Gene loci information

Transcript annotation

  • This transcript has been annotated as Sodium- and chloride-dependent glycine transporter 1.

Parent gene

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.t4 TSS g9869.t4 5770746 5770746
chr_1 g9869 g9869.t4 isoform g9869.t4 5771012 5775513
chr_1 g9869 g9869.t4 exon g9869.t4.exon1 5771012 5771169
chr_1 g9869 g9869.t4 cds g9869.t4.CDS1 5771012 5771169
chr_1 g9869 g9869.t4 exon g9869.t4.exon2 5771721 5771768
chr_1 g9869 g9869.t4 cds g9869.t4.CDS2 5771721 5771768
chr_1 g9869 g9869.t4 exon g9869.t4.exon3 5771825 5771970
chr_1 g9869 g9869.t4 cds g9869.t4.CDS3 5771825 5771970
chr_1 g9869 g9869.t4 exon g9869.t4.exon4 5774693 5774836
chr_1 g9869 g9869.t4 cds g9869.t4.CDS4 5774693 5774836
chr_1 g9869 g9869.t4 exon g9869.t4.exon5 5774898 5775120
chr_1 g9869 g9869.t4 cds g9869.t4.CDS5 5774898 5775120
chr_1 g9869 g9869.t4 exon g9869.t4.exon6 5775173 5775513
chr_1 g9869 g9869.t4 cds g9869.t4.CDS6 5775173 5775512
chr_1 g9869 g9869.t4 TTS g9869.t4 NA NA

Sequences

>g9869.t4 Gene=g9869 Length=1060
ATGGATGTGAAATCTTTTGATGTGCCAAATATTAGTGGCATAGAAAAATCCTCGAATAAT
GGAAGCAATGTTGAAATTTCAACGTCATCTACTGTCAATTTAATTGAAGATCGAACAAAT
TGGAGTCGACCAATTGAATTTATTTTATCGTGCTTGAGTTTCGAAGGATTGGGGAACATT
TGGAGATTTCCTCATCTTGCTTATAGGAATGGCGGTGGAGCTTTTTTACTGCCATATTTT
CTTGCAGCAGTTTTTATTGGTTTGCCAATATTTTTTGCTGAACTGATTACAGGACAATAT
AGTGGACTTGGGCCGATTAAAGCTTATAGTTATCTTGCTCCGCTCTTTAAAGGCTTGGGC
TACTGCACATTTATGGTAATTTCTTTCGTCAGCATTTACTATCAACTGATTATTGCGTGG
GTCTTATTTTATCTTTATTCGTCATTCTTTCCATCTCTTCGTTGGGGCACATGTGACAAT
GATTGGAATTCTGAAAACTGTTTCAGTACAATTGAAGATTTATATTGTCGTCAAGAAAAT
GTTGGTAGTGCAAGTGATCAAATTTTCTATCGTGGTGGATGCAGAGAGATTAACGAAATT
TGTTCAATTCACGATTTGGTGGGCGTTAATGCTAGCAATTGTATGAATACAACAACAAAT
GAACTTGTTCCCATTAATGATGTCATCACAAGAAGCCTCTCATCTGAAGAGTTTTTCTAT
GAACATGTTCTTGGTATTGGTGATGCGAGATGGGACAACTTTGGTTATCCTCGATGGCAA
ATGGTCATTTTTCTATTTCTTGGTTGGACACTTACATATTTGTGTTTAATCAAAGGCGTT
CAGTCAATGGGAAAAGTCGTCTATTTTACTGCCACATTTCCTTATGTCATTTTAACAGCT
CTCTTAATTCGCTCATTAACATTAGAAGGTTCTTATGAAGGCATCATGTTTTATATTACT
CCACAATGGGAAAGATTACTTTCACCTGGTGTTTGGGGTGATGCCAGCAGTCAAATTTTC
TACTCATTTGGCTTAGCTTGTGGCAGTCTTGTGGCTTTAG

>g9869.t4 Gene=g9869 Length=353
MDVKSFDVPNISGIEKSSNNGSNVEISTSSTVNLIEDRTNWSRPIEFILSCLSFEGLGNI
WRFPHLAYRNGGGAFLLPYFLAAVFIGLPIFFAELITGQYSGLGPIKAYSYLAPLFKGLG
YCTFMVISFVSIYYQLIIAWVLFYLYSSFFPSLRWGTCDNDWNSENCFSTIEDLYCRQEN
VGSASDQIFYRGGCREINEICSIHDLVGVNASNCMNTTTNELVPINDVITRSLSSEEFFY
EHVLGIGDARWDNFGYPRWQMVIFLFLGWTLTYLCLIKGVQSMGKVVYFTATFPYVILTA
LLIRSLTLEGSYEGIMFYITPQWERLLSPGVWGDASSQIFYSFGLACGSLVAL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
3 g9869.t4 PANTHER PTHR11616 SODIUM/CHLORIDE DEPENDENT TRANSPORTER 28 353 1.2E-102
4 g9869.t4 PANTHER PTHR11616:SF241 TRANSPORTER 28 353 1.2E-102
6 g9869.t4 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 45 66 2.3E-32
8 g9869.t4 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 74 93 2.3E-32
7 g9869.t4 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 118 144 2.3E-32
5 g9869.t4 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 286 303 2.3E-32
2 g9869.t4 Pfam PF00209 Sodium:neurotransmitter symporter family 38 181 5.3E-51
1 g9869.t4 Pfam PF00209 Sodium:neurotransmitter symporter family 209 353 5.1E-44
19 g9869.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 75 -
23 g9869.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 76 97 -
16 g9869.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 98 117 -
22 g9869.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 118 146 -
18 g9869.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 147 258 -
20 g9869.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 259 277 -
15 g9869.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 278 285 -
21 g9869.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 286 306 -
17 g9869.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 307 353 -
14 g9869.t4 ProSiteProfiles PS50267 Sodium:neurotransmitter symporter family profile. 37 353 48.671
13 g9869.t4 SUPERFAMILY SSF161070 SNF-like 38 352 3.14E-84
12 g9869.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 71 93 -
10 g9869.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 124 146 -
11 g9869.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 259 281 -
9 g9869.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 286 308 -

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