELWYAAVTQVFYALGICFGSIIMYSSYNRF
DQNVYRDVNIITTMDYLTSLLAGLIIFGILGHLKFVMGIEDIQEVTTSFMGLTFIAYPEA
IAKFDYIPQFFAIVFFLMLFFFCVGSNMGMASCILTVIRDRYPEIKCWKIVLGIVIFGIT
IGTFYTTPSGQYLINFLDFYGASFVALILAIIELLTVSWIYGVDRFCKDIEFMLKRKTGL
YWRLCWKYITPFIMISIFVYFLATWKPITYGKIEYSNKMHAFGSCISLFGLLQLPIWMMY
AFLKQPEGNFIEKFKTIFKPNKKWGPVDSRIRTQYNRFMEIKFKETK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
39 g590.t5 CDD cd10324 SLC6sbd 30 502 1.18469E-155
13 g590.t5 Coils Coil Coil 5 28 -
2 g590.t5 PANTHER PTHR11616 SODIUM/CHLORIDE DEPENDENT TRANSPORTER 12 575 8.6E-245
3 g590.t5 PANTHER PTHR11616:SF269 TRANSPORTER 12 575 8.6E-245
8 g590.t5 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 36 57 8.7E-46
10 g590.t5 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 65 84 8.7E-46
5 g590.t5 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 108 134 8.7E-46
9 g590.t5 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 227 244 8.7E-46
11 g590.t5 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 309 329 8.7E-46
4 g590.t5 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 365 384 8.7E-46
7 g590.t5 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 443 463 8.7E-46
6 g590.t5 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 483 503 8.7E-46
1 g590.t5 Pfam PF00209 Sodium:neurotransmitter symporter family 29 544 1.3E-142
15 g590.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 34 -
32 g590.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 35 54 -
21 g590.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 55 65 -
33 g590.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 66 88 -
20 g590.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 89 108 -
31 g590.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 109 136 -
25 g590.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 137 199 -
28 g590.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 200 218 -
17 g590.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 219 229 -
30 g590.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 230 261 -
22 g590.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 262 272 -
27 g590.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 273 295 -
16 g590.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 296 315 -
35 g590.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 316 337 -
24 g590.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 338 369 -
29 g590.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 370 398 -
19 g590.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 399 409 -
38 g590.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 410 427 -
23 g590.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 428 438 -
36 g590.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 439 463 -
14 g590.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 464 483 -
37 g590.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 484 501 -
26 g590.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 502 520 -
34 g590.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 521 543 -
18 g590.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 544 587 -
51 g590.t5 ProSiteProfiles PS50267 Sodium:neurotransmitter symporter family profile. 27 547 77.306
12 g590.t5 SUPERFAMILY SSF161070 SNF-like 29 542 4.71E-140
43 g590.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 56 78 -
45 g590.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 115 137 -
46 g590.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 196 218 -
42 g590.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 227 249 -
41 g590.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 275 297 -
50 g590.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 317 339 -
48 g590.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 373 395 -
49 g590.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 407 426 -
47 g590.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 441 463 -
40 g590.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 484 506 -
44 g590.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 521 543 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g590/g590.t5; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g590.t5.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