General information for g24.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 g24 is located on chr_3: 336403..338823 (+ 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 | g24 | g24.t1 | isoform | g24.t1 | 336403 | 338823 |
| chr_3 | g24 | g24.t1 | exon | g24.t1.exon1 | 336403 | 336637 |
| chr_3 | g24 | g24.t1 | cds | g24.t1.CDS1 | 336403 | 336637 |
| chr_3 | g24 | g24.t1 | exon | g24.t1.exon2 | 336712 | 336727 |
| chr_3 | g24 | g24.t1 | cds | g24.t1.CDS2 | 336712 | 336727 |
| chr_3 | g24 | g24.t1 | exon | g24.t1.exon3 | 336831 | 337660 |
| chr_3 | g24 | g24.t1 | cds | g24.t1.CDS3 | 336831 | 337660 |
| chr_3 | g24 | g24.t1 | exon | g24.t1.exon4 | 337811 | 338112 |
| chr_3 | g24 | g24.t1 | cds | g24.t1.CDS4 | 337811 | 338112 |
| chr_3 | g24 | g24.t1 | exon | g24.t1.exon5 | 338173 | 338476 |
| chr_3 | g24 | g24.t1 | cds | g24.t1.CDS5 | 338173 | 338476 |
| chr_3 | g24 | g24.t1 | exon | g24.t1.exon6 | 338599 | 338666 |
| chr_3 | g24 | g24.t1 | cds | g24.t1.CDS6 | 338599 | 338666 |
| chr_3 | g24 | g24.t1 | exon | g24.t1.exon7 | 338728 | 338823 |
| chr_3 | g24 | g24.t1 | cds | g24.t1.CDS7 | 338728 | 338823 |
| chr_3 | g24 | g24.t1 | TTS | g24.t1 | 338953 | 338953 |
| chr_3 | g24 | g24.t1 | TSS | g24.t1 | NA | NA |
Sequences
>g24.t1 Gene=g24 Length=1851
ATGAATGGACACGACAATCCGACATTTATTGGTGATACTGTTTTCACTATACCTGGTGAA
TATCGAAGAAATCTCACACAATTTTATCCTGGTAAATATCAACAAACATTTCAAACAACA
ACACCAGCAACTTTGCAAATTAGTGATATAAAAACAGAAAAGAAACCACCAAAAGAACGC
GACAGTTGGGGACATGGACTAGAATTCTTGATGTCATGTATCGCGATGAGCGTAGGACTT
GGCAACATTTGGCGGTTCCCTTTTGTTGCTCTTGATAATGGAGGTGGAGCTTTTGTTATT
CCTTATCTCATAGTTCTGTTACTTATTGGAAAACCCATTTATTTTATGGAGATGGTTTTT
GGTCAATTTTCATCACGTGGATCAATCAAAGTCTTTGATTGTGTACCTGCAATGAGAGGC
GTTGGTGTTGGTCAAATTGTTTCAGTTGCAATTGTCGCCACATATTACAGCTCACTTATG
GCATTGACTTTAAATTACTTTGCAAATTCATTTAATGAAATTTTACCATGGGGAAGTTGC
AAAGAAGAATGGAATACAACTTGTATACCGAGTAGTCATCAAGAAAATGGAAATATGACT
TGGTCAAATAGCACAAAATCTTCAGCTGAATTATATTTCCTAAAAGATGTTCTAAGATCT
AAAGACAATATTAATGATGGAATTGGTGAACCAAATTGGACACTCGTCATCTTTCTTGCT
ATTTCTTGGTCAATTGTTTTTCTTACATTAATTAAAGGTGTTAGAAGCAGTGGAAAAGCT
TCTTATGTTCTCGCTATTTTTCCTTATCTGGTTTTATCAATTTTATTTGTACGTGCTATT
ACTCTTCCTGGTTCATTGAATGGAATTAAATACTTTCTAACACCACAATGGGATAAAATT
CTTGAAATAAAAGTTTGGTATGCAGCTGTGACACAATGCTTTTTTTCGCTTTCTGTTTGC
TTTGGAAATATCATCATGTATTCTTCATATAATAAATTCAGTCACAACGTTTATCGAGAT
GCAAATATTGTGACAACACTCGATACTTTTACATCACTTCTTGCTGGTTGTTGCATATTT
GGTATTCTTGGTAATCTCGCATATGAACTTGATGTTGATGATATTTCAACTGTTGTTAAA
AGTGGATCAGGATTGGCATTCATTTCTTATCCTGATGCGATTGCAAAATTCAAAGCATTT
CCACAAGTTTTTTCAGTTCTTTTCTTTTTGATGTTGTATTTACTTGGAATTGGCAGTAAT
GTCGCAATGATGAGTTGTATTATGACTGTAATAAGAGACAGATTTAAGAAAGTTAAAAAT
TGGCATGCAGCTCTTGGTTTTGCTATTTTTGGTACTCTTTGTGGATCAATTTATATGACA
CCGGGAGGACAATCAGTTTTAAAACTTGTCGATTATTATGGAGCATCATTTATTGCCTTC
GTATTAGCTATTGCTGAACTTTACACATTTAGTTATATTTATGGTGTTGATCGATTTTGC
AAAGATATTGAATTCATGTTAGGCTTCAGACCAAATATTTACTGGAGAACTTGCTGGCGA
TTTATTACACCTGGTTTAATGAGCATAATTTTAGCTTACACACTTTTTACGTTAGAACCA
CTTCAAGATAATGGAGCAGATTATCCACAAATTGCATATATAATTGGTTGGTGTATTTCT
GCTTTAGGTTTAATTCAATTGCCTGCATTTGCTATTTTTGCAATTTGCAAACAGAAAGGT
GACAACTTATGGGAGAAAATCAAAGGAGCATTTAGTCCTATGCATAAATGGGGACCACGT
GATCCAGCAACAAATGCCAAGTATAAAGAATTTCTTAATTCCACCGATTGA
>g24.t1 Gene=g24 Length=616
MNGHDNPTFIGDTVFTIPGEYRRNLTQFYPGKYQQTFQTTTPATLQISDIKTEKKPPKER
DSWGHGLEFLMSCIAMSVGLGNIWRFPFVALDNGGGAFVIPYLIVLLLIGKPIYFMEMVF
GQFSSRGSIKVFDCVPAMRGVGVGQIVSVAIVATYYSSLMALTLNYFANSFNEILPWGSC
KEEWNTTCIPSSHQENGNMTWSNSTKSSAELYFLKDVLRSKDNINDGIGEPNWTLVIFLA
ISWSIVFLTLIKGVRSSGKASYVLAIFPYLVLSILFVRAITLPGSLNGIKYFLTPQWDKI
LEIKVWYAAVTQCFFSLSVCFGNIIMYSSYNKFSHNVYRDANIVTTLDTFTSLLAGCCIF
GILGNLAYELDVDDISTVVKSGSGLAFISYPDAIAKFKAFPQVFSVLFFLMLYLLGIGSN
VAMMSCIMTVIRDRFKKVKNWHAALGFAIFGTLCGSIYMTPGGQSVLKLVDYYGASFIAF
VLAIAELYTFSYIYGVDRFCKDIEFMLGFRPNIYWRTCWRFITPGLMSIILAYTLFTLEP
LQDNGADYPQIAYIIGWCISALGLIQLPAFAIFAICKQKGDNLWEKIKGAFSPMHKWGPR
DPATNAKYKEFLNSTD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 38 | g24.t1 | CDD | cd10324 | SLC6sbd | 61 | 535 | 0.0 |
| 2 | g24.t1 | PANTHER | PTHR11616 | SODIUM/CHLORIDE DEPENDENT TRANSPORTER | 36 | 607 | 6.7E-269 |
| 3 | g24.t1 | PANTHER | PTHR11616:SF269 | TRANSPORTER | 36 | 607 | 6.7E-269 |
