General information for g19.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Sodium-dependent nutrient amino acid transporter 1.
Parent gene
- The parent gene g19 is located on chr_3: 318753..319629 (+ strand)
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.t3 | isoform | g19.t3 | 313665 | 319629 |
| chr_3 | g19 | g19.t3 | exon | g19.t3.exon1 | 313665 | 314165 |
| chr_3 | g19 | g19.t3 | exon | g19.t3.exon2 | 315358 | 315440 |
| chr_3 | g19 | g19.t3 | exon | g19.t3.exon3 | 315511 | 315600 |
| chr_3 | g19 | g19.t3 | exon | g19.t3.exon4 | 316632 | 316736 |
| chr_3 | g19 | g19.t3 | exon | g19.t3.exon5 | 316791 | 316878 |
| chr_3 | g19 | g19.t3 | exon | g19.t3.exon6 | 317115 | 317524 |
| chr_3 | g19 | g19.t3 | cds | g19.t3.CDS1 | 317376 | 317524 |
| chr_3 | g19 | g19.t3 | exon | g19.t3.exon7 | 317607 | 317877 |
| chr_3 | g19 | g19.t3 | cds | g19.t3.CDS2 | 317607 | 317877 |
| chr_3 | g19 | g19.t3 | exon | g19.t3.exon8 | 318303 | 318362 |
| chr_3 | g19 | g19.t3 | cds | g19.t3.CDS3 | 318303 | 318362 |
| chr_3 | g19 | g19.t3 | exon | g19.t3.exon9 | 318426 | 318534 |
| chr_3 | g19 | g19.t3 | cds | g19.t3.CDS4 | 318426 | 318534 |
| chr_3 | g19 | g19.t3 | exon | g19.t3.exon10 | 318592 | 318679 |
| chr_3 | g19 | g19.t3 | cds | g19.t3.CDS5 | 318592 | 318679 |
| chr_3 | g19 | g19.t3 | exon | g19.t3.exon11 | 318823 | 319058 |
| chr_3 | g19 | g19.t3 | cds | g19.t3.CDS6 | 318823 | 318832 |
| chr_3 | g19 | g19.t3 | exon | g19.t3.exon12 | 319118 | 319629 |
| chr_3 | g19 | g19.t3 | TTS | g19.t3 | 319710 | 319710 |
| chr_3 | g19 | g19.t3 | TSS | g19.t3 | NA | NA |
Sequences
>g19.t3 Gene=g19 Length=2553
AGATAATTGAAGTTATTATTGTTTATAATTAATAAATCTTTTATGAGTTCATTTTAGGAT
GTAACTTGCTTACTCTAGAAATTTTTATCAGAAATAATAAAAAGTTAAGACCACAATGAA
GTAATAAATTAATTCATCTATCACATTATTGTCGCACTTATAGCAGCAATTTGAAATAAT
TTTCATTCATCAATGTGATTAACTCAAATTGCTTTTTTTTTAATTTATCGTTTTCCTGCA
AAATCAAACTCTCAACACGGTAGAAATGACAGCTGTGTATGGTTTTTTTTAAATTTTTTT
AAACTCACTTTACTAACACCTTGCAATTATAATAGTATTATTTTATTCACTTGCTCAAAT
AGTACTGTTTAAACTTTTTTTATCTATACAATAACGCATTATGTGAAATGTTCACTTCAG
TTCATATTCTGAGCTCGAGTTGTTCACACATTTGGTATTTAAACTTAAAATATTTTACGA
ATTGTGGTGATATTTTATTAGCTCAAAACATTTTTTTGAATAAAATATAGTAAAAAGTAT
CTGTAATGTGGTATTTCTATGGAAACATCCTATTTTAATGAACAACATTCATCATAGAAA
GGGAGCAAAATAAGTTTATTACAAAAATGGGTAAACAAGGTTCATATAACATGGGATTTG
ACGCATCTAATGAGGACATAAAAACAGTCAATGGTATATCAAACGGTGTGTCATCATCGC
CAACCAATATGATGGCAATAAATGTCAGCGATAAAGCTTCTACAAATAACCATGATGAGA
TTAATCATGATTTGGAGCATGGACCTGAAAGAGCAACATGGGGACATGGATTAGAATTTT
TGATGAGTTGCATTTCTCTTTCAGTTGTTCAATATTTCTTTCAAATTTATGAGATAAAAT
ATTTTATGCACAGGTGGAGCATTTTTAATTCCATACATCATTGTACTCATACTCATTGGA
AAACCGATTTATTATTACGAGATGGTTCTCGGTCAATTTGTTTCTAAAGCTTCAGTAAAA
GCTACATCAGTAATTCCAGCTTTGAAAGGAATAGCAATTGGACAACAACTAGGAGTTTTA
TGCATCGTCACATATTATACTTCACTTATCGCTCTCACACTTTTTTATATGATTAAAAGT
TTCTCTGAAACATTACCTTGGAGTTTCTGTTGGGATAAATGGACTGATGTAATTTGTATT
CCTGCTGATCCTAAATTTCAAACAAATGATGGTGAAAAAGTTGTCAATGGAACAAGTTCA
AGTGAACTTTATTTTATTCGAGAAGTGATAAAAGAGAAAAATGATATAAGTGACGGTCTA
GGTTTTCCTGATTGGCAGCTGACAATTTACTTGCTTTTAGCATGGATTGTAATTTATCTG
ATTATTATAAAAGGTGTCAAAAGTAGTGGAAAAGTAAGCTATTTTCTCGCTTGCTTCCCT
TATGTTGTGTTGATAATTCTATTGATTCGAGCCTCAACTTTAAATGGAACTTGGGATGGC
