General information for g21.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Sodium-dependent nutrient amino acid transporter 1.
Parent gene
- The parent gene g21 is located on chr_3: 323486..324340 (+ 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_3 | g21 | g21.t1 | TSS | g21.t1 | 321722 | 321722 |
| chr_3 | g21 | g21.t1 | isoform | g21.t1 | 321870 | 324340 |
| chr_3 | g21 | g21.t1 | exon | g21.t1.exon1 | 321870 | 322056 |
| chr_3 | g21 | g21.t1 | cds | g21.t1.CDS1 | 321870 | 322056 |
| chr_3 | g21 | g21.t1 | exon | g21.t1.exon2 | 322120 | 322135 |
| chr_3 | g21 | g21.t1 | cds | g21.t1.CDS2 | 322120 | 322135 |
| chr_3 | g21 | g21.t1 | exon | g21.t1.exon3 | 322239 | 322273 |
| chr_3 | g21 | g21.t1 | cds | g21.t1.CDS3 | 322239 | 322273 |
| chr_3 | g21 | g21.t1 | exon | g21.t1.exon4 | 322378 | 322735 |
| chr_3 | g21 | g21.t1 | cds | g21.t1.CDS4 | 322378 | 322735 |
| chr_3 | g21 | g21.t1 | exon | g21.t1.exon5 | 322795 | 323303 |
| chr_3 | g21 | g21.t1 | cds | g21.t1.CDS5 | 322795 | 323303 |
| chr_3 | g21 | g21.t1 | exon | g21.t1.exon6 | 323359 | 323591 |
| chr_3 | g21 | g21.t1 | cds | g21.t1.CDS6 | 323359 | 323591 |
| chr_3 | g21 | g21.t1 | exon | g21.t1.exon7 | 323644 | 323794 |
| chr_3 | g21 | g21.t1 | cds | g21.t1.CDS7 | 323644 | 323794 |
| chr_3 | g21 | g21.t1 | exon | g21.t1.exon8 | 323853 | 324005 |
| chr_3 | g21 | g21.t1 | cds | g21.t1.CDS8 | 323853 | 324005 |
| chr_3 | g21 | g21.t1 | exon | g21.t1.exon9 | 324126 | 324193 |
| chr_3 | g21 | g21.t1 | cds | g21.t1.CDS9 | 324126 | 324193 |
| chr_3 | g21 | g21.t1 | exon | g21.t1.exon10 | 324248 | 324340 |
| chr_3 | g21 | g21.t1 | cds | g21.t1.CDS10 | 324248 | 324340 |
| chr_3 | g21 | g21.t1 | TTS | g21.t1 | 324375 | 324375 |
Sequences
>g21.t1 Gene=g21 Length=1803
ATGGCAAGAGGTCATGATAATCCATCCTTCTCAGATATTCCTGATAGTGAAAAATTCTCA
AATCATTACATCATAAACAATGAAAATGACAGCGAGCAAAGTAGTAGAAATGCAGAAGAT
GAAAACGACCGCGATCAATGGGGAAAAGGGATCCAATTTACATTGTCATGTATCGCGTGT
TGTGTTGGGCTAGGAAACGTATGGCGGTTTCCATTTATTGCTTTGCAGAATGGAGGAGGT
GCTTTTGTGATACCTTACATAATTATGCTTTTATTAGTTGGTAGACCTGGATATTTCTTA
GAGATGATCATGGGACAATTTTCATCACGTGGTACAATCAAAGTGTATGATTGTGCACCA
GCTATGAGAGGAGTTGGAATGGGTCAAATGGTTACAATTCTTGCAGTTTCTACTTATTAT
TCAAGCATTTTAGCTATCGCTTTACGATATTTCTTTTATTCTTTTAATACTGTCTTACCA
TGGAGTGAATGCAAACCTGAATGGACAGAACCATGCTATTCAGCAAATGGAATTCAAACA
AATGATGATGAATCTGGAAATATTACGAGAAAATCTTCTACTGAACTTTATTTCTTAAAA
GAAGTTCTTCATGCAAGAGAAAATATAAATGATGGAATTGGATCAATAAATTGGAACCTT
TTTGGTTTTCTAGCTCTTACTTGGATTACCGTCTGTTTGATTTTAATGCGTGGAGTTCGA
AGTTCTGGAAAAGCAGCTTATATTACAGGAATAGTGCCATTTATATTTCTTTTTATCTTT
CTTATTCGTGCTCTCACTCTTCCTGGTGCTTTCAATGGCATTGCTTTCTTTTTTACTCCT
AAATGGGAAGATATTTTAAAGCCAGGTGTTTGGTATGCTGCTGTAACTCAACTATTTTTC
TCTCTCAATGTTTTCTTTGCAAATATTATCATGTATGCTTCTTATAACAAATTTTCACAC
AAAATTCATCGAGATTCAAATATTATTACTATAATTGACACTGGAACTTCTTTACTTGCT
GGTTGTATTAGTTTTGGTATTATTGGTCATTTAGCTCATGAATTAGGTGTCGATGATATT
TCCAAAGTTTTTCAAGGTGGTCCTGGTTTGGTCTTTGTAACTTATGCCGAAACGATCTCA
AAATTTAGAGTACTTCCACAAGTATTTTCAGTATTATTTTTTCTTATGCTTTATATTCTT
GGATTAGGAAGTTTAATAGCACAAACATCATGTGTGATAACAGTCATAAGAGATCAATTT
AAAAATGTTAAAAATTGGCATGCAGCTGTTGGGTATTCAATTTTTGGTGCTCTTTGTGGA
AGTTTATATACAACTGAAGGGGGACAATCAGTTTTAAATTTAGTCGATCATTATGGAACA
ACATTTGTTAATTTTTTGTTAGCTGTTTTTGAAATTATGGCATTTTGTCATATTTATGGA
GTTAATAGAATATGCAAAGATGTAAAATTCATGCTTGGATTTATACCAGGAATTTATTGG
ACTGTATGTTGGCGGGTAGTAACACCACTTATTATGATGGCAATTATTGTTTATCATTTC
ATTTACTATGAAAATCCAAAAGATAATGGAGCTGAATTTCCATTTATTGCTCATGTTGTT
GGTTGGTGTATTACTGCTTCAGGTTTAATTTGGTTGCCTTTAATAATAATTTGGAGTATT
TCAAAACAAAATGAGAAAACTTTTGTTGACAGGGTAAAATCAGCTTTTAGACCAACAAAA
AATTGGGGACCATTGAACTCTTCACTTTTATTAAAATATCAAGAATTTCTTAAAACAAAC
TAA
>g21.t1 Gene=g21 Length=600
MARGHDNPSFSDIPDSEKFSNHYIINNENDSEQSSRNAEDENDRDQWGKGIQFTLSCIAC
CVGLGNVWRFPFIALQNGGGAFVIPYIIMLLLVGRPGYFLEMIMGQFSSRGTIKVYDCAP
AMRGVGMGQMVTILAVSTYYSSILAIALRYFFYSFNTVLPWSECKPEWTEPCYSANGIQT
NDDESGNITRKSSTELYFLKEVLHARENINDGIGSINWNLFGFLALTWITVCLILMRGVR
SSGKAAYITGIVPFIFLFIFLIRALTLPGAFNGIAFFFTPKWEDILKPGVWYAAVTQLFF
SLNVFFANIIMYASYNKFSHKIHRDSNIITIIDTGTSLLAGCISFGIIGHLAHELGVDDI
SKVFQGGPGLVFVTYAETISKFRVLPQVFSVLFFLMLYILGLGSLIAQTSCVITVIRDQF
KNVKNWHAAVGYSIFGALCGSLYTTEGGQSVLNLVDHYGTTFVNFLLAVFEIMAFCHIYG
VNRICKDVKFMLGFIPGIYWTVCWRVVTPLIMMAIIVYHFIYYENPKDNGAEFPFIAHVV
GWCITASGLIWLPLIIIWSISKQNEKTFVDRVKSAFRPTKNWGPLNSSLLLKYQEFLKTN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 38 | g21.t1 | CDD | cd10324 | SLC6sbd | 45 | 520 | 4.68147E-163 |
