General information for g9869.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Sodium- and chloride-dependent glycine transporter 1.
Parent gene
- The parent gene g9869 is located on chr_1: 5774709..5776427 (+ 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_1 | g9869 | g9869.t1 | TSS | g9869.t1 | 5770746 | 5770746 |
| chr_1 | g9869 | g9869.t1 | isoform | g9869.t1 | 5771012 | 5776427 |
| chr_1 | g9869 | g9869.t1 | exon | g9869.t1.exon1 | 5771012 | 5771169 |
| chr_1 | g9869 | g9869.t1 | cds | g9869.t1.CDS1 | 5771012 | 5771169 |
| chr_1 | g9869 | g9869.t1 | exon | g9869.t1.exon2 | 5771654 | 5771664 |
| chr_1 | g9869 | g9869.t1 | cds | g9869.t1.CDS2 | 5771654 | 5771664 |
| chr_1 | g9869 | g9869.t1 | exon | g9869.t1.exon3 | 5771729 | 5771768 |
| chr_1 | g9869 | g9869.t1 | cds | g9869.t1.CDS3 | 5771729 | 5771768 |
| chr_1 | g9869 | g9869.t1 | exon | g9869.t1.exon4 | 5771825 | 5771970 |
| chr_1 | g9869 | g9869.t1 | cds | g9869.t1.CDS4 | 5771825 | 5771970 |
| chr_1 | g9869 | g9869.t1 | exon | g9869.t1.exon5 | 5774693 | 5774836 |
| chr_1 | g9869 | g9869.t1 | cds | g9869.t1.CDS5 | 5774693 | 5774836 |
| chr_1 | g9869 | g9869.t1 | exon | g9869.t1.exon6 | 5774898 | 5775120 |
| chr_1 | g9869 | g9869.t1 | cds | g9869.t1.CDS6 | 5774898 | 5775120 |
| chr_1 | g9869 | g9869.t1 | exon | g9869.t1.exon7 | 5775173 | 5775527 |
| chr_1 | g9869 | g9869.t1 | cds | g9869.t1.CDS7 | 5775173 | 5775527 |
| chr_1 | g9869 | g9869.t1 | exon | g9869.t1.exon8 | 5775591 | 5776427 |
| chr_1 | g9869 | g9869.t1 | cds | g9869.t1.CDS8 | 5775591 | 5776427 |
| chr_1 | g9869 | g9869.t1 | TTS | g9869.t1 | 5776568 | 5776568 |
Sequences
>g9869.t1 Gene=g9869 Length=1914
ATGGATGTGAAATCTTTTGATGTGCCAAATATTAGTGGCATAGAAAAATCCTCGAATAAT
GGAAGCAATGTTGAAATTTCAACGTCATCTACTGTCAATTTAATTGAAGATCGAACAAAT
TGGAGTCGACCAATTGAATTTATTTTATCGTGCTTGAGTTATGCAATAGGATTGGGGAAC
ATTTGGAGATTTCCTCATCTTGCTTATAGGAATGGCGGTGGAGCTTTTTTACTGCCATAT
TTTCTTGCAGCAGTTTTTATTGGTTTGCCAATATTTTTTGCTGAACTGATTACAGGACAA
TATAGTGGACTTGGGCCGATTAAAGCTTATAGTTATCTTGCTCCGCTCTTTAAAGGCTTG
GGCTACTGCACATTTATGGTAATTTCTTTCGTCAGCATTTACTATCAACTGATTATTGCG
TGGGTCTTATTTTATCTTTATTCGTCATTCTTTCCATCTCTTCGTTGGGGCACATGTGAC
AATGATTGGAATTCTGAAAACTGTTTCAGTACAATTGAAGATTTATATTGTCGTCAAGAA
AATGTTGGTAGTGCAAGTGATCAAATTTTCTATCGTGGTGGATGCAGAGAGATTAACGAA
ATTTGTTCAATTCACGATTTGGTGGGCGTTAATGCTAGCAATTGTATGAATACAACAACA
AATGAACTTGTTCCCATTAATGATGTCATCACAAGAAGCCTCTCATCTGAAGAGTTTTTC
TATGAACATGTTCTTGGTATTGGTGATGCGAGATGGGACAACTTTGGTTATCCTCGATGG
CAAATGGTCATTTTTCTATTTCTTGGTTGGACACTTACATATTTGTGTTTAATCAAAGGC
GTTCAGTCAATGGGAAAAGTCGTCTATTTTACTGCCACATTTCCTTATGTCATTTTAACA
GCTCTCTTAATTCGCTCATTAACATTAGAAGGTTCTTATGAAGGCATCATGTTTTATATT
ACTCCACAATGGGAAAGATTACTTTCACCTGGTGTTTGGGGTGATGCCAGCAGTCAAATT
TTCTACTCATTTGGCTTAGCTTGTGGCAGTCTTGTGGCTTTAGCTTCGTATAATAAATTT
AAAAATAATTGCCATTTTGATGCAGTATTTATATCAATCATAAATTTTGGCACTGCTATT
TTCGGTGGTTTTGTAGTTTTTGCGACTCTTGGATTTTTATCAAATTCAATGCAACAACCT
ATTGATAATGTCGTAACTGGTGGCCCTGGTTTAACATTTATTACATATCCTGAAGCTATC
