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 g9870 g9870.t3 isoform g9870.t3 5779252 5780639
chr_1 g9870 g9870.t3 exon g9870.t3.exon1 5779252 5779261
chr_1 g9870 g9870.t3 exon g9870.t3.exon2 5779320 5779674
chr_1 g9870 g9870.t3 cds g9870.t3.CDS1 5779381 5779674
chr_1 g9870 g9870.t3 exon g9870.t3.exon3 5779746 5780425
chr_1 g9870 g9870.t3 cds g9870.t3.CDS2 5779746 5780425
chr_1 g9870 g9870.t3 exon g9870.t3.exon4 5780483 5780639
chr_1 g9870 g9870.t3 cds g9870.t3.CDS3 5780483 5780639
chr_1 g9870 g9870.t3 TTS g9870.t3 5780673 5780673
chr_1 g9870 g9870.t3 TSS g9870.t3 NA NA

Sequences

>g9870.t3 Gene=g9870 Length=1202
AATTTTTTTATGAACATGTCCTTGGCATTGGTGATGCGAGATGGGACAACTTTGGTTATC
CTCGTTGGCAAATGGTCATTTGTCTGTTCTCAGCTTGGGCACTTTCAGCACTTTGTTTGC
TTGGTGGTGTCAAATCAGTTGGAAAAATTGTTTATTTTACTGCCACATTTCCTTATGTGA
TTCTTACTGCCTTACTTGTTCGTGCATTAACATTAGAAGGTTCTATTGATGGTATTATGT
TTTATATCACTCCACAATGGGAAAGATTACTTTCACCTGGTGTTTGGGGTGATGCCAGCA
GCCAGATTTTCTACTCTTTCAGTTTGGCTTTAGGATCTCTGATTACACTTGCTTCTTATA
ATAAGTTCAAAAATAATGCACATTTTGATGCGACAATAGTTTCCTTGATCAATTATTTGA
CTGCATTCTATTCAGGTCTTGCAGTTTTCGCAATTCTTGGATTTCTTGCACATCAAATGA
ATGTTCCTGTTGATTCTGTTGCTTCATCTGGGCCTGGACTTAGTTTTATTACATTTCCTG
AAGCAATTCTTCTTATGCCTGGTTCACAAATTTGGGCGATTTTATTTTTCTTCATGATGA
TCATTTTGGGCTTAGGAAGTACATTTGCAGGAGTGCAAGCAATAACTACAGCAATAATTG
ATCGTTGGCCAAGATTAAGAAAAGATGAATGGAAAGTAACAATTGCAACATGTTTATCTG
GATTTATTCTTGGTTTACCAATGACTTGTCATGGTGGAATTTATCTTTTTACTCTTATGG
AATGGCACACAGCTAGTTGGGCAATTTTATTAATTGGTTTTGCTGAAGTTGTGATATTAT
CATGGGTTTATGGAATAAATAACACAATGGAAATGATTAAAGAGATGGGAATGAAAATAT
GGAAAGTTGTGCAATATTATTGGAAAGCAACTTGGGTTGTCATCACACCTTTTTATGCAG
TTGGTGTCTTTATCTTTATTCTAACAGGTATCGGACCAACACAATTTCGTGGTTATATTT
TCCCTGTTTGGGCTGATGTTCTTGGTTGGCTATTTGGCACAGCAACATTAGTTCCATTTG
TAGTGTTTGCAATAATTGAATTAATCAAGACAGATGACATAAAAAAATCATTTAGACCTA
CTGAAAATTGGGGGCCACAAGAGGTCGATGGAAGAAGAGTTGATCGGGCTGTTTTAACAT
GA

>g9870.t3 Gene=g9870 Length=376
MVICLFSAWALSALCLLGGVKSVGKIVYFTATFPYVILTALLVRALTLEGSIDGIMFYIT
PQWERLLSPGVWGDASSQIFYSFSLALGSLITLASYNKFKNNAHFDATIVSLINYLTAFY
SGLAVFAILGFLAHQMNVPVDSVASSGPGLSFITFPEAILLMPGSQIWAILFFFMMIILG
LGSTFAGVQAITTAIIDRWPRLRKDEWKVTIATCLSGFILGLPMTCHGGIYLFTLMEWHT
ASWAILLIGFAEVVILSWVYGINNTMEMIKEMGMKIWKVVQYYWKATWVVITPFYAVGVF
IFILTGIGPTQFRGYIFPVWADVLGWLFGTATLVPFVVFAIIELIKTDDIKKSFRPTENW
GPQEVDGRRVDRAVLT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g9870.t3 PANTHER PTHR11616 SODIUM/CHLORIDE DEPENDENT TRANSPORTER 1 363 1.1E-119
4 g9870.t3 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 26 43 3.8E-36
5 g9870.t3 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 108 128 3.8E-36
7 g9870.t3 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 162 181 3.8E-36
3 g9870.t3 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 242 262 3.8E-36
6 g9870.t3 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 285 305 3.8E-36
1 g9870.t3 Pfam PF00209 Sodium:neurotransmitter symporter family 1 346 9.2E-109
20 g9870.t3 Phobius SIGNAL_PEPTIDE Signal peptide region 1 22 -
21 g9870.t3 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 1 -
22 g9870.t3 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 2 17 -
32 g9870.t3 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 18 22 -
16 g9870.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 23 31 -
25 g9870.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 32 59 -
12 g9870.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 60 78 -
29 g9870.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 79 97 -
18 g9870.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 98 108 -
28 g9870.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 109 131 -
14 g9870.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 132 142 -
23 g9870.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 143 161 -
19 g9870.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 162 166 -
27 g9870.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 167 188 -
13 g9870.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 189 208 -
30 g9870.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 209 234 -
15 g9870.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 235 239 -
24 g9870.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 240 261 -
11 g9870.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 262 281 -
31 g9870.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 282 303 -
17 g9870.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 304 322 -
26 g9870.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 323 345 -
10 g9870.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 346 376 -
42 g9870.t3 ProSiteProfiles PS50267 Sodium:neurotransmitter symporter family profile. 1 349 58.697
8 g9870.t3 SUPERFAMILY SSF161070 SNF-like 1 344 1.44E-91
9 g9870.t3 SignalP_EUK SignalP-TM SignalP-TM 1 22 -
35 g9870.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 5 24 -
37 g9870.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 26 48 -
39 g9870.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 75 97 -
34 g9870.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 110 132 -
41 g9870.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 166 188 -
36 g9870.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 209 231 -
40 g9870.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 241 263 -
33 g9870.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 286 308 -
38 g9870.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 323 345 -

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