| 2 | g21.t1 | PANTHER | PTHR11616 | SODIUM/CHLORIDE DEPENDENT TRANSPORTER | 22 | 591 | 4.5E-235 |
| 3 | g21.t1 | PANTHER | PTHR11616:SF269 | TRANSPORTER | 22 | 591 | 4.5E-235 |
| 8 | g21.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 52 | 73 | 1.2E-44 |
| 9 | g21.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 81 | 100 | 1.2E-44 |
| 7 | g21.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 124 | 150 | 1.2E-44 |
| 11 | g21.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 245 | 262 | 1.2E-44 |
| 6 | g21.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 327 | 347 | 1.2E-44 |
| 10 | g21.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 383 | 402 | 1.2E-44 |
| 5 | g21.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 461 | 481 | 1.2E-44 |
| 4 | g21.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 501 | 521 | 1.2E-44 |
| 1 | g21.t1 | Pfam | PF00209 | Sodium:neurotransmitter symporter family | 44 | 560 | 2.6E-145 |
| 16 | g21.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 52 | - |
| 27 | g21.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 53 | 74 | - |
| 22 | g21.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 75 | 79 | - |
| 33 | g21.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 80 | 100 | - |
| 17 | g21.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 101 | 130 | - |
| 36 | g21.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 131 | 152 | - |
| 21 | g21.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 153 | 219 | - |
| 34 | g21.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 220 | 239 | - |
| 13 | g21.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 240 | 250 | - |
| 28 | g21.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 251 | 278 | - |
| 20 | g21.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 279 | 289 | - |
| 31 | g21.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 290 | 315 | - |
| 15 | g21.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 316 | 326 | - |
| 29 | g21.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 327 | 348 | - |
| 23 | g21.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 349 | 390 | - |
| 37 | g21.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 391 | 416 | - |
| 14 | g21.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 417 | 427 | - |
| 30 | g21.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 428 | 445 | - |
| 24 | g21.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 446 | 456 | - |
| 26 | g21.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 457 | 481 | - |
| 18 | g21.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 482 | 501 | - |
| 35 | g21.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 502 | 523 | - |
| 25 | g21.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 524 | 534 | - |
| 32 | g21.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 535 | 558 | - |
| 19 | g21.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 559 | 600 | - |
| 50 | g21.t1 | ProSitePatterns | PS00610 | Sodium:neurotransmitter symporter family signature 1. | 68 | 82 | - |
| 51 | g21.t1 | ProSiteProfiles | PS50267 | Sodium:neurotransmitter symporter family profile. | 43 | 565 | 76.018 |
| 12 | g21.t1 | SUPERFAMILY | SSF161070 | SNF-like | 44 | 560 | 2.62E-146 |
| 40 | g21.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 72 | 94 | - |
| 44 | g21.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 131 | 153 | - |
| 48 | g21.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 213 | 235 | - |
| 49 | g21.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 256 | 278 | - |
| 43 | g21.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 293 | 315 | - |
| 47 | g21.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 327 | 349 | - |
| 39 | g21.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 384 | 406 | - |
| 41 | g21.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 426 | 444 | - |
| 46 | g21.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 459 | 481 | - |
| 45 | g21.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 501 | 523 | - |
| 42 | g21.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 538 | 560 | - |
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.
