General information for g19.t1
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.t1 | isoform | g19.t1 | 315553 | 319629 |
| chr_3 | g19 | g19.t1 | exon | g19.t1.exon1 | 315553 | 315600 |
| chr_3 | g19 | g19.t1 | cds | g19.t1.CDS1 | 315553 | 315600 |
| chr_3 | g19 | g19.t1 | exon | g19.t1.exon2 | 316632 | 316736 |
| chr_3 | g19 | g19.t1 | cds | g19.t1.CDS2 | 316632 | 316736 |
| chr_3 | g19 | g19.t1 | exon | g19.t1.exon3 | 316791 | 316878 |
| chr_3 | g19 | g19.t1 | cds | g19.t1.CDS3 | 316791 | 316878 |
| chr_3 | g19 | g19.t1 | exon | g19.t1.exon4 | 316956 | 316971 |
| chr_3 | g19 | g19.t1 | cds | g19.t1.CDS4 | 316956 | 316971 |
| chr_3 | g19 | g19.t1 | exon | g19.t1.exon5 | 317075 | 317106 |
| chr_3 | g19 | g19.t1 | cds | g19.t1.CDS5 | 317075 | 317106 |
| chr_3 | g19 | g19.t1 | exon | g19.t1.exon6 | 317161 | 317524 |
| chr_3 | g19 | g19.t1 | cds | g19.t1.CDS6 | 317161 | 317524 |
| chr_3 | g19 | g19.t1 | exon | g19.t1.exon7 | 317607 | 317877 |
| chr_3 | g19 | g19.t1 | cds | g19.t1.CDS7 | 317607 | 317877 |
| chr_3 | g19 | g19.t1 | exon | g19.t1.exon8 | 318303 | 318362 |
| chr_3 | g19 | g19.t1 | cds | g19.t1.CDS8 | 318303 | 318362 |
| chr_3 | g19 | g19.t1 | exon | g19.t1.exon9 | 318426 | 318534 |
| chr_3 | g19 | g19.t1 | cds | g19.t1.CDS9 | 318426 | 318534 |
| chr_3 | g19 | g19.t1 | exon | g19.t1.exon10 | 318592 | 318679 |
| chr_3 | g19 | g19.t1 | cds | g19.t1.CDS10 | 318592 | 318679 |
| chr_3 | g19 | g19.t1 | exon | g19.t1.exon11 | 318753 | 318792 |
| chr_3 | g19 | g19.t1 | cds | g19.t1.CDS11 | 318753 | 318792 |
| chr_3 | g19 | g19.t1 | exon | g19.t1.exon12 | 318857 | 319058 |
| chr_3 | g19 | g19.t1 | cds | g19.t1.CDS12 | 318857 | 319058 |
| chr_3 | g19 | g19.t1 | exon | g19.t1.exon13 | 319118 | 319629 |
| chr_3 | g19 | g19.t1 | cds | g19.t1.CDS13 | 319118 | 319629 |
| chr_3 | g19 | g19.t1 | TTS | g19.t1 | 319710 | 319710 |
| chr_3 | g19 | g19.t1 | TSS | g19.t1 | NA | NA |
Sequences
>g19.t1 Gene=g19 Length=1935
ATGGGTAAACAAGGTTCATATAACATGGGATTTGACGCATCTAATGAGGACATAAAAACA
GTCAATGGTATATCAAACGGTGTGTCATCATCGCCAACCAATATGATGGCAATAAATGTC
AGCGATAAAGCTTCTACAAATAACCATGATGAGATTAATCATGATTTGGAGCATGGACCT
GAAAGAGCAACATGGGGACATGGATTAGAATTTTTGATGAGTTGCATTTCTCTTTCAGTT
GGGCTTGGGAATATTTGGCGGTTTCCATTTACTTGTTATGAAAATGGAGGTGGAGCATTT
TTAATTCCATACATCATTGTACTCATACTCATTGGAAAACCGATTTATTATTACGAGATG
GTTCTCGGTCAATTTGTTTCTAAAGCTTCAGTAAAAGCTACATCAGTAATTCCAGCTTTG
AAAGGAATAGCAATTGGACAACAACTAGGAGTTTTATGCATCGTCACATATTATACTTCA
CTTATCGCTCTCACACTTTTTTATATGATTAAAAGTTTCTCTGAAACATTACCTTGGAGT
TTCTGTTGGGATAAATGGACTGATGTAATTTGTATTCCTGCTGATCCTAAATTTCAAACA
AATGATGGTGAAAAAGTTGTCAATGGAACAAGTTCAAGTGAACTTTATTTTATTCGAGAA
GTGATAAAAGAGAAAAATGATATAAGTGACGGTCTAGGTTTTCCTGATTGGCAGCTGACA
ATTTACTTGCTTTTAGCATGGATTGTAATTTATCTGATTATTATAAAAGGTGTCAAAAGT
AGTGGAAAAGTAAGCTATTTTCTCGCTTGCTTCCCTTATGTTGTGTTGATAATTCTATTG
ATTCGAGCCTCAACTTTAAATGGAACTTGGGATGGCATTAGGTATTTCATCACACCAGAC
TTTAAGCGGCTTATCGAACCACAAGTATGGTATGCTGCCACAACTCAGTTATTCTTCTCT
CTTTCAGTGGGCCAAGGGACTATAATTATGTTTGCATCTTTTAATCGATTTGATCATAAT
ATTCATAGAGATGCAATGATTGTCACAACTATGGATACTTTTACAAGTTTACTTGGAGGC
TTTACGATTTTTGGTATTTTGGGAAATTTGGCATATAGCATTGGTGAAGAGGATATTGGA
