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.t2 TSS g9870.t2 5777999 5777999
chr_1 g9870 g9870.t2 isoform g9870.t2 5778175 5780074
chr_1 g9870 g9870.t2 exon g9870.t2.exon1 5778175 5778362
chr_1 g9870 g9870.t2 cds g9870.t2.CDS1 5778175 5778362
chr_1 g9870 g9870.t2 exon g9870.t2.exon2 5778461 5778499
chr_1 g9870 g9870.t2 cds g9870.t2.CDS2 5778461 5778499
chr_1 g9870 g9870.t2 exon g9870.t2.exon3 5778561 5778706
chr_1 g9870 g9870.t2 cds g9870.t2.CDS3 5778561 5778706
chr_1 g9870 g9870.t2 exon g9870.t2.exon4 5778778 5778831
chr_1 g9870 g9870.t2 cds g9870.t2.CDS4 5778778 5778831
chr_1 g9870 g9870.t2 exon g9870.t2.exon5 5778898 5778987
chr_1 g9870 g9870.t2 cds g9870.t2.CDS5 5778898 5778987
chr_1 g9870 g9870.t2 exon g9870.t2.exon6 5779045 5779261
chr_1 g9870 g9870.t2 cds g9870.t2.CDS6 5779045 5779261
chr_1 g9870 g9870.t2 exon g9870.t2.exon7 5779320 5779674
chr_1 g9870 g9870.t2 cds g9870.t2.CDS7 5779320 5779674
chr_1 g9870 g9870.t2 exon g9870.t2.exon8 5779746 5780074
chr_1 g9870 g9870.t2 cds g9870.t2.CDS8 5779746 5780072
chr_1 g9870 g9870.t2 TTS g9870.t2 5780673 5780673

Sequences

>g9870.t2 Gene=g9870 Length=1418
ATGGAGGAAAAAAGTGTTCGGTCATATGACTTTCCACAGGAAGCTTCTTATATAGACAAA
AAATTTGGTGACTCTTCAGAACCAGTGGAAAATTTGACGGCTAACTCCGAAGATAATTTA
ATTGCTGATCGTGGAAATTGGTCTCGACCTATTGAATTTATTTTATCATGTATGAATTTT
GCAATAGGATTGGGGAACGTGTGGAGGTACCCATATTTAGCCTACAGAAATGGCGGCGGT
GCTTTTTTGATTCCTTATCTTTTAGCTGCTTGTTTCATTGGATTACCAATTTTTTTTGCC
GAACTGATTGTTGGTCAATACAGTGCTTTAGGCCCGATTAAAGCATTTGCTTTTTTAGCT
CCATTCTTCAAAGGACTGGGTTATTGCACACTACTTGTAATCACATTCATAGAAATTTAT
TATTTTGTTATCATCGCGTGGGTCCTTTTTTACTTTTATACATCAATGTTTCCAAGTTTA
TTATGGGGTTCTTGTGATAACGATTGGAATACTGATTATTGTTATAATTTAATTGCTGAC
ATTGAATGTCAATCAGGAAATAATAATGATGCCTTTGACCAACTTTTCTTTCAAGATCGT
TGCCAAACTGTTACAGAAATTTGTGAACCAAGAAATTTGATTCCACTCAATGCAAGTTTC
TGTTCAAATGCTACACATGTTTTACCAATGAGTGACATAATTACAAGAGTTCTTTCATCT
GAAGAATTTTTTTATGAACATGTCCTTGGCATTGGTGATGCGAGATGGGACAACTTTGGT
TATCCTCGTTGGCAAATGGTCATTTGTCTGTTCTCAGCTTGGGCACTTTCAGCACTTTGT
TTGCTTGGTGGTGTCAAATCAGTTGGAAAAATTGTTTATTTTACTGCCACATTTCCTTAT
GTGATTCTTACTGCCTTACTTGTTCGTGCATTAACATTAGAAGGTTCTATTGATGGTATT
ATGTTTTATATCACTCCACAATGGGAAAGATTACTTTCACCTGGTGTTTGGGGTGATGCC
AGCAGCCAGATTTTCTACTCTTTCAGTTTGGCTTTAGGATCTCTGATTACACTTGCTTCT
TATAATAAGTTCAAAAATAATGCACATTTTGATGCGACAATAGTTTCCTTGATCAATTAT
TTGACTGCATTCTATTCAGGTCTTGCAGTTTTCGCAATTCTTGGATTTCTTGCACATCAA
ATGAATGTTCCTGTTGATTCTGTTGCTTCATCTGGGCCTGGACTTAGTTTTATTACATTT
CCTGAAGCAATTCTTCTTATGCCTGGTTCACAAATTTGGGCGATTTTATTTTTCTTCATG
ATGATCATTTTGGGCTTAGGAAGTACATTTGCAGGAGTGCAAGCAATAACTACAGCAATA
ATTGATCGTTGGCCAAGATTAAGAAAAGATGAATGGAA

