General information for g16309.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cystinosin-like protein.
Parent gene
- The parent gene g16309 is located on chr_4: 9040136..9041220 (- 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_4 | g16309 | g16309.t1 | TTS | g16309.t1 | 9038698 | 9038698 |
| chr_4 | g16309 | g16309.t1 | isoform | g16309.t1 | 9038760 | 9041220 |
| chr_4 | g16309 | g16309.t1 | exon | g16309.t1.exon1 | 9038760 | 9038962 |
| chr_4 | g16309 | g16309.t1 | cds | g16309.t1.CDS1 | 9038760 | 9038962 |
| chr_4 | g16309 | g16309.t1 | exon | g16309.t1.exon2 | 9039367 | 9039460 |
| chr_4 | g16309 | g16309.t1 | cds | g16309.t1.CDS2 | 9039367 | 9039460 |
| chr_4 | g16309 | g16309.t1 | exon | g16309.t1.exon3 | 9040019 | 9040213 |
| chr_4 | g16309 | g16309.t1 | cds | g16309.t1.CDS3 | 9040019 | 9040213 |
| chr_4 | g16309 | g16309.t1 | exon | g16309.t1.exon4 | 9040336 | 9040882 |
| chr_4 | g16309 | g16309.t1 | cds | g16309.t1.CDS4 | 9040336 | 9040882 |
| chr_4 | g16309 | g16309.t1 | exon | g16309.t1.exon5 | 9041078 | 9041220 |
| chr_4 | g16309 | g16309.t1 | cds | g16309.t1.CDS5 | 9041078 | 9041220 |
| chr_4 | g16309 | g16309.t1 | TSS | g16309.t1 | 9041243 | 9041243 |
Sequences
>g16309.t1 Gene=g16309 Length=1182
ATGAAAAATTATTTTGTGACAATTTTGGTGCTATTTTGTTGCTTCTATGAGTTTCATGGA
GCAGATTTACCAAGTTTTGAGCTCTCTACTGATGGATTTACATTAATTGTTGGGGAAAGT
GAAGAAATTCGATTGTCATTGAATTCTCCTGTAACTCGAGCAGTCACATTTAATTTCGAG
ACAGATCGCGATGAAATCATCACACTTAATCCAAAATCTTTCACAGTTCTACCTTCTGTG
CCTGTTACAAATCAAACAATAAAAGTTGAAACACATAAAGCTGGAAAAGTTGAAGTTGAT
GGACATGCAACACCTGTAGAAATTATCGATGACTTCAATCTTTTCTTCAGGATTGTTGTA
GCAAATTCTCGACCTTTAATAATAATTTCATCAGTTGTTGGTTGGATTTATTTTGTAGCA
TGGAGTGTTTCTTTTTATCCGCAAGTTTGGTTAAATTTCAAAAGAAAATCTGTGGTTGGA
TTGAGTTTTGACTTTTTGGCATTAAATATTGTTGGTCATACTCTTTATGCTGTATTTAAT
TCATCATTGTATTTTATCAAATATTTCCAAGATGAATATTTTGTTCGATTTCCTCATGGA
TTGAATCCTGTTGAACTTAATGATGTTTTCTTCAGTATTCATGCTTCAGTTTTGACATTT
TTGACTATTTGTCAATGTTTTTATTATGAAAGTGGAACACAAAGGGTTTCAAAAATATCA
TGGTCTATTATTGGAATTTTCACAATTACTGCTCTTGTTATAATTATTCTATGCTCAATT
GGAAATCTTCATTGGTTGGACTTTTTGTATACATGCAGTTATATCAAATTGGCTGTGACT
TTAACTAAATATGTTCCACAAGCTTTCTTGAATTATAAGAGAAAAAGCACTGTAGGCTGG
AGTATTGAGAATATTCTTCTTGATTTTACTGGAGGAATTTTGTCAATGTTGCAAATGATC
TTCAACTCTTATAATTACAATGACTGGGCTTCAATCTTTGGTGATCCAACAAAATTCGGT
CTTGGACTCTTTTCAGTTCTTTTCGATATTGTTTTTATTGTACAACATTATGTGCTTTAC
AAAGATGCAAGACATCAAAAGAATAATGACAATAACACAACAGAAGTTGAAAATACGGAA
GTCACAATTGAACCAGAAGATAAAGAAAAAGAAAATATTTAA
>g16309.t1 Gene=g16309 Length=393
MKNYFVTILVLFCCFYEFHGADLPSFELSTDGFTLIVGESEEIRLSLNSPVTRAVTFNFE
TDRDEIITLNPKSFTVLPSVPVTNQTIKVETHKAGKVEVDGHATPVEIIDDFNLFFRIVV
ANSRPLIIISSVVGWIYFVAWSVSFYPQVWLNFKRKSVVGLSFDFLALNIVGHTLYAVFN
SSLYFIKYFQDEYFVRFPHGLNPVELNDVFFSIHASVLTFLTICQCFYYESGTQRVSKIS
WSIIGIFTITALVIIILCSIGNLHWLDFLYTCSYIKLAVTLTKYVPQAFLNYKRKSTVGW
SIENILLDFTGGILSMLQMIFNSYNYNDWASIFGDPTKFGLGLFSVLFDIVFIVQHYVLY
KDARHQKNNDNNTTEVENTEVTIEPEDKEKENI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 32 | g16309.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 370 | 393 | - |
| 3 | g16309.t1 | PANTHER | PTHR13131 | CYSTINOSIN | 120 | 373 | 5.7E-111 |
| 2 | g16309.t1 | Pfam | PF04193 | PQ loop repeat | 129 | 183 | 2.3E-19 |
| 1 | g16309.t1 | Pfam | PF04193 | PQ loop repeat | 269 | 325 | 4.8E-19 |
| 13 | g16309.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 20 | - |
| 14 | g16309.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 4 | - |
| 15 | g16309.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 5 | 15 | - |
| 23 | g16309.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 16 | 20 | - |
| 11 | g16309.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 21 | 125 | - |
| 22 | g16309.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 126 | 146 | - |
| 7 | g16309.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 147 | 157 | - |
| 20 | g16309.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 158 | 179 | - |
| 12 | g16309.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 180 | 208 | - |
| 19 | g16309.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 209 | 229 | - |
| 8 | g16309.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 230 | 240 | - |
| 18 | g16309.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 241 | 262 | - |
| 9 | g16309.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 263 | 267 | - |
| 17 | g16309.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 268 | 286 | - |
| 6 | g16309.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 287 | 297 | - |
| 21 | g16309.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 298 | 321 | - |
| 10 | g16309.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 322 | 340 | - |
| 16 | g16309.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 341 | 360 | - |
| 5 | g16309.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 361 | 393 | - |
| 30 | g16309.t1 | SMART | SM00679 | ctns | 143 | 174 | 1.4E-10 |
| 31 | g16309.t1 | SMART | SM00679 | ctns | 282 | 313 | 2.8E-8 |
| 4 | g16309.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 20 | - |
| 33 | g16309.t1 | TIGRFAM | TIGR00951 | 2A43: lysosomal Cystine Transporter | 128 | 360 | 2.4E-84 |
| 28 | g16309.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 125 | 147 | - |
| 27 | g16309.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 167 | 189 | - |
| 29 | g16309.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 210 | 229 | - |
| 26 | g16309.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 244 | 266 | - |
| 25 | g16309.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 299 | 321 | - |
| 24 | g16309.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 341 | 360 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K12386 (cystinosin)
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