AACGTTATTAAAAGCGGGGGCAGTGGGTTAGCGTTTATTTCATACCCTGAAGCAATTTCA
AAGTTCAAATTTGTTCCACAGCTCTTTGCCGTTCTCTTCTTCTTTATGCTTTTTACACTG
GGAGTTGGTAGTGCTGTTGGATTACAAAGTGCCATAGTAGCAAATTTAATGGACTTTTTC
CCAAAAATAAAGCAATGGATGATGGCTTTAATCTGCTGCTTGATTGGATTTGTAATTGGC
CTTTTATATGTCACGCCAGGAGGACAATGGATTCTAAATTTGGTTGACCATTTTGGAGGA
ACATTTTTGATTTTCACTCTTGCCATCTTTCAAATTGTAGGAATATTTTGGGTATATGGA
ATTGAAAACTTTTGCTGGGATGTTGAATTTATGTTAAATAGAAAAGTTACAAAGTTTTGG
CGATTTTCTTGGTTTATTGTCACTCCTGTCTTGCTTATCATCATTTTCATATATTTTTTG
ATAAAAACCGAAAATCCTACTTATGGTGCTCGAGAATATCCAGTCACAGTTTTAGCTACA
GGTTGGATTATTTTTGGTGTTGGAATGTTCCAAATACTCTTGTGGATTTCATGGTCAATT
ATTAGAGATCCAAATAAATGTGAAGCCTTTAAATCTCTCTTCAGACAAAATTCAGAATGG
GGACCAAAATCTCCAAAAGTTTTCAAAGAATGGAAAACATATAAAAGCGAAAGACTTGAA
AAACGCAGAGCAAAAAGCAATGGAGATTCAAAGATTAAAAAATGTTTAAACATTTTACTC
GATAAATATGAATAG
>g19.t1 Gene=g19 Length=644
MGKQGSYNMGFDASNEDIKTVNGISNGVSSSPTNMMAINVSDKASTNNHDEINHDLEHGP
ERATWGHGLEFLMSCISLSVGLGNIWRFPFTCYENGGGAFLIPYIIVLILIGKPIYYYEM
VLGQFVSKASVKATSVIPALKGIAIGQQLGVLCIVTYYTSLIALTLFYMIKSFSETLPWS
FCWDKWTDVICIPADPKFQTNDGEKVVNGTSSSELYFIREVIKEKNDISDGLGFPDWQLT
IYLLLAWIVIYLIIIKGVKSSGKVSYFLACFPYVVLIILLIRASTLNGTWDGIRYFITPD
FKRLIEPQVWYAATTQLFFSLSVGQGTIIMFASFNRFDHNIHRDAMIVTTMDTFTSLLGG
FTIFGILGNLAYSIGEEDIGNVIKSGGSGLAFISYPEAISKFKFVPQLFAVLFFFMLFTL
GVGSAVGLQSAIVANLMDFFPKIKQWMMALICCLIGFVIGLLYVTPGGQWILNLVDHFGG
TFLIFTLAIFQIVGIFWVYGIENFCWDVEFMLNRKVTKFWRFSWFIVTPVLLIIIFIYFL
IKTENPTYGAREYPVTVLATGWIIFGVGMFQILLWISWSIIRDPNKCEAFKSLFRQNSEW
GPKSPKVFKEWKTYKSERLEKRRAKSNGDSKIKKCLNILLDKYE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 38 | g19.t1 | CDD | cd10324 | SLC6sbd | 63 | 530 | 8.77028E-169 |
| 2 | g19.t1 | PANTHER | PTHR11616 | SODIUM/CHLORIDE DEPENDENT TRANSPORTER | 26 | 615 | 6.2E-224 |
| 3 | g19.t1 | PANTHER | PTHR11616:SF269 | TRANSPORTER | 26 | 615 | 6.2E-224 |
| 8 | g19.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 70 | 91 | 3.4E-52 |
| 9 | g19.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 99 | 118 | 3.4E-52 |
| 5 | g19.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 142 | 168 | 3.4E-52 |
| 7 | g19.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 264 | 281 | 3.4E-52 |
| 11 | g19.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 346 | 366 | 3.4E-52 |
| 4 | g19.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 403 | 422 | 3.4E-52 |
| 6 | g19.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 481 | 501 | 3.4E-52 |
| 10 | g19.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 521 | 541 | 3.4E-52 |
| 1 | g19.t1 | Pfam | PF00209 | Sodium:neurotransmitter symporter family | 62 | 578 | 1.7E-149 |
| 15 | g19.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 67 | - |
| 34 | g19.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 68 | 86 | - |
| 24 | g19.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 87 | 97 | - |
| 27 | g19.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 98 | 118 | - |
| 14 | g19.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 119 | 148 | - |
| 29 | g19.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 149 | 170 | - |
| 21 | g19.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 171 | 236 | - |
