General information for g683.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 g683 is located on chr_3: 5240802..5243287 (+ 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 | g683 | g683.t1 | TSS | g683.t1 | 5240282 | 5240282 |
| chr_3 | g683 | g683.t1 | isoform | g683.t1 | 5240802 | 5243287 |
| chr_3 | g683 | g683.t1 | exon | g683.t1.exon1 | 5240802 | 5240994 |
| chr_3 | g683 | g683.t1 | cds | g683.t1.CDS1 | 5240802 | 5240994 |
| chr_3 | g683 | g683.t1 | exon | g683.t1.exon2 | 5241070 | 5241085 |
| chr_3 | g683 | g683.t1 | cds | g683.t1.CDS2 | 5241070 | 5241085 |
| chr_3 | g683 | g683.t1 | exon | g683.t1.exon3 | 5241189 | 5241223 |
| chr_3 | g683 | g683.t1 | cds | g683.t1.CDS3 | 5241189 | 5241223 |
| chr_3 | g683 | g683.t1 | exon | g683.t1.exon4 | 5241327 | 5241401 |
| chr_3 | g683 | g683.t1 | cds | g683.t1.CDS4 | 5241327 | 5241401 |
| chr_3 | g683 | g683.t1 | exon | g683.t1.exon5 | 5241585 | 5241641 |
| chr_3 | g683 | g683.t1 | cds | g683.t1.CDS5 | 5241585 | 5241641 |
| chr_3 | g683 | g683.t1 | exon | g683.t1.exon6 | 5241694 | 5242424 |
| chr_3 | g683 | g683.t1 | cds | g683.t1.CDS6 | 5241694 | 5242424 |
| chr_3 | g683 | g683.t1 | exon | g683.t1.exon7 | 5242475 | 5242702 |
| chr_3 | g683 | g683.t1 | cds | g683.t1.CDS7 | 5242475 | 5242702 |
| chr_3 | g683 | g683.t1 | exon | g683.t1.exon8 | 5242755 | 5243129 |
| chr_3 | g683 | g683.t1 | cds | g683.t1.CDS8 | 5242755 | 5243129 |
| chr_3 | g683 | g683.t1 | exon | g683.t1.exon9 | 5243195 | 5243287 |
| chr_3 | g683 | g683.t1 | cds | g683.t1.CDS9 | 5243195 | 5243287 |
| chr_3 | g683 | g683.t1 | TTS | g683.t1 | NA | NA |
Sequences
>g683.t1 Gene=g683 Length=1803
ATGACTCAAGAAATTTACGACAATCCAGCATTTTCATCTGAAAATTCATTGTCTGTAATT
GAAGGAAATTTAACATCTGTGAATAATGAAGATAAAAATGAAGATCGAAAAATTGTCACA
AAAGATGGTGTTATTCGACAAAAATGGGGAAGAGATATAGAATTTCTTTTATCATGCATA
GCTATGGCCATAGGATTAGGCAACGTTTGGAGGTTTCCTTTTATTGCCTTGGAAAATGGA
GGAGGTGCTTTTGTTATTCCATATATTATTGTACTAATTTTAATTGGAAAACCTGGTTAT
TATTTGGAAATGATTATGGGCCAATTTTCTTCACGTGGCACAGTTAAAGTTTATGATTGT
GTTCCAGCTATGAGAGGTGTTGGATTAGGTCAAATGATTTGCCTTGCAATGGTTGCAACT
TATTATTCAGCAATTGTTGCCATCATATTATATTTCCTTATCGTTTCTTTTTTTCCTACT
CTGCCATGGAGTGAATGCAAAGATTATTGGGATGTTCCATGCTATTCATCAAGTGGCAGC
AACTCAAATATCACTTGGAATAATAACACAAAATCATCTGCGGAACTTTATTTTTTAAAA
GACGTTCTTAATGCTAGAGATACACTTGAAGATGGAATTGGTTTACCAAATTGGAATTTA
GTTGGACTTTTGGTTTTTTCATGGACAATAATGTTTATTCTTCTTTTTAAAGGAGTGAGA
ATTACTGGAAAAGCTTCCTATGTCACAGGAACAGCTCCATTTATTTTTCTAGCAATTTTT
TTTATTCGAGCTATCACACTTGAGGGCTCATATGAAGGAATTGCTTATTTTTTCAAACCA
AAATGGAATGATATTTTGAAGCCAAAAGTTTGGTTTGAAGCTTGCACTCAAGTATTTTTC
ACTCTTAATGTTTTTTTTGTCAATGTCATCATGTGTGCTTCATATAATAGATTTGAACAT
AAAATACAACGTGATTCAGCTATTGTTACAACATTAGACACATTTACATCACTTCTTGTT
GGTTCGATTACCTTTGGTATTGTTGGTCATTTATCACATGAACTTAATAGACCAATTAAA
GAGGTTTTCAGAGGAGGTCCTGGCTTGGTATTTGTCACTTATCCTGAAACGATAGCAAAA
TTTAAATTTTGGCCACAATTCTTTTCTGTAATGTTTTTCCTGATGCTTTTTATTCTTTCA
TTTGGAAGTTTACTTGCAACTTCATTATCGGCAATGACAGTAATTCGCGATCGATTTAAA
AGAATTAAAGATTGGCAAGCTGCTCTTGGATTTGCCATTTTTGGAACTATTTTTGGATGT
TTTTACACTACACCTGCCGGATTGTTGATTCTTAATTTAGTCGACAGCTATTGTGCAACT
TTTGTAATTTTTATCTTAGCCTGTCTTGAAATTTACACATTCTCCTATATTTATGGAGTT
GCCAGAATTTGTAAAGATGTAAAATTTATGCTGGGTTTCAGACCAAATATTTTTTGGAGA
GTAACTTGGAAATTTATAACACCACTTATTATGACAGCAATTGTTATTTACACATTTGTA
TATTTTGAACTTCCAAGTGATGGTGATTATCAATATCCAGTAGGAGCTCACATTTTTGGT
TGGTTTATAGCTTTATTAGGACTGATTTGGGTACCTGTAATTTTTACTACAAGAGTTTGG
AAACAAAAGCAAGAAACTAAATTGATTGAAAAAATTCGTGCTGCATTAAGACCAACAAAA
AACTGGGGTCCATTAGATCCTGTAACTAATGCAAAATACAAGGAATTTATGACAAAAAAT
TAG
>g683.t1 Gene=g683 Length=600
MTQEIYDNPAFSSENSLSVIEGNLTSVNNEDKNEDRKIVTKDGVIRQKWGRDIEFLLSCI
AMAIGLGNVWRFPFIALENGGGAFVIPYIIVLILIGKPGYYLEMIMGQFSSRGTVKVYDC
VPAMRGVGLGQMICLAMVATYYSAIVAIILYFLIVSFFPTLPWSECKDYWDVPCYSSSGS
NSNITWNNNTKSSAELYFLKDVLNARDTLEDGIGLPNWNLVGLLVFSWTIMFILLFKGVR
ITGKASYVTGTAPFIFLAIFFIRAITLEGSYEGIAYFFKPKWNDILKPKVWFEACTQVFF
TLNVFFVNVIMCASYNRFEHKIQRDSAIVTTLDTFTSLLVGSITFGIVGHLSHELNRPIK
EVFRGGPGLVFVTYPETIAKFKFWPQFFSVMFFLMLFILSFGSLLATSLSAMTVIRDRFK
RIKDWQAALGFAIFGTIFGCFYTTPAGLLILNLVDSYCATFVIFILACLEIYTFSYIYGV
ARICKDVKFMLGFRPNIFWRVTWKFITPLIMTAIVIYTFVYFELPSDGDYQYPVGAHIFG
WFIALLGLIWVPVIFTTRVWKQKQETKLIEKIRAALRPTKNWGPLDPVTNAKYKEFMTKN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 38 | g683.t1 | CDD | cd10324 | SLC6sbd | 47 | 519 | 1.45422E-151 |
| 2 | g683.t1 | PANTHER | PTHR11616 | SODIUM/CHLORIDE DEPENDENT TRANSPORTER | 21 | 591 | 5.4E-215 |