CTATTGATGCCATTGCCAAACCTTTGGGCAATTTTGTTTTTCCTCATGATGCTCATTTTG
GGTTTAGGTTCTCAATTCCCTGGTGTTCAAATGATTTCAACTTCAATTGTTGATCATTGG
CCACATTTGAGAAATAAGGAATGGAAAGTGACAGCTGGAGTATGCATGAGTTGTTTTGTT
CTCGGTTTACCAATGACTTGTCATGGTGGAATTTATCTTTTTACTCTTATGGAATGGCAT
ACAGCAAGTTGGGCAATTTTATTAATTGGTGCAGCTGAAATTGTCATCTTTTCATGGGTC
TATGGAATAAATAACACACTCGATATGATTAAAGAGATGGGAATGAAATTCGTAAAAGTT
ACGAGATATTTCTGGAAAGCAGTATGGGTTGTTATAACACCAATTGGATCAGTTGCAATT
TTCATCTTTATTTTAACTGATTTGGGACCAAGTGAATTTCGTGATTATGTTTTTCCTCTT
TGGGCTGATATCTTAGGTTGGATGTTTGGACTTGCAACGCTTGTTCCTTTTATTGTTTTC
GCTATTTATCAATTAATTGTTGTAAAAGATAAGAAAACACTACTCAAACCAACAGATCTT
TGGGGCCCACAAGAAATCGATGGACAAAGGATTGATAGAGCAGTATTAGCTTAA
>g9869.t1 Gene=g9869 Length=637
MDVKSFDVPNISGIEKSSNNGSNVEISTSSTVNLIEDRTNWSRPIEFILSCLSYAIGLGN
IWRFPHLAYRNGGGAFLLPYFLAAVFIGLPIFFAELITGQYSGLGPIKAYSYLAPLFKGL
GYCTFMVISFVSIYYQLIIAWVLFYLYSSFFPSLRWGTCDNDWNSENCFSTIEDLYCRQE
NVGSASDQIFYRGGCREINEICSIHDLVGVNASNCMNTTTNELVPINDVITRSLSSEEFF
YEHVLGIGDARWDNFGYPRWQMVIFLFLGWTLTYLCLIKGVQSMGKVVYFTATFPYVILT
ALLIRSLTLEGSYEGIMFYITPQWERLLSPGVWGDASSQIFYSFGLACGSLVALASYNKF
KNNCHFDAVFISIINFGTAIFGGFVVFATLGFLSNSMQQPIDNVVTGGPGLTFITYPEAI
LLMPLPNLWAILFFLMMLILGLGSQFPGVQMISTSIVDHWPHLRNKEWKVTAGVCMSCFV
LGLPMTCHGGIYLFTLMEWHTASWAILLIGAAEIVIFSWVYGINNTLDMIKEMGMKFVKV
TRYFWKAVWVVITPIGSVAIFIFILTDLGPSEFRDYVFPLWADILGWMFGLATLVPFIVF
AIYQLIVVKDKKTLLKPTDLWGPQEIDGQRIDRAVLA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g9869.t1 | PANTHER | PTHR11616 | SODIUM/CHLORIDE DEPENDENT TRANSPORTER | 28 | 610 | 8.5E-189 |
| 4 | g9869.t1 | PANTHER | PTHR11616:SF241 | TRANSPORTER | 28 | 610 | 8.5E-189 |
| 11 | g9869.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 46 | 67 | 5.0E-66 |
| 5 | g9869.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 75 | 94 | 5.0E-66 |
| 9 | g9869.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 119 | 145 | 5.0E-66 |
| 6 | g9869.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 287 | 304 | 5.0E-66 |
| 7 | g9869.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 369 | 389 | 5.0E-66 |
| 10 | g9869.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 423 | 442 | 5.0E-66 |
| 12 | g9869.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 503 | 523 | 5.0E-66 |
| 8 | g9869.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 546 | 566 | 5.0E-66 |
| 2 | g9869.t1 | Pfam | PF00209 | Sodium:neurotransmitter symporter family | 38 | 182 | 2.7E-53 |
| 1 | g9869.t1 | Pfam | PF00209 | Sodium:neurotransmitter symporter family | 210 | 606 | 6.6E-118 |
| 28 | g9869.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 46 | - |
| 52 | g9869.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 47 | 65 | - |
| 39 | g9869.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 66 | 76 | - |
| 41 | g9869.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 77 | 98 | - |
| 31 | g9869.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 99 | 118 | - |
| 48 | g9869.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 119 | 147 | - |