| 31 | g19.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 237 | 254 | - |
| 17 | g19.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 255 | 265 | - |
| 35 | g19.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 266 | 290 | - |
| 20 | g19.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 291 | 309 | - |
| 28 | g19.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 310 | 334 | - |
| 19 | g19.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 335 | 353 | - |
| 32 | g19.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 354 | 374 | - |
| 25 | g19.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 375 | 407 | - |
| 37 | g19.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 408 | 434 | - |
| 16 | g19.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 435 | 445 | - |
| 30 | g19.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 446 | 465 | - |
| 23 | g19.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 466 | 476 | - |
| 33 | g19.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 477 | 501 | - |
| 13 | g19.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 502 | 521 | - |
| 26 | g19.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 522 | 541 | - |
| 22 | g19.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 542 | 552 | - |
| 36 | g19.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 553 | 576 | - |
| 18 | g19.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 577 | 644 | - |
| 52 | g19.t1 | ProSitePatterns | PS00610 | Sodium:neurotransmitter symporter family signature 1. | 86 | 100 | - |
| 51 | g19.t1 | ProSitePatterns | PS00754 | Sodium:neurotransmitter symporter family signature 2. | 168 | 187 | - |
| 53 | g19.t1 | ProSiteProfiles | PS50267 | Sodium:neurotransmitter symporter family profile. | 61 | 585 | 81.398 |
| 12 | g19.t1 | SUPERFAMILY | SSF161070 | SNF-like | 62 | 580 | 1.57E-146 |
| 46 | g19.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 68 | 90 | - |
| 44 | g19.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 100 | 122 | - |
| 48 | g19.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 148 | 170 | - |
| 41 | g19.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 237 | 255 | - |
| 42 | g19.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 264 | 286 | - |
| 47 | g19.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 310 | 332 | - |
| 49 | g19.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 353 | 375 | - |
| 50 | g19.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 411 | 433 | - |
| 39 | g19.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 446 | 468 | - |
| 45 | g19.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 478 | 500 | - |
| 43 | g19.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 519 | 541 | - |
| 40 | g19.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 556 | 578 | - |
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 transcript has been annotated with K05038 (solute carrier family 6 (neurotransmitter transporter, glycine) member 5/9)
Pathway
- This transcript belongs to the following pathways
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.
