General information for g9870.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 g9870 is located on chr_1: 5779325..5780639 (+ 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 | g9870 | g9870.t1 | TSS | g9870.t1 | 5777999 | 5777999 |
| chr_1 | g9870 | g9870.t1 | isoform | g9870.t1 | 5778175 | 5780639 |
| chr_1 | g9870 | g9870.t1 | exon | g9870.t1.exon1 | 5778175 | 5778362 |
| chr_1 | g9870 | g9870.t1 | cds | g9870.t1.CDS1 | 5778175 | 5778362 |
| chr_1 | g9870 | g9870.t1 | exon | g9870.t1.exon2 | 5778461 | 5778499 |
| chr_1 | g9870 | g9870.t1 | cds | g9870.t1.CDS2 | 5778461 | 5778499 |
| chr_1 | g9870 | g9870.t1 | exon | g9870.t1.exon3 | 5778561 | 5778706 |
| chr_1 | g9870 | g9870.t1 | cds | g9870.t1.CDS3 | 5778561 | 5778706 |
| chr_1 | g9870 | g9870.t1 | exon | g9870.t1.exon4 | 5778778 | 5778831 |
| chr_1 | g9870 | g9870.t1 | cds | g9870.t1.CDS4 | 5778778 | 5778831 |
| chr_1 | g9870 | g9870.t1 | exon | g9870.t1.exon5 | 5778898 | 5778987 |
| chr_1 | g9870 | g9870.t1 | cds | g9870.t1.CDS5 | 5778898 | 5778987 |
| chr_1 | g9870 | g9870.t1 | exon | g9870.t1.exon6 | 5779045 | 5779261 |
| chr_1 | g9870 | g9870.t1 | cds | g9870.t1.CDS6 | 5779045 | 5779261 |
| chr_1 | g9870 | g9870.t1 | exon | g9870.t1.exon7 | 5779320 | 5779674 |
| chr_1 | g9870 | g9870.t1 | cds | g9870.t1.CDS7 | 5779320 | 5779674 |
| chr_1 | g9870 | g9870.t1 | exon | g9870.t1.exon8 | 5779746 | 5780425 |
| chr_1 | g9870 | g9870.t1 | cds | g9870.t1.CDS8 | 5779746 | 5780425 |
| chr_1 | g9870 | g9870.t1 | exon | g9870.t1.exon9 | 5780483 | 5780639 |
| chr_1 | g9870 | g9870.t1 | cds | g9870.t1.CDS9 | 5780483 | 5780639 |
| chr_1 | g9870 | g9870.t1 | TTS | g9870.t1 | 5780673 | 5780673 |
Sequences
>g9870.t1 Gene=g9870 Length=1926
ATGGAGGAAAAAAGTGTTCGGTCATATGACTTTCCACAGGAAGCTTCTTATATAGACAAA
AAATTTGGTGACTCTTCAGAACCAGTGGAAAATTTGACGGCTAACTCCGAAGATAATTTA
ATTGCTGATCGTGGAAATTGGTCTCGACCTATTGAATTTATTTTATCATGTATGAATTTT
GCAATAGGATTGGGGAACGTGTGGAGGTACCCATATTTAGCCTACAGAAATGGCGGCGGT
GCTTTTTTGATTCCTTATCTTTTAGCTGCTTGTTTCATTGGATTACCAATTTTTTTTGCC
GAACTGATTGTTGGTCAATACAGTGCTTTAGGCCCGATTAAAGCATTTGCTTTTTTAGCT
CCATTCTTCAAAGGACTGGGTTATTGCACACTACTTGTAATCACATTCATAGAAATTTAT
TATTTTGTTATCATCGCGTGGGTCCTTTTTTACTTTTATACATCAATGTTTCCAAGTTTA
TTATGGGGTTCTTGTGATAACGATTGGAATACTGATTATTGTTATAATTTAATTGCTGAC
ATTGAATGTCAATCAGGAAATAATAATGATGCCTTTGACCAACTTTTCTTTCAAGATCGT
TGCCAAACTGTTACAGAAATTTGTGAACCAAGAAATTTGATTCCACTCAATGCAAGTTTC
TGTTCAAATGCTACACATGTTTTACCAATGAGTGACATAATTACAAGAGTTCTTTCATCT
GAAGAATTTTTTTATGAACATGTCCTTGGCATTGGTGATGCGAGATGGGACAACTTTGGT
TATCCTCGTTGGCAAATGGTCATTTGTCTGTTCTCAGCTTGGGCACTTTCAGCACTTTGT
TTGCTTGGTGGTGTCAAATCAGTTGGAAAAATTGTTTATTTTACTGCCACATTTCCTTAT
GTGATTCTTACTGCCTTACTTGTTCGTGCATTAACATTAGAAGGTTCTATTGATGGTATT
ATGTTTTATATCACTCCACAATGGGAAAGATTACTTTCACCTGGTGTTTGGGGTGATGCC
AGCAGCCAGATTTTCTACTCTTTCAGTTTGGCTTTAGGATCTCTGATTACACTTGCTTCT
TATAATAAGTTCAAAAATAATGCACATTTTGATGCGACAATAGTTTCCTTGATCAATTAT
TTGACTGCATTCTATTCAGGTCTTGCAGTTTTCGCAATTCTTGGATTTCTTGCACATCAA