| 11 | g24.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 68 | 89 | 1.7E-46 |
| 6 | g24.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 97 | 116 | 1.7E-46 |
| 9 | g24.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 140 | 166 | 1.7E-46 |
| 7 | g24.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 260 | 277 | 1.7E-46 |
| 8 | g24.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 342 | 362 | 1.7E-46 |
| 10 | g24.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 398 | 417 | 1.7E-46 |
| 5 | g24.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 476 | 496 | 1.7E-46 |
| 4 | g24.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 516 | 536 | 1.7E-46 |
| 1 | g24.t1 | Pfam | PF00209 | Sodium:neurotransmitter symporter family | 60 | 577 | 1.2E-154 |
| 16 | g24.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 62 | - |
| 32 | g24.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 63 | 84 | - |
| 22 | g24.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 85 | 95 | - |
| 27 | g24.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 96 | 116 | - |
| 14 | g24.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 117 | 136 | - |
| 35 | g24.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 137 | 156 | - |
| 25 | g24.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 157 | 232 | - |
| 33 | g24.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 233 | 251 | - |
| 19 | g24.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 252 | 262 | - |
| 28 | g24.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 263 | 285 | - |
| 21 | g24.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 286 | 304 | - |
| 36 | g24.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 305 | 326 | - |
| 13 | g24.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 327 | 346 | - |
| 31 | g24.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 347 | 368 | - |
| 24 | g24.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 369 | 405 | - |
| 26 | g24.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 406 | 431 | - |
| 17 | g24.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 432 | 442 | - |
| 37 | g24.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 443 | 460 | - |
| 20 | g24.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 461 | 471 | - |
| 30 | g24.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 472 | 496 | - |
| 18 | g24.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 497 | 516 | - |
| 29 | g24.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 517 | 536 | - |
| 23 | g24.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 537 | 550 | - |
| 34 | g24.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 551 | 576 | - |
| 15 | g24.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 577 | 616 | - |
| 51 | g24.t1 | ProSitePatterns | PS00610 | Sodium:neurotransmitter symporter family signature 1. | 84 | 98 | - |
| 52 | g24.t1 | ProSiteProfiles | PS50267 | Sodium:neurotransmitter symporter family profile. | 59 | 580 | 81.943 |
| 12 | g24.t1 | SUPERFAMILY | SSF161070 | SNF-like | 60 | 576 | 1.44E-151 |
| 39 | g24.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 62 | 84 | - |
| 49 | g24.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 99 | 121 | - |
| 41 | g24.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 141 | 163 | - |
| 44 | g24.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 231 | 253 | - |
| 45 | g24.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 260 | 282 | - |
| 50 | g24.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 306 | 328 | - |
| 40 | g24.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 341 | 363 | - |
| 42 | g24.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 399 | 421 | - |
| 48 | g24.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 441 | 463 | - |
| 47 | g24.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 473 | 495 | - |
| 43 | g24.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 516 | 538 | - |
| 46 | g24.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 553 | 575 | - |
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.