ATTAGGTATTTCATCACACCAGACTTTAAGCGGCTTATCGAACCACAAGTATGGTATGCT
GCCACAACTCAGTTATTCTTCTCTCTTTCAGTGGGCCAAGGGACTATAATTATGTTTGCA
TCTTTTAATCGATTTGATCATAATATTCATAGAGATGCAATGATTGTCACAACTATGGAT
ACTTTTACAAGTTTACTTGGAGGCTTTACGATTTTTGGTATTTTGGGAAATTTGGCATAT
AGCATTGGTGAAGAGGATATTGGAAACGTTATTAAAAGCGGGGGCAGTGGGTTAGCGTTT
ATTTCACAGTTTTGAAATTAAATTTTTCATCACATAAAGCTCTTTGCCGTTCTCTTCTTC
TTTATGCTTTTTACACTGGGAGTTGGTAGTGCTGTTGGATTACAAAGTGCCATAGTAGCA
AATTTAATGGACTTTTTCCCAAAAATAAAGCAATGGATGATGGCTTTAATCTGCTGCTTG
ATTGGATTTGTAATTGGCCTTTTATATGTCACGCCAGGAGGACAATGGATTCTAAATTTG
GTTGACCATTTTGGAGGAACATTTTTGATTTTCACTCTTGCCATCTTTCAAATTGTAGGA
ATATTTTGGGTATATGGAATTGAAAACTTTTGCTGGGATGTTGAATTTATGTTAAATAGA
AAAGTTACAAAGTTTTGGCGATTTTCTTGGTTTATTGTCACTCCTGTCTTGCTTATCATC
ATTTTCATATATTTTTTGATAAAAACCGAAAATCCTACTTATGGTGCTCGAGAATATCCA
GTCACAGTTTTAGCTACAGGTTGGATTATTTTTGGTGTTGGAATGTTCCAAATACTCTTG
TGGATTTCATGGTCAATTATTAGAGATCCAAATAAATGTGAAGCCTTTAAATCTCTCTTC
AGACAAAATTCAGAATGGGGACCAAAATCTCCAAAAGTTTTCAAAGAATGGAAAACATAT
AAAAGCGAAAGACTTGAAAAACGCAGAGCAAAAAGCAATGGAGATTCAAAGATTAAAAAA
TGTTTAAACATTTTACTCGATAAATATGAATAG
>g19.t3 Gene=g19 Length=228
MIKSFSETLPWSFCWDKWTDVICIPADPKFQTNDGEKVVNGTSSSELYFIREVIKEKNDI
SDGLGFPDWQLTIYLLLAWIVIYLIIIKGVKSSGKVSYFLACFPYVVLIILLIRASTLNG
TWDGIRYFITPDFKRLIEPQVWYAATTQLFFSLSVGQGTIIMFASFNRFDHNIHRDAMIV
TTMDTFTSLLGGFTIFGILGNLAYSIGEEDIGNVIKSGGSGLAFISQF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g19.t3 | PANTHER | PTHR11616 | SODIUM/CHLORIDE DEPENDENT TRANSPORTER | 2 | 226 | 2.5E-91 |
| 3 | g19.t3 | PANTHER | PTHR11616:SF269 | TRANSPORTER | 2 | 226 | 2.5E-91 |
| 4 | g19.t3 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 96 | 113 | 1.3E-11 |
| 5 | g19.t3 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 178 | 198 | 1.3E-11 |
| 1 | g19.t3 | Pfam | PF00209 | Sodium:neurotransmitter symporter family | 2 | 225 | 8.2E-68 |
| 16 | g19.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 68 | - |
| 17 | g19.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 69 | 86 | - |
| 12 | g19.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 87 | 97 | - |
| 18 | g19.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 98 | 122 | - |
| 15 | g19.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 123 | 141 | - |
| 19 | g19.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 142 | 166 | - |
| 13 | g19.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 167 | 185 | - |
| 20 | g19.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 186 | 206 | - |
| 14 | g19.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 207 | 228 | - |
| 11 | g19.t3 | ProSiteProfiles | PS50267 | Sodium:neurotransmitter symporter family profile. | 1 | 228 | 32.947 |
| 10 | g19.t3 | SUPERFAMILY | SSF161070 | SNF-like | 2 | 226 | 1.44E-59 |
| 8 | g19.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 69 | 87 | - |
| 6 | g19.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 96 | 118 | - |
| 7 | g19.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 142 | 164 | - |
| 9 | g19.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 185 | 207 | - |
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