General information for g23.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 g23 is located on chr_3: 331854..332566 (+ 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 | g23 | g23.t1 | TSS | g23.t1 | 329342 | 329342 |
| chr_3 | g23 | g23.t1 | isoform | g23.t1 | 329745 | 332566 |
| chr_3 | g23 | g23.t1 | exon | g23.t1.exon1 | 329745 | 329931 |
| chr_3 | g23 | g23.t1 | cds | g23.t1.CDS1 | 329745 | 329931 |
| chr_3 | g23 | g23.t1 | exon | g23.t1.exon2 | 330009 | 330024 |
| chr_3 | g23 | g23.t1 | cds | g23.t1.CDS2 | 330009 | 330024 |
| chr_3 | g23 | g23.t1 | exon | g23.t1.exon3 | 330128 | 330162 |
| chr_3 | g23 | g23.t1 | cds | g23.t1.CDS3 | 330128 | 330162 |
| chr_3 | g23 | g23.t1 | exon | g23.t1.exon4 | 330831 | 330962 |
| chr_3 | g23 | g23.t1 | cds | g23.t1.CDS4 | 330831 | 330962 |
| chr_3 | g23 | g23.t1 | exon | g23.t1.exon5 | 331025 | 331983 |
| chr_3 | g23 | g23.t1 | cds | g23.t1.CDS5 | 331025 | 331983 |
| chr_3 | g23 | g23.t1 | exon | g23.t1.exon6 | 332040 | 332414 |
| chr_3 | g23 | g23.t1 | cds | g23.t1.CDS6 | 332040 | 332414 |
| chr_3 | g23 | g23.t1 | exon | g23.t1.exon7 | 332474 | 332566 |
| chr_3 | g23 | g23.t1 | cds | g23.t1.CDS7 | 332474 | 332566 |
| chr_3 | g23 | g23.t1 | TTS | g23.t1 | 332670 | 332670 |
Sequences
>g23.t1 Gene=g23 Length=1797
ATGACTCAAGCATACGATAACCCAACATTTGCAAACGATAAATCAGTTGTTGCCAATAGC
ACTTTGGCATTCACAATTGATCACAAAAGTGACGAATACAATGCACAGACAAAAAAACAT
GGAACAACTCGCGATACATGGGGAAAAGATGTAGAATTTCTTTTGTCATGCATTGCTATG
GCAGTAGGACTTGGGAACGTTTGGCGATTCCCTTTCACTGCTTTAAGGAATGGAGGAGCA
TCGTTTTTGATTCCATACATTATTGTTCTTGTATTGGTTGGCAAGCCTGGATATTTCTTA
GAGATGATCATGGGACAGTTTTCGTCACGTGGAACAGTAAAAGTATATGACAGTGTTCCT
GCTATGAGAGGAATTGGCATCGGTCAAACGTTATGCATCATGGTAGTTGCTACTTATTAC
AGTTTTATTATCGGCGTCATTTCGCGTTATCTTTTTGACTCATTTAGTTTCACTCTACCT
TGGAGTGAATGTAATCCTAATTGGAATGTCTCATGTTATTCTTCAAATGGAAATAATGGG
TCAAATGTTGTTATGAATGGTACAACCAAATCATCAGCTGAACTTTATTTTTTCAAAGAA
GTTCTTCATGAAAGAAAATTAGAAGATGGAATAGGAATGCCAAACTGGAATCTTGTTTTA
TTTCTGTTCCTTTCATGGGCAATTGTTTTCTTCATTCTCTTCAAAGGAGTCAAAATGTCT
GGCAAAGCTTCATACATAACTGGAATTGCTCCATTCATCTTTCTTGCAATTTTCCTCGTC
CGTGCGCTTACACTTGAAGGAGCTTGGGATGGTATTGAATATCTTATTAAACCAAGATGG
GGAGAATTACTCGATCCAAAAGTTTGGTACGAAGCGTGTACTCAAGTATTTTTTACACTC
AATGTTTTCTTCGTAAATGTCATCATGTATGCTTCATACAATAAATTTGAACATAACATT
CATCGTGATTCAAACATAGTCACGACATTAGACACTTTGACATCTATAGTTGTTGGTTCA
ATCACTTTTGGTATTATTGGTCATTTATCACATGAACTTAATACTCCAATTGAGACAGTA
ATCAAATCTGGTCCTGGTTTAGTTTTCATAACATACCCCGAAACTATTTCAAAATTCAAA
TTCTGGCCACAACTTTTTTCTATAATGTTTTTTTTGATGCTTTATATCATTGCTCTTGGT
AGTCTATTTGCAATTACATCATCTGCTATCACCGTTATTCGTGATCAATTTAAGAAGGTC
AAAGATTGGCAAGCAGCATTAGGAATCGCAATTTTCGGAACTATTTCTGGATCAATTTAT
ACAACACCAGCTGGGTTAAGTATTCTTGATCTCGTCGATCATTATTGTGCTACTTTTGTG
ATTTTCATTCTGGCCTGTTTTGAAATATGTACATTCTGTTATATTTATGGTGTTGATCGT
ATTTGCAATGATGTTAAATTCATGCTTGGATTTAGACCAAATATTTTCTGGAGAACTTGC
TGGCGATATATTACACCTTCAATTTTGACAGCATTAGTTATTTATTTACTGATGAAAGCT
AAATTTATCAAAGATGATGCAAGCACATTTCCTGCGTCAGCACATGCAGTTGGCGTGTGC
ATAGCTGTTATGGGTATTATTTGGTTACCTATTGTATTTATTTGGAGAGTTTTAAAACAA
ACACATGAAAAGACTTTAATCGATAAAATCAAAAGCGCCTGCAAACCAACAAAAAATTGG
GGACCAATGGATCCTGTTAAAAATGCTAGGTACAAAGAATATATGGCCACAAATTAA
>g23.t1 Gene=g23 Length=598
MTQAYDNPTFANDKSVVANSTLAFTIDHKSDEYNAQTKKHGTTRDTWGKDVEFLLSCIAM
AVGLGNVWRFPFTALRNGGASFLIPYIIVLVLVGKPGYFLEMIMGQFSSRGTVKVYDSVP
AMRGIGIGQTLCIMVVATYYSFIIGVISRYLFDSFSFTLPWSECNPNWNVSCYSSNGNNG
SNVVMNGTTKSSAELYFFKEVLHERKLEDGIGMPNWNLVLFLFLSWAIVFFILFKGVKMS
GKASYITGIAPFIFLAIFLVRALTLEGAWDGIEYLIKPRWGELLDPKVWYEACTQVFFTL
NVFFVNVIMYASYNKFEHNIHRDSNIVTTLDTLTSIVVGSITFGIIGHLSHELNTPIETV
IKSGPGLVFITYPETISKFKFWPQLFSIMFFLMLYIIALGSLFAITSSAITVIRDQFKKV
KDWQAALGIAIFGTISGSIYTTPAGLSILDLVDHYCATFVIFILACFEICTFCYIYGVDR
ICNDVKFMLGFRPNIFWRTCWRYITPSILTALVIYLLMKAKFIKDDASTFPASAHAVGVC
IAVMGIIWLPIVFIWRVLKQTHEKTLIDKIKSACKPTKNWGPMDPVKNARYKEYMATN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 38 | g23.t1 | CDD | cd10324 | SLC6sbd | 45 | 517 | 1.16576E-165 |
| 2 | g23.t1 | PANTHER | PTHR11616 | SODIUM/CHLORIDE DEPENDENT TRANSPORTER | 22 | 590 | 4.0E-223 |
| 3 | g23.t1 | PANTHER | PTHR11616:SF269 | TRANSPORTER | 22 | 590 | 4.0E-223 |
