General information for g3080.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cystinosin-like protein.
Parent gene
- The parent gene g3080 is located on chr_3: 22590736..22597282 (- 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 | g3080 | g3080.t4 | TTS | g3080.t4 | 22587336 | 22587336 |
| chr_3 | g3080 | g3080.t4 | isoform | g3080.t4 | 22587565 | 22597196 |
| chr_3 | g3080 | g3080.t4 | exon | g3080.t4.exon1 | 22587565 | 22588264 |
| chr_3 | g3080 | g3080.t4 | cds | g3080.t4.CDS1 | 22588135 | 22588264 |
| chr_3 | g3080 | g3080.t4 | exon | g3080.t4.exon2 | 22589302 | 22589404 |
| chr_3 | g3080 | g3080.t4 | cds | g3080.t4.CDS2 | 22589302 | 22589404 |
| chr_3 | g3080 | g3080.t4 | exon | g3080.t4.exon3 | 22589459 | 22589747 |
| chr_3 | g3080 | g3080.t4 | cds | g3080.t4.CDS3 | 22589459 | 22589747 |
| chr_3 | g3080 | g3080.t4 | exon | g3080.t4.exon4 | 22589806 | 22590346 |
| chr_3 | g3080 | g3080.t4 | cds | g3080.t4.CDS4 | 22589806 | 22590346 |
| chr_3 | g3080 | g3080.t4 | exon | g3080.t4.exon5 | 22590417 | 22590513 |
| chr_3 | g3080 | g3080.t4 | cds | g3080.t4.CDS5 | 22590417 | 22590513 |
| chr_3 | g3080 | g3080.t4 | exon | g3080.t4.exon6 | 22590685 | 22590931 |
| chr_3 | g3080 | g3080.t4 | cds | g3080.t4.CDS6 | 22590685 | 22590736 |
| chr_3 | g3080 | g3080.t4 | exon | g3080.t4.exon7 | 22596975 | 22597196 |
| chr_3 | g3080 | g3080.t4 | TSS | g3080.t4 | 22597311 | 22597311 |
Sequences
>g3080.t4 Gene=g3080 Length=2199
AAGAGTTAATTTCTAAGTTATTGTACAAATAAGTGAAGTGTGACAAAATAATTCTATTGT
GTTTGTGGAAGTTTTAAATTATAGCAATTCATTCTTGTCATTAAGTAAATTCATTGTGAT
AGTTCTTTTTTGTAAGTGATTGAATCAAATATTACCGTGAAGGGCACTTGTTATACCAAA
GAAAGAGGAAGAAATTAAGAGCAAAAAGCGAAAACCAAATTGACGTAAAAATTTTATTTT
CTTCTCTCACTCACTCAAGTGATCATCATCAAGTAATTGTTATTTTGCGAAGAAAGGAAT
TCATTCTGTTGGTGTTTATCATCGAATTAAGACAAAATATTCAGTTTCTCTATTTTATTG
TGCATAATTAAAAGCAACGAGTGAGAAAATAGGAAAAAGGAATATAAAAATTAGAATATG
TTTCTTAGTAAATTTAATTTGCTACTTGTAGCATTGACTACATTTTTTTATGTTGCAAAA
TGCCAAAGTTTACCAAAATTTGCTGTGTCGTCAAGTGAATTGACTTTGATTATAAATGAA
ACTGAACAAATTTCACTTTATTTGAATGAACCATTAAACCAAAATGTGACAATAACCTTC
TCACTAAATCACTATGACTTGGTCACAATTGTTCCAATGTCAATGAAAATAGCGGCAAAT
ACTTCAGGAAACTTTAATATCTCAGTGCTTGCTGAATCACCAGGCCATGTCGATGTCACT
GGAGTAGCTCTTCCAAAAGTCGTTGACGATTTTAACTTATTCTTTCGAATAATCGTTGCC
AACTCTCGAATCATAATTATTGTCTCAGCTGTTGTTGGATGGATTTATTTTGTTGCATGG
TCAATTTCATTTTATCCACAATTGGTCATCAATTACAAGCGTAAATCAGTTGTTGGATTG
AGTTTTGATTTTATGGCATTGAACTTTATGGGACACACTCTCTATGCCATTTTCAACACT
TGCCTCTATTTTGTGCCATTTTTTCAAGAAGAATATTTTAATCGATTCCCAAGAGGATTA
AATCCTGTTGAATTGAATGACGTTTTCTTTTCAATTCATGCATCAGCCATTACTGCATTG
ACTATTTTGCAATGCTTCTTTTATGAGCGGGGTGAACAAAGAGTTTCAGATATTGCTCGT
GGAATTCTTGGAATTTTCACAACAATCATAATTGTAGTGACGATTCTCTCAGCAATTGGT
CAAATTCATTGGTTAGATTTCCTCAACACTTGCAGTTACATTAAACTTGCCATAACACTC
ATCAAATATGTGCCACAAGCGATTTTAAATTACAAAAGAAAATCAACAGTTGGATGGAGC
ATAGGAAATATTTTATTGGATTTTACTGGTGGAATTTTATCAATGCTTCAAATGATTCTT
AACTCATACAACTACAATGATTGGCAATCAATTTTTGGTGATCCAACAAAATTCGGTCTT
GGTTTATTTTCAGTTCTATTTGATATTCTCTTTATTATTCAGCACTATGTCTTGTATAGA
AACTTAGAGGCTTATAGGACAATCCCTGGAAATGAATCGGAAGCTAATTTGACTGAAAAA
GATGAAGAAAATAGTAATGAAGAGGAAGAAGATCAAAATCAGGTTCCTTCAGGGATAAGA
TATCAGTAATCGAATAATTAATGAATTTACTTGTCATAGGAATATTTAGTAATAGGAAAT
TTAAAGATTTGAAAAAAAAAATTATTGAGATTCAAAAAACTAGACAATTTTATTGAAATT
TAATTCAATTTAGTAGAAAACTCTTACTCAGTTACATCGAATTCAATACTTAATTAGAAC
TTTAATTTTGTCAACTGTCATTCATTGACGACTTCAAAACAATCTTAACTTGAGGCTAAT
TAATTTTTTAAATAGAAATATTTTCATATCACAATAACTATATATTATTCACATGTGCAT
TAACGTAAATGACAATATTTTGATAAAAGAAATTTATTGACTAACAAAATTATAAAAATT
TAACCCGAAATAGTTTGATAAAAAAGTTTTGATGGAATAAGCTCGAAGTCTAATACTTTT
AAGAAAACTTTTCAGACTTTATATCACAAGACTTGAAATTAAAAATATTGTTATGAATTT