ATGAATGTTCCTGTTGATTCTGTTGCTTCATCTGGGCCTGGACTTAGTTTTATTACATTT
CCTGAAGCAATTCTTCTTATGCCTGGTTCACAAATTTGGGCGATTTTATTTTTCTTCATG
ATGATCATTTTGGGCTTAGGAAGTACATTTGCAGGAGTGCAAGCAATAACTACAGCAATA
ATTGATCGTTGGCCAAGATTAAGAAAAGATGAATGGAAAGTAACAATTGCAACATGTTTA
TCTGGATTTATTCTTGGTTTACCAATGACTTGTCATGGTGGAATTTATCTTTTTACTCTT
ATGGAATGGCACACAGCTAGTTGGGCAATTTTATTAATTGGTTTTGCTGAAGTTGTGATA
TTATCATGGGTTTATGGAATAAATAACACAATGGAAATGATTAAAGAGATGGGAATGAAA
ATATGGAAAGTTGTGCAATATTATTGGAAAGCAACTTGGGTTGTCATCACACCTTTTTAT
GCAGTTGGTGTCTTTATCTTTATTCTAACAGGTATCGGACCAACACAATTTCGTGGTTAT
ATTTTCCCTGTTTGGGCTGATGTTCTTGGTTGGCTATTTGGCACAGCAACATTAGTTCCA
TTTGTAGTGTTTGCAATAATTGAATTAATCAAGACAGATGACATAAAAAAATCATTTAGA
CCTACTGAAAATTGGGGGCCACAAGAGGTCGATGGAAGAAGAGTTGATCGGGCTGTTTTA
ACATGA
>g9870.t1 Gene=g9870 Length=641
MEEKSVRSYDFPQEASYIDKKFGDSSEPVENLTANSEDNLIADRGNWSRPIEFILSCMNF
AIGLGNVWRYPYLAYRNGGGAFLIPYLLAACFIGLPIFFAELIVGQYSALGPIKAFAFLA
PFFKGLGYCTLLVITFIEIYYFVIIAWVLFYFYTSMFPSLLWGSCDNDWNTDYCYNLIAD
IECQSGNNNDAFDQLFFQDRCQTVTEICEPRNLIPLNASFCSNATHVLPMSDIITRVLSS
EEFFYEHVLGIGDARWDNFGYPRWQMVICLFSAWALSALCLLGGVKSVGKIVYFTATFPY
VILTALLVRALTLEGSIDGIMFYITPQWERLLSPGVWGDASSQIFYSFSLALGSLITLAS
YNKFKNNAHFDATIVSLINYLTAFYSGLAVFAILGFLAHQMNVPVDSVASSGPGLSFITF
PEAILLMPGSQIWAILFFFMMIILGLGSTFAGVQAITTAIIDRWPRLRKDEWKVTIATCL
SGFILGLPMTCHGGIYLFTLMEWHTASWAILLIGFAEVVILSWVYGINNTMEMIKEMGMK
IWKVVQYYWKATWVVITPFYAVGVFIFILTGIGPTQFRGYIFPVWADVLGWLFGTATLVP
FVVFAIIELIKTDDIKKSFRPTENWGPQEVDGRRVDRAVLT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g9870.t1 | PANTHER | PTHR11616 | SODIUM/CHLORIDE DEPENDENT TRANSPORTER | 33 | 628 | 6.2E-189 |
| 6 | g9870.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 52 | 73 | 2.6E-68 |
| 9 | g9870.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 81 | 100 | 2.6E-68 |
| 7 | g9870.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 125 | 151 | 2.6E-68 |
| 3 | g9870.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 291 | 308 | 2.6E-68 |
| 5 | g9870.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 373 | 393 | 2.6E-68 |
| 4 | g9870.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 427 | 446 | 2.6E-68 |
| 8 | g9870.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 507 | 527 | 2.6E-68 |
| 10 | g9870.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 550 | 570 | 2.6E-68 |
| 1 | g9870.t1 | Pfam | PF00209 | Sodium:neurotransmitter symporter family | 44 | 611 | 1.2E-166 |
| 30 | g9870.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 52 | - |
| 48 | g9870.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 53 | 71 | - |
| 32 | g9870.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 72 | 82 | - |
| 41 | g9870.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 83 | 104 | - |
| 31 | g9870.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 105 | 124 | - |
| 46 | g9870.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 125 | 153 | - |
| 37 | g9870.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 154 | 263 | - |