| 35 | g9869.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 148 | 259 | - |
| 43 | g9869.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 260 | 278 | - |
| 34 | g9869.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 279 | 286 | - |
| 46 | g9869.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 287 | 307 | - |
| 40 | g9869.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 308 | 339 | - |
| 44 | g9869.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 340 | 357 | - |
| 33 | g9869.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 358 | 368 | - |
| 47 | g9869.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 369 | 393 | - |
| 36 | g9869.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 394 | 427 | - |
| 45 | g9869.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 428 | 449 | - |
| 32 | g9869.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 450 | 469 | - |
| 49 | g9869.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 470 | 495 | - |
| 38 | g9869.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 496 | 500 | - |
| 50 | g9869.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 501 | 522 | - |
| 30 | g9869.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 523 | 542 | - |
| 51 | g9869.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 543 | 564 | - |
| 37 | g9869.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 565 | 583 | - |
| 42 | g9869.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 584 | 606 | - |
| 29 | g9869.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 607 | 637 | - |
| 27 | g9869.t1 | ProSiteProfiles | PS50267 | Sodium:neurotransmitter symporter family profile. | 37 | 610 | 88.358 |
| 26 | g9869.t1 | SUPERFAMILY | SSF161070 | SNF-like | 38 | 605 | 1.23E-153 |
| 22 | g9869.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 45 | 64 | - |
| 19 | g9869.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 76 | 98 | - |
| 18 | g9869.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 113 | 135 | - |
| 20 | g9869.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 137 | 159 | - |
| 17 | g9869.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 260 | 278 | - |
| 16 | g9869.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 287 | 309 | - |
| 14 | g9869.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 336 | 358 | - |
| 21 | g9869.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 371 | 393 | - |
| 15 | g9869.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 420 | 442 | - |
| 25 | g9869.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 474 | 496 | - |
| 23 | g9869.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 501 | 523 | - |
| 13 | g9869.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 543 | 565 | - |
| 24 | g9869.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 585 | 607 | - |
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