>g9870.t2 Gene=g9870 Length=472
MEEKSVRSYDFPQEASYIDKKFGDSSEPVENLTANSEDNLIADRGNWSRPIEFILSCMNF
AIGLGNVWRYPYLAYRNGGGAFLIPYLLAACFIGLPIFFAELIVGQYSALGPIKAFAFLA
PFFKGLGYCTLLVITFIEIYYFVIIAWVLFYFYTSMFPSLLWGSCDNDWNTDYCYNLIAD
IECQSGNNNDAFDQLFFQDRCQTVTEICEPRNLIPLNASFCSNATHVLPMSDIITRVLSS
EEFFYEHVLGIGDARWDNFGYPRWQMVICLFSAWALSALCLLGGVKSVGKIVYFTATFPY
VILTALLVRALTLEGSIDGIMFYITPQWERLLSPGVWGDASSQIFYSFSLALGSLITLAS
YNKFKNNAHFDATIVSLINYLTAFYSGLAVFAILGFLAHQMNVPVDSVASSGPGLSFITF
PEAILLMPGSQIWAILFFFMMIILGLGSTFAGVQAITTAIIDRWPRLRKDEW

Protein features from InterProScan

Transcript Database ID Name Start End E.value
3 g9870.t2 PANTHER PTHR11616 SODIUM/CHLORIDE DEPENDENT TRANSPORTER 33 468 7.6E-155
5 g9870.t2 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 52 73 9.0E-58
7 g9870.t2 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 81 100 9.0E-58
6 g9870.t2 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 125 151 9.0E-58
4 g9870.t2 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 291 308 9.0E-58
9 g9870.t2 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 373 393 9.0E-58
8 g9870.t2 PRINTS PR00176 Sodium/chloride neurotransmitter symporter signature 427 446 9.0E-58
2 g9870.t2 Pfam PF00209 Sodium:neurotransmitter symporter family 44 187 1.2E-52
1 g9870.t2 Pfam PF00209 Sodium:neurotransmitter symporter family 233 467 2.0E-89
23 g9870.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 52 -
35 g9870.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 53 71 -
25 g9870.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 72 82 -
30 g9870.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 83 104 -
24 g9870.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 105 124 -
34 g9870.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 125 153 -
28 g9870.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 154 263 -
32 g9870.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 264 285 -
20 g9870.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 286 296 -
36 g9870.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 297 324 -
26 g9870.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 325 343 -
31 g9870.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 344 362 -
22 g9870.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 363 373 -
29 g9870.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 374 398 -
27 g9870.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 399 431 -
33 g9870.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 432 461 -
21 g9870.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 462 472 -
19 g9870.t2 ProSiteProfiles PS50267 Sodium:neurotransmitter symporter family profile. 43 472 72.751
18 g9870.t2 SUPERFAMILY SSF161070 SNF-like 44 469 9.55E-132
15 g9870.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 78 100 -
12 g9870.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 115 137 -
16 g9870.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 139 161 -
11 g9870.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 262 284 -
14 g9870.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 291 313 -
13 g9870.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 340 362 -
17 g9870.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 375 397 -
10 g9870.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 431 453 -

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