| 43 | g9870.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 264 | 285 | - |
| 27 | g9870.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 286 | 296 | - |
| 49 | g9870.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 297 | 324 | - |
| 33 | g9870.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 325 | 343 | - |
| 42 | g9870.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 344 | 362 | - |
| 29 | g9870.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 363 | 373 | - |
| 39 | g9870.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 374 | 398 | - |
| 34 | g9870.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 399 | 431 | - |
| 38 | g9870.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 432 | 453 | - |
| 26 | g9870.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 454 | 473 | - |
| 44 | g9870.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 474 | 499 | - |
| 35 | g9870.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 500 | 504 | - |
| 40 | g9870.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 505 | 526 | - |
| 28 | g9870.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 527 | 546 | - |
| 47 | g9870.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 547 | 568 | - |
| 36 | g9870.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 569 | 587 | - |
| 45 | g9870.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 588 | 610 | - |
| 25 | g9870.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 611 | 641 | - |
| 24 | g9870.t1 | ProSiteProfiles | PS50267 | Sodium:neurotransmitter symporter family profile. | 43 | 614 | 88.612 |
| 23 | g9870.t1 | SUPERFAMILY | SSF161070 | SNF-like | 44 | 609 | 5.1E-153 |
| 20 | g9870.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 78 | 100 | - |
| 16 | g9870.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 115 | 137 | - |
| 21 | g9870.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 139 | 161 | - |
| 12 | g9870.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 262 | 284 | - |
| 18 | g9870.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 291 | 313 | - |
| 17 | g9870.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 340 | 362 | - |
| 22 | g9870.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 375 | 397 | - |
| 11 | g9870.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 431 | 453 | - |
| 19 | g9870.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 474 | 496 | - |
| 13 | g9870.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 506 | 528 | - |
| 15 | g9870.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 551 | 573 | - |
| 14 | g9870.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 588 | 610 | - |
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 transcript has been annotated with K05038 (solute carrier family 6 (neurotransmitter transporter, glycine) member 5/9)
Pathway
- This transcript belongs to the following pathways
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