Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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 g21 g21.t4 TSS g21.t4 321722 321722
chr_3 g21 g21.t4 isoform g21.t4 322724 324340
chr_3 g21 g21.t4 exon g21.t4.exon1 322724 323303
chr_3 g21 g21.t4 cds g21.t4.CDS1 322904 323303
chr_3 g21 g21.t4 exon g21.t4.exon2 323853 324340
chr_3 g21 g21.t4 cds g21.t4.CDS2 323853 324037
chr_3 g21 g21.t4 TTS g21.t4 324375 324375

Sequences

>g21.t4 Gene=g21 Length=1068
ACTTTATTTCTTGTGAGTTTTCTTTTAATCTTATTTTTCAATAATTTTGAATGTGTCACT
TATTTTATTAGAAAAGAAGTTCTTCATGCAAGAGAAAATATAAATGATGGAATTGGATCA
ATAAATTGGAACCTTTTTGGTTTTCTAGCTCTTACTTGGATTACCGTCTGTTTGATTTTA
ATGCGTGGAGTTCGAAGTTCTGGAAAAGCAGCTTATATTACAGGAATAGTGCCATTTATA
TTTCTTTTTATCTTTCTTATTCGTGCTCTCACTCTTCCTGGTGCTTTCAATGGCATTGCT
TTCTTTTTTACTCCTAAATGGGAAGATATTTTAAAGCCAGGTGTTTGGTATGCTGCTGTA
ACTCAACTATTTTTCTCTCTCAATGTTTTCTTTGCAAATATTATCATGTATGCTTCTTAT
AACAAATTTTCACACAAAATTCATCGAGATTCAAATATTATTACTATAATTGACACTGGA
ACTTCTTTACTTGCTGGTTGTATTAGTTTTGGTATTATTGGTCATTTAGCTCATGAATTA
GGTGTCGATGATATTTCCAAAGTTTTTCAAGGTGGTCCTGGAATTTATTGGACTGTATGT
TGGCGGGTAGTAACACCACTTATTATGATGGCAATTATTGTTTATCATTTCATTTACTAT
GAAAATCCAAAAGATAATGGAGCTGAATTTCCATTTATTGCTCATGTTGTTGGTTGGTGT
ATTACTGCTTCAGGTAAGTTTACAAACATTTGTATCACATTATAAAGTCTTAATGCTTTA
AAAGGATACTTTAATAATTATTCATTTTGTAAGTATAGAGAGTCACATGAATTTAATTAT
TTATACATTTTAGGTTTAATTTGGTTGCCTTTAATAATAATTTGGAGTATTTCAAAACAA
AATGAGAAAACTTTTGTTGACGTAACATAAAAATCATTTTGAAAAATTTAATTATTAAAT
TTAAATTATTTTTAGAGGGTAAAATCAGCTTTTAGACCAACAAAAAATTGGGGACCATTG
AACTCTTCACTTTTATTAAAATATCAAGAATTTCTTAAAACAAACTAA

>g21.t4 Gene=g21 Length=194
MRGVRSSGKAAYITGIVPFIFLFIFLIRALTLPGAFNGIAFFFTPKWEDILKPGVWYAAV
TQLFFSLNVFFANIIMYASYNKFSHKIHRDSNIITIIDTGTSLLAGCISFGIIGHLAHEL
GVDDISKVFQGGPGIYWTVCWRVVTPLIMMAIIVYHFIYYENPKDNGAEFPFIAHVVGWC
ITASGKFTNICITL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g21.t4 PANTHER PTHR11616 SODIUM/CHLORIDE DEPENDENT TRANSPORTER 1 135 7.2E-67
4 g21.t4 PANTHER PTHR11616:SF269 TRANSPORTER 1 135 7.2E-67
3 g21.t4 PANTHER PTHR11616 SODIUM/CHLORIDE DEPENDENT TRANSPORTER 134 185 7.2E-67
5 g21.t4 PANTHER PTHR11616:SF269 TRANSPORTER 134 185 7.2E-67
6 g21.t4 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 10 27 5.9E-6
7 g21.t4 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 92 112 5.9E-6
1 g21.t4 Pfam PF00209 Sodium:neurotransmitter symporter family 1 135 1.0E-39
15 g21.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
21 g21.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 36 -
18 g21.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 37 55 -
22 g21.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 56 80 -
16 g21.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 81 91 -
20 g21.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 92 114 -
17 g21.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 115 133 -
19 g21.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 134 158 -
14 g21.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 159 194 -
13 g21.t4 ProSiteProfiles PS50267 Sodium:neurotransmitter symporter family profile. 1 160 25.262
12 g21.t4 SUPERFAMILY SSF161070 SNF-like 2 185 8.5E-45
9 g21.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 21 43 -
11 g21.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 58 80 -
8 g21.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 93 115 -
10 g21.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 135 157 -

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