Gene loci information

Transcript annotation

  • This transcript has been annotated as Sodium- and chloride-dependent glycine transporter 2.

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.t9 isoform g9869.t9 5774709 5776427
chr_1 g9869 g9869.t9 exon g9869.t9.exon1 5774709 5774836
chr_1 g9869 g9869.t9 cds g9869.t9.CDS1 5774713 5774836
chr_1 g9869 g9869.t9 exon g9869.t9.exon2 5774898 5775120
chr_1 g9869 g9869.t9 cds g9869.t9.CDS2 5774898 5775120
chr_1 g9869 g9869.t9 exon g9869.t9.exon3 5775173 5775527
chr_1 g9869 g9869.t9 cds g9869.t9.CDS3 5775173 5775527
chr_1 g9869 g9869.t9 exon g9869.t9.exon4 5775591 5776427
chr_1 g9869 g9869.t9 cds g9869.t9.CDS4 5775591 5776427
chr_1 g9869 g9869.t9 TTS g9869.t9 5776568 5776568
chr_1 g9869 g9869.t9 TSS g9869.t9 NA NA

Sequences

>g9869.t9 Gene=g9869 Length=1543
ATTTATGGTAATTTCTTTCGTCAGCATTTACTATCAACTGATTATTGCGTGGGTCTTATT
TTATCTTTATTCGTCATTCTTTCCATCTCTTCGTTGGGGCACATGTGACAATGATTGGAA
TTCTGAAAACTGTTTCAGTACAATTGAAGATTTATATTGTCGTCAAGAAAATGTTGGTAG
TGCAAGTGATCAAATTTTCTATCGTGGTGGATGCAGAGAGATTAACGAAATTTGTTCAAT
TCACGATTTGGTGGGCGTTAATGCTAGCAATTGTATGAATACAACAACAAATGAACTTGT
TCCCATTAATGATGTCATCACAAGAAGCCTCTCATCTGAAGAGTTTTTCTATGAACATGT
TCTTGGTATTGGTGATGCGAGATGGGACAACTTTGGTTATCCTCGATGGCAAATGGTCAT
TTTTCTATTTCTTGGTTGGACACTTACATATTTGTGTTTAATCAAAGGCGTTCAGTCAAT
GGGAAAAGTCGTCTATTTTACTGCCACATTTCCTTATGTCATTTTAACAGCTCTCTTAAT
TCGCTCATTAACATTAGAAGGTTCTTATGAAGGCATCATGTTTTATATTACTCCACAATG
GGAAAGATTACTTTCACCTGGTGTTTGGGGTGATGCCAGCAGTCAAATTTTCTACTCATT
TGGCTTAGCTTGTGGCAGTCTTGTGGCTTTAGCTTCGTATAATAAATTTAAAAATAATTG
CCATTTTGATGCAGTATTTATATCAATCATAAATTTTGGCACTGCTATTTTCGGTGGTTT
TGTAGTTTTTGCGACTCTTGGATTTTTATCAAATTCAATGCAACAACCTATTGATAATGT
CGTAACTGGTGGCCCTGGTTTAACATTTATTACATATCCTGAAGCTATCCTATTGATGCC
ATTGCCAAACCTTTGGGCAATTTTGTTTTTCCTCATGATGCTCATTTTGGGTTTAGGTTC
TCAATTCCCTGGTGTTCAAATGATTTCAACTTCAATTGTTGATCATTGGCCACATTTGAG
AAATAAGGAATGGAAAGTGACAGCTGGAGTATGCATGAGTTGTTTTGTTCTCGGTTTACC
AATGACTTGTCATGGTGGAATTTATCTTTTTACTCTTATGGAATGGCATACAGCAAGTTG
GGCAATTTTATTAATTGGTGCAGCTGAAATTGTCATCTTTTCATGGGTCTATGGAATAAA
TAACACACTCGATATGATTAAAGAGATGGGAATGAAATTCGTAAAAGTTACGAGATATTT
CTGGAAAGCAGTATGGGTTGTTATAACACCAATTGGATCAGTTGCAATTTTCATCTTTAT
TTTAACTGATTTGGGACCAAGTGAATTTCGTGATTATGTTTTTCCTCTTTGGGCTGATAT
CTTAGGTTGGATGTTTGGACTTGCAACGCTTGTTCCTTTTATTGTTTTCGCTATTTATCA
ATTAATTGTTGTAAAAGATAAGAAAACACTACTCAAACCAACAGATCTTTGGGGCCCACA
AGAAATCGATGGACAAAGGATTGATAGAGCAGTATTAGCTTAA