AATTATAAGCAGGAACTTTCAAAGAAGGCATTTATTTAATAGGAAGTAGGTACCTTCTTT
TGAAATTCTTTCAGTAATTTTGAAGTATTAATCAAAAAT
>g3080.t4 Gene=g3080 Length=403
MFLSKFNLLLVALTTFFYVAKCQSLPKFAVSSSELTLIINETEQISLYLNEPLNQNVTIT
FSLNHYDLVTIVPMSMKIAANTSGNFNISVLAESPGHVDVTGVALPKVVDDFNLFFRIIV
ANSRIIIIVSAVVGWIYFVAWSISFYPQLVINYKRKSVVGLSFDFMALNFMGHTLYAIFN
TCLYFVPFFQEEYFNRFPRGLNPVELNDVFFSIHASAITALTILQCFFYERGEQRVSDIA
RGILGIFTTIIIVVTILSAIGQIHWLDFLNTCSYIKLAITLIKYVPQAILNYKRKSTVGW
SIGNILLDFTGGILSMLQMILNSYNYNDWQSIFGDPTKFGLGLFSVLFDILFIIQHYVLY
RNLEAYRTIPGNESEANLTEKDEENSNEEEEDQNQVPSGIRYQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g3080.t4 | Coils | Coil | Coil | 371 | 391 | - |
| 35 | g3080.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 374 | 403 | - |
| 3 | g3080.t4 | PANTHER | PTHR13131 | CYSTINOSIN | 120 | 386 | 1.4E-113 |
| 4 | g3080.t4 | PANTHER | PTHR13131:SF5 | CYSTINOSIN | 120 | 386 | 1.4E-113 |
| 1 | g3080.t4 | Pfam | PF04193 | PQ loop repeat | 130 | 187 | 2.8E-19 |
| 2 | g3080.t4 | Pfam | PF04193 | PQ loop repeat | 269 | 325 | 6.0E-21 |
| 15 | g3080.t4 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 22 | - |
| 16 | g3080.t4 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 7 | - |
| 17 | g3080.t4 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 8 | 17 | - |
| 25 | g3080.t4 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 18 | 22 | - |
| 13 | g3080.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 23 | 124 | - |
| 24 | g3080.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 125 | 146 | - |
| 8 | g3080.t4 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 147 | 166 | - |
| 21 | g3080.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 167 | 189 | - |
| 14 | g3080.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 190 | 208 | - |
| 22 | g3080.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 209 | 230 | - |
| 10 | g3080.t4 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 231 | 241 | - |
| 20 | g3080.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 242 | 262 | - |
| 11 | g3080.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 263 | 267 | - |
| 19 | g3080.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 268 | 286 | - |
| 9 | g3080.t4 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 287 | 297 | - |
| 23 | g3080.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 298 | 321 | - |
| 12 | g3080.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 322 | 340 | - |
| 18 | g3080.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 341 | 360 | - |
| 7 | g3080.t4 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 361 | 403 | - |
| 33 | g3080.t4 | SMART | SM00679 | ctns | 143 | 174 | 8.4E-8 |
| 34 | g3080.t4 | SMART | SM00679 | ctns | 282 | 313 | 4.6E-10 |
| 5 | g3080.t4 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 22 | - |
| 36 | g3080.t4 | TIGRFAM | TIGR00951 | 2A43: lysosomal Cystine Transporter | 128 | 360 | 7.2E-86 |
| 27 | g3080.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 125 | 147 | - |
| 29 | g3080.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 168 | 190 | - |
| 31 | g3080.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 210 | 229 | - |
| 32 | g3080.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 242 | 264 | - |
| 28 | g3080.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 274 | 291 | - |
| 26 | g3080.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 298 | 320 | - |
| 30 | g3080.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 340 | 359 | - |
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.