| 5 | g23.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 52 | 73 | 1.8E-40 |
| 9 | g23.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 81 | 100 | 1.8E-40 |
| 4 | g23.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 124 | 150 | 1.8E-40 |
| 10 | g23.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 243 | 260 | 1.8E-40 |
| 6 | g23.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 325 | 345 | 1.8E-40 |
| 7 | g23.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 380 | 399 | 1.8E-40 |
| 11 | g23.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 458 | 478 | 1.8E-40 |
| 8 | g23.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 498 | 518 | 1.8E-40 |
| 1 | g23.t1 | Pfam | PF00209 | Sodium:neurotransmitter symporter family | 44 | 559 | 1.3E-143 |
| 13 | g23.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 52 | - |
| 28 | g23.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 53 | 70 | - |
| 23 | g23.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 71 | 81 | - |
| 34 | g23.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 82 | 100 | - |
| 17 | g23.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 101 | 130 | - |
| 36 | g23.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 131 | 152 | - |
| 22 | g23.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 153 | 215 | - |
| 33 | g23.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 216 | 234 | - |
| 16 | g23.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 235 | 245 | - |
| 31 | g23.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 246 | 269 | - |
| 24 | g23.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 270 | 288 | - |
| 26 | g23.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 289 | 313 | - |
| 19 | g23.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 314 | 324 | - |
| 37 | g23.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 325 | 346 | - |
| 21 | g23.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 347 | 387 | - |
| 35 | g23.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 388 | 413 | - |
| 18 | g23.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 414 | 424 | - |
| 27 | g23.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 425 | 449 | - |
| 20 | g23.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 450 | 454 | - |
| 30 | g23.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 455 | 478 | - |
| 14 | g23.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 479 | 498 | - |
| 29 | g23.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 499 | 518 | - |
| 25 | g23.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 519 | 529 | - |
| 32 | g23.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 530 | 555 | - |
| 15 | g23.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 556 | 598 | - |
| 51 | g23.t1 | ProSitePatterns | PS00610 | Sodium:neurotransmitter symporter family signature 1. | 68 | 82 | - |
| 52 | g23.t1 | ProSiteProfiles | PS50267 | Sodium:neurotransmitter symporter family profile. | 43 | 562 | 75.51 |
| 12 | g23.t1 | SUPERFAMILY | SSF161070 | SNF-like | 44 | 558 | 1.23E-144 |
| 40 | g23.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 53 | 72 | - |
| 47 | g23.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 82 | 104 | - |
| 48 | g23.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 125 | 147 | - |
| 45 | g23.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 212 | 234 | - |
| 42 | g23.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 243 | 265 | - |
| 44 | g23.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 292 | 314 | - |
| 49 | g23.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 326 | 348 | - |
| 43 | g23.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 385 | 407 | - |
| 50 | g23.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 427 | 449 | - |
| 39 | g23.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 459 | 478 | - |
| 41 | g23.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 499 | 518 | - |
| 46 | g23.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 533 | 555 | - |
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.