>g9869.t9 Gene=g9869 Length=512
MVISFVSIYYQLIIAWVLFYLYSSFFPSLRWGTCDNDWNSENCFSTIEDLYCRQENVGSA
SDQIFYRGGCREINEICSIHDLVGVNASNCMNTTTNELVPINDVITRSLSSEEFFYEHVL
GIGDARWDNFGYPRWQMVIFLFLGWTLTYLCLIKGVQSMGKVVYFTATFPYVILTALLIR
SLTLEGSYEGIMFYITPQWERLLSPGVWGDASSQIFYSFGLACGSLVALASYNKFKNNCH
FDAVFISIINFGTAIFGGFVVFATLGFLSNSMQQPIDNVVTGGPGLTFITYPEAILLMPL
PNLWAILFFLMMLILGLGSQFPGVQMISTSIVDHWPHLRNKEWKVTAGVCMSCFVLGLPM
TCHGGIYLFTLMEWHTASWAILLIGAAEIVIFSWVYGINNTLDMIKEMGMKFVKVTRYFW
KAVWVVITPIGSVAIFIFILTDLGPSEFRDYVFPLWADILGWMFGLATLVPFIVFAIYQL
IVVKDKKTLLKPTDLWGPQEIDGQRIDRAVLA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
3 g9869.t9 PANTHER PTHR11616 SODIUM/CHLORIDE DEPENDENT TRANSPORTER 2 499 1.2E-146
8 g9869.t9 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 162 179 2.3E-33
6 g9869.t9 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 244 264 2.3E-33
7 g9869.t9 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 298 317 2.3E-33
5 g9869.t9 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 378 398 2.3E-33
4 g9869.t9 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 421 441 2.3E-33
2 g9869.t9 Pfam PF00209 Sodium:neurotransmitter symporter family 1 57 2.2E-12
1 g9869.t9 Pfam PF00209 Sodium:neurotransmitter symporter family 85 481 3.8E-118
21 g9869.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 6 -
35 g9869.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 7 26 -
29 g9869.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 27 134 -
33 g9869.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 135 153 -
25 g9869.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 154 161 -
36 g9869.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 162 182 -
31 g9869.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 183 214 -
38 g9869.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 215 232 -
26 g9869.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 233 243 -
39 g9869.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 244 268 -
28 g9869.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 269 302 -
32 g9869.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 303 324 -
23 g9869.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 325 344 -
34 g9869.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 345 370 -
30 g9869.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 371 375 -
40 g9869.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 376 397 -
24 g9869.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 398 417 -
41 g9869.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 418 439 -
27 g9869.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 440 458 -
37 g9869.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 459 481 -
22 g9869.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 482 512 -
20 g9869.t9 ProSiteProfiles PS50267 Sodium:neurotransmitter symporter family profile. 1 485 64.504
19 g9869.t9 SUPERFAMILY SSF161070 SNF-like 3 480 1.05E-112
13 g9869.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 7 29 -
9 g9869.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 135 153 -
12 g9869.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 162 184 -
17 g9869.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 211 233 -
18 g9869.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 246 268 -
16 g9869.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 295 317 -
10 g9869.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 349 371 -
11 g9869.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 376 398 -
15 g9869.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 418 440 -
14 g9869.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 460 482 -

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.

Raw TPM values