| 3 | g683.t1 | PANTHER | PTHR11616:SF269 | TRANSPORTER | 21 | 591 | 5.4E-215 |
| 6 | g683.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 54 | 75 | 2.3E-43 |
| 8 | g683.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 83 | 102 | 2.3E-43 |
| 9 | g683.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 126 | 152 | 2.3E-43 |
| 10 | g683.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 245 | 262 | 2.3E-43 |
| 5 | g683.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 327 | 347 | 2.3E-43 |
| 4 | g683.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 382 | 401 | 2.3E-43 |
| 7 | g683.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 460 | 480 | 2.3E-43 |
| 11 | g683.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 500 | 520 | 2.3E-43 |
| 1 | g683.t1 | Pfam | PF00209 | Sodium:neurotransmitter symporter family | 46 | 561 | 2.2E-138 |
| 13 | g683.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 54 | - |
| 30 | g683.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 55 | 76 | - |
| 20 | g683.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 77 | 81 | - |
| 29 | g683.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 82 | 102 | - |
| 17 | g683.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 103 | 132 | - |
| 26 | g683.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 133 | 154 | - |
| 25 | g683.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 155 | 217 | - |
| 32 | g683.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 218 | 236 | - |
| 16 | g683.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 237 | 247 | - |
| 35 | g683.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 248 | 271 | - |
| 24 | g683.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 272 | 290 | - |
| 27 | g683.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 291 | 315 | - |
| 15 | g683.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 316 | 326 | - |
| 28 | g683.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 327 | 348 | - |
| 23 | g683.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 349 | 389 | - |
| 33 | g683.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 390 | 415 | - |
| 19 | g683.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 416 | 426 | - |
| 37 | g683.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 427 | 453 | - |
| 21 | g683.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 454 | 458 | - |
| 34 | g683.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 459 | 481 | - |
| 14 | g683.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 482 | 500 | - |
| 36 | g683.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 501 | 522 | - |
| 22 | g683.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 523 | 533 | - |
| 31 | g683.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 534 | 555 | - |
| 18 | g683.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 556 | 600 | - |
| 51 | g683.t1 | ProSitePatterns | PS00610 | Sodium:neurotransmitter symporter family signature 1. | 70 | 84 | - |
| 52 | g683.t1 | ProSiteProfiles | PS50267 | Sodium:neurotransmitter symporter family profile. | 45 | 564 | 74.947 |
| 12 | g683.t1 | SUPERFAMILY | SSF161070 | SNF-like | 46 | 560 | 3.92E-137 |
| 42 | g683.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 53 | 75 | - |
| 40 | g683.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 80 | 102 | - |
| 43 | g683.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 133 | 155 | - |
| 45 | g683.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 214 | 236 | - |
| 41 | g683.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 245 | 267 | - |
| 48 | g683.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 291 | 313 | - |
| 49 | g683.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 326 | 348 | - |
| 39 | g683.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 384 | 406 | - |
| 50 | g683.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 427 | 449 | - |
| 47 | g683.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 459 | 481 | - |
| 46 | g683.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 501 | 523 | - |
| 44 | g683.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 538 | 560 | - |
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.
