Gene loci information

Transcript annotation

  • This transcript has been annotated as Cystinosin-like protein.

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_3 g3080 g3080.t11 TTS g3080.t11 22588625 22588625
chr_3 g3080 g3080.t11 isoform g3080.t11 22589464 22596373
chr_3 g3080 g3080.t11 exon g3080.t11.exon1 22589464 22589747
chr_3 g3080 g3080.t11 cds g3080.t11.CDS1 22589466 22589747
chr_3 g3080 g3080.t11 exon g3080.t11.exon2 22589806 22590346
chr_3 g3080 g3080.t11 cds g3080.t11.CDS2 22589806 22590346
chr_3 g3080 g3080.t11 exon g3080.t11.exon3 22590417 22590513
chr_3 g3080 g3080.t11 cds g3080.t11.CDS3 22590417 22590513
chr_3 g3080 g3080.t11 exon g3080.t11.exon4 22590685 22590931
chr_3 g3080 g3080.t11 cds g3080.t11.CDS4 22590685 22590736
chr_3 g3080 g3080.t11 exon g3080.t11.exon5 22596075 22596373
chr_3 g3080 g3080.t11 TSS g3080.t11 22597311 22597311

Sequences

>g3080.t11 Gene=g3080 Length=1468
CCTTCGACAGTTGAGTAAATTAGTTGAGCTTTAAGAGCTAAGAATAAAAAAATTATTTTT
TATTTGATAGAATTTTATAGAATTTTTTTATTTTTCTCGATTCGTCTTTTACTGATAAGA
TAAAATATTTTAAAAAGTCTGATAAAAAATTGCAATTAAAAAAAATTGCAAATATCAACA
AGTTTAAGCAAATTCAACCTCTTAATTCAACTTTTGAAGGCTACAAAATCACACATATTT
TTTATTTATATCATTGAGATATATTTTTAATATTTTGTGATTGTGCTGAAAAGCGAAAGA
CGTAAAAATTTTATTTTCTTCTCTCACTCACTCAAGTGATCATCATCAAGTAATTGTTAT
TTTGCGAAGAAAGGAATTCATTCTGTTGGTGTTTATCATCGAATTAAGACAAAATATTCA
GTTTCTCTATTTTATTGTGCATAATTAAAAGCAACGAGTGAGAAAATAGGAAAAAGGAAT
ATAAAAATTAGAATATGTTTCTTAGTAAATTTAATTTGCTACTTGTAGCATTGACTACAT
TTTTTTATGTTGCAAAATGCCAAAGTTTACCAAAATTTGCTGTGTCGTCAAGTGAATTGA
CTTTGATTATAAATGAAACTGAACAAATTTCACTTTATTTGAATGAACCATTAAACCAAA
ATGTGACAATAACCTTCTCACTAAATCACTATGACTTGGTCACAATTGTTCCAATGTCAA
TGAAAATAGCGGCAAATACTTCAGGAAACTTTAATATCTCAGTGCTTGCTGAATCACCAG
GCCATGTCGATGTCACTGGAGTAGCTCTTCCAAAAGTCGTTGACGATTTTAACTTATTCT
TTCGAATAATCGTTGCCAACTCTCGAATCATAATTATTGTCTCAGCTGTTGTTGGATGGA
TTTATTTTGTTGCATGGTCAATTTCATTTTATCCACAATTGGTCATCAATTACAAGCGTA
AATCAGTTGTTGGATTGAGTTTTGATTTTATGGCATTGAACTTTATGGGACACACTCTCT
ATGCCATTTTCAACACTTGCCTCTATTTTGTGCCATTTTTTCAAGAAGAATATTTTAATC
GATTCCCAAGAGGATTAAATCCTGTTGAATTGAATGACGTTTTCTTTTCAATTCATGCAT
CAGCCATTACTGCATTGACTATTTTGCAATGCTTCTTTTATGAGCGGGGTGAACAAAGAG
TTTCAGATATTGCTCGTGGAATTCTTGGAATTTTCACAACAATCATAATTGTAGTGACGA
TTCTCTCAGCAATTGGTCAAATTCATTGGTTAGATTTCCTCAACACTTGCAGTTACATTA
AACTTGCCATAACACTCATCAAATATGTGCCACAAGCGATTTTAAATTACAAAAGAAAAT
CAACAGTTGGATGGAGCATAGGAAATATTTTATTGGATTTTACTGGTGGAATTTTATCAA
TGCTTCAAATGATTCTTAACTCATACAA

>g3080.t11 Gene=g3080 Length=324
MFLSKFNLLLVALTTFFYVAKCQSLPKFAVSSSELTLIINETEQISLYLNEPLNQNVTIT
FSLNHYDLVTIVPMSMKIAANTSGNFNISVLAESPGHVDVTGVALPKVVDDFNLFFRIIV
ANSRIIIIVSAVVGWIYFVAWSISFYPQLVINYKRKSVVGLSFDFMALNFMGHTLYAIFN
TCLYFVPFFQEEYFNRFPRGLNPVELNDVFFSIHASAITALTILQCFFYERGEQRVSDIA
RGILGIFTTIIIVVTILSAIGQIHWLDFLNTCSYIKLAITLIKYVPQAILNYKRKSTVGW
SIGNILLDFTGGILSMLQMILNSY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
3 g3080.t11 PANTHER PTHR13131 CYSTINOSIN 120 324 4.8E-88
2 g3080.t11 Pfam PF04193 PQ loop repeat 130 187 2.0E-19
1 g3080.t11 Pfam PF04193 PQ loop repeat 269 324 5.0E-20
21 g3080.t11 Phobius SIGNAL_PEPTIDE Signal peptide region 1 22 -
22 g3080.t11 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 7 -
23 g3080.t11 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 8 17 -
30 g3080.t11 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 18 22 -
19 g3080.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 23 124 -
29 g3080.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 125 146 -
14 g3080.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 147 166 -
26 g3080.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 167 189 -
20 g3080.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 190 208 -
27 g3080.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 209 230 -
16 g3080.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 231 241 -
25 g3080.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 242 262 -
18 g3080.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 263 267 -
24 g3080.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 268 286 -
15 g3080.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 287 297 -
28 g3080.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 298 321 -
17 g3080.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 322 324 -
10 g3080.t11 SMART SM00679 ctns 143 174 8.4E-8
11 g3080.t11 SMART SM00679 ctns 282 313 4.6E-10
12 g3080.t11 SignalP_EUK SignalP-noTM SignalP-noTM 1 22 -
13 g3080.t11 TIGRFAM TIGR00951 2A43: lysosomal Cystine Transporter 128 324 2.8E-68
5 g3080.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 125 147 -
7 g3080.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 168 190 -
8 g3080.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 210 229 -
9 g3080.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 242 264 -
6 g3080.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 274 291 -
4 g3080.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 298 320 -

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 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.

Raw TPM values