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.t7 isoform g3080.t7 22588593 22596076
chr_3 g3080 g3080.t7 exon g3080.t7.exon1 22588593 22588904
chr_3 g3080 g3080.t7 TTS g3080.t7 22588625 22588625
chr_3 g3080 g3080.t7 cds g3080.t7.CDS1 22588829 22588904
chr_3 g3080 g3080.t7 exon g3080.t7.exon2 22589308 22589404
chr_3 g3080 g3080.t7 cds g3080.t7.CDS2 22589308 22589404
chr_3 g3080 g3080.t7 exon g3080.t7.exon3 22589459 22589747
chr_3 g3080 g3080.t7 cds g3080.t7.CDS3 22589459 22589747
chr_3 g3080 g3080.t7 exon g3080.t7.exon4 22589806 22590346
chr_3 g3080 g3080.t7 cds g3080.t7.CDS4 22589806 22590346
chr_3 g3080 g3080.t7 exon g3080.t7.exon5 22590417 22590513
chr_3 g3080 g3080.t7 cds g3080.t7.CDS5 22590417 22590513
chr_3 g3080 g3080.t7 exon g3080.t7.exon6 22590685 22590931
chr_3 g3080 g3080.t7 cds g3080.t7.CDS6 22590685 22590736
chr_3 g3080 g3080.t7 exon g3080.t7.exon7 22596075 22596076
chr_3 g3080 g3080.t7 TSS g3080.t7 22596379 22596379

Sequences

>g3080.t7 Gene=g3080 Length=1585
AGACGTAAAAATTTTATTTTCTTCTCTCACTCACTCAAGTGATCATCATCAAGTAATTGT
TATTTTGCGAAGAAAGGAATTCATTCTGTTGGTGTTTATCATCGAATTAAGACAAAATAT
TCAGTTTCTCTATTTTATTGTGCATAATTAAAAGCAACGAGTGAGAAAATAGGAAAAAGG
AATATAAAAATTAGAATATGTTTCTTAGTAAATTTAATTTGCTACTTGTAGCATTGACTA
CATTTTTTTATGTTGCAAAATGCCAAAGTTTACCAAAATTTGCTGTGTCGTCAAGTGAAT
TGACTTTGATTATAAATGAAACTGAACAAATTTCACTTTATTTGAATGAACCATTAAACC
AAAATGTGACAATAACCTTCTCACTAAATCACTATGACTTGGTCACAATTGTTCCAATGT
CAATGAAAATAGCGGCAAATACTTCAGGAAACTTTAATATCTCAGTGCTTGCTGAATCAC
CAGGCCATGTCGATGTCACTGGAGTAGCTCTTCCAAAAGTCGTTGACGATTTTAACTTAT
TCTTTCGAATAATCGTTGCCAACTCTCGAATCATAATTATTGTCTCAGCTGTTGTTGGAT
GGATTTATTTTGTTGCATGGTCAATTTCATTTTATCCACAATTGGTCATCAATTACAAGC
GTAAATCAGTTGTTGGATTGAGTTTTGATTTTATGGCATTGAACTTTATGGGACACACTC
TCTATGCCATTTTCAACACTTGCCTCTATTTTGTGCCATTTTTTCAAGAAGAATATTTTA
ATCGATTCCCAAGAGGATTAAATCCTGTTGAATTGAATGACGTTTTCTTTTCAATTCATG
CATCAGCCATTACTGCATTGACTATTTTGCAATGCTTCTTTTATGAGCGGGGTGAACAAA
GAGTTTCAGATATTGCTCGTGGAATTCTTGGAATTTTCACAACAATCATAATTGTAGTGA
CGATTCTCTCAGCAATTGGTCAAATTCATTGGTTAGATTTCCTCAACACTTGCAGTTACA
TTAAACTTGCCATAACACTCATCAAATATGTGCCACAAGCGATTTTAAATTACAAAAGAA
AATCAACAGTTGGATGGAGCATAGGAAATATTTTATTGGATTTTACTGGTGGAATTTTAT
CAATGCTTCAAATGATTCTTAACTCATACAACTACAATGATTGGCAATCAATTTTTGGTG
ATCCAACAAAATTCGGTCTTGGTTTATTTTCAGTTCTATTTGATATTCTCTTTATTATTC
AGCACTATGTCTTAAAATCAGGCCTCCCGGAAGATAGCTCGCGTGCTGATCTTACAAAAG
TGCCAACTGATAAAACCCAAAGATATTGAATTTCATAAGATTCTCTTCTTATCTTAATCC
CTTCATATTTTTATCCACTTATTTTGTTGACACTCTTATTTTTATTACAGTTGATAAGAA
GAGTTTTAAAGTATTTTATATATTAATGAATATTGTATTTTACATAATCTCTCACATTTT
GTACAGTAAATAAATTTAGAAAATATAAAATGAATTTTAATAAAAAGAATATTTTATAAG
CTCTCTTTTTATCTTCATTTAAAAA

>g3080.t7 Gene=g3080 Length=383
MFLSKFNLLLVALTTFFYVAKCQSLPKFAVSSSELTLIINETEQISLYLNEPLNQNVTIT
FSLNHYDLVTIVPMSMKIAANTSGNFNISVLAESPGHVDVTGVALPKVVDDFNLFFRIIV
ANSRIIIIVSAVVGWIYFVAWSISFYPQLVINYKRKSVVGLSFDFMALNFMGHTLYAIFN
TCLYFVPFFQEEYFNRFPRGLNPVELNDVFFSIHASAITALTILQCFFYERGEQRVSDIA
RGILGIFTTIIIVVTILSAIGQIHWLDFLNTCSYIKLAITLIKYVPQAILNYKRKSTVGW
SIGNILLDFTGGILSMLQMILNSYNYNDWQSIFGDPTKFGLGLFSVLFDILFIIQHYVLK
SGLPEDSSRADLTKVPTDKTQRY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
3 g3080.t7 PANTHER PTHR13131 CYSTINOSIN 120 361 7.4E-110
1 g3080.t7 Pfam PF04193 PQ loop repeat 130 187 2.6E-19
2 g3080.t7 Pfam PF04193 PQ loop repeat 269 325 5.5E-21
23 g3080.t7 Phobius SIGNAL_PEPTIDE Signal peptide region 1 22 -
24 g3080.t7 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 7 -
25 g3080.t7 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 8 17 -
33 g3080.t7 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 18 22 -
21 g3080.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 23 124 -
32 g3080.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 125 146 -
16 g3080.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 147 166 -
29 g3080.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 167 189 -
22 g3080.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 190 208 -
30 g3080.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 209 230 -
18 g3080.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 231 241 -
28 g3080.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 242 262 -
19 g3080.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 263 267 -
27 g3080.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 268 286 -
17 g3080.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 287 297 -
31 g3080.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 298 321 -
20 g3080.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 322 340 -
26 g3080.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 341 359 -
15 g3080.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 360 383 -
11 g3080.t7 SMART SM00679 ctns 143 174 8.4E-8
12 g3080.t7 SMART SM00679 ctns 282 313 4.6E-10
13 g3080.t7 SignalP_EUK SignalP-noTM SignalP-noTM 1 22 -
14 g3080.t7 TIGRFAM TIGR00951 2A43: lysosomal Cystine Transporter 128 359 1.5E-85
5 g3080.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 125 147 -
7 g3080.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 168 190 -
9 g3080.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 210 229 -
10 g3080.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 242 264 -
6 g3080.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 274 291 -
4 g3080.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 298 320 -
8 g3080.t7 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

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.

Raw TPM values