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.t9 isoform g3080.t9 22588593 22596373
chr_3 g3080 g3080.t9 exon g3080.t9.exon1 22588593 22588904
chr_3 g3080 g3080.t9 TTS g3080.t9 22588625 22588625
chr_3 g3080 g3080.t9 cds g3080.t9.CDS1 22588881 22588904
chr_3 g3080 g3080.t9 exon g3080.t9.exon2 22589298 22589404
chr_3 g3080 g3080.t9 cds g3080.t9.CDS2 22589298 22589404
chr_3 g3080 g3080.t9 exon g3080.t9.exon3 22589459 22589747
chr_3 g3080 g3080.t9 cds g3080.t9.CDS3 22589459 22589747
chr_3 g3080 g3080.t9 exon g3080.t9.exon4 22589806 22590346
chr_3 g3080 g3080.t9 cds g3080.t9.CDS4 22589806 22590346
chr_3 g3080 g3080.t9 exon g3080.t9.exon5 22590417 22590513
chr_3 g3080 g3080.t9 cds g3080.t9.CDS5 22590417 22590513
chr_3 g3080 g3080.t9 exon g3080.t9.exon6 22590685 22590931
chr_3 g3080 g3080.t9 cds g3080.t9.CDS6 22590685 22590736
chr_3 g3080 g3080.t9 exon g3080.t9.exon7 22596075 22596373
chr_3 g3080 g3080.t9 TSS g3080.t9 22597311 22597311

Sequences

>g3080.t9 Gene=g3080 Length=1892
CCTTCGACAGTTGAGTAAATTAGTTGAGCTTTAAGAGCTAAGAATAAAAAAATTATTTTT
TATTTGATAGAATTTTATAGAATTTTTTTATTTTTCTCGATTCGTCTTTTACTGATAAGA
TAAAATATTTTAAAAAGTCTGATAAAAAATTGCAATTAAAAAAAATTGCAAATATCAACA
AGTTTAAGCAAATTCAACCTCTTAATTCAACTTTTGAAGGCTACAAAATCACACATATTT
TTTATTTATATCATTGAGATATATTTTTAATATTTTGTGATTGTGCTGAAAAGCGAAAGA
CGTAAAAATTTTATTTTCTTCTCTCACTCACTCAAGTGATCATCATCAAGTAATTGTTAT
TTTGCGAAGAAAGGAATTCATTCTGTTGGTGTTTATCATCGAATTAAGACAAAATATTCA
GTTTCTCTATTTTATTGTGCATAATTAAAAGCAACGAGTGAGAAAATAGGAAAAAGGAAT
ATAAAAATTAGAATATGTTTCTTAGTAAATTTAATTTGCTACTTGTAGCATTGACTACAT
TTTTTTATGTTGCAAAATGCCAAAGTTTACCAAAATTTGCTGTGTCGTCAAGTGAATTGA
CTTTGATTATAAATGAAACTGAACAAATTTCACTTTATTTGAATGAACCATTAAACCAAA
ATGTGACAATAACCTTCTCACTAAATCACTATGACTTGGTCACAATTGTTCCAATGTCAA
TGAAAATAGCGGCAAATACTTCAGGAAACTTTAATATCTCAGTGCTTGCTGAATCACCAG
GCCATGTCGATGTCACTGGAGTAGCTCTTCCAAAAGTCGTTGACGATTTTAACTTATTCT
TTCGAATAATCGTTGCCAACTCTCGAATCATAATTATTGTCTCAGCTGTTGTTGGATGGA
TTTATTTTGTTGCATGGTCAATTTCATTTTATCCACAATTGGTCATCAATTACAAGCGTA
AATCAGTTGTTGGATTGAGTTTTGATTTTATGGCATTGAACTTTATGGGACACACTCTCT
ATGCCATTTTCAACACTTGCCTCTATTTTGTGCCATTTTTTCAAGAAGAATATTTTAATC
GATTCCCAAGAGGATTAAATCCTGTTGAATTGAATGACGTTTTCTTTTCAATTCATGCAT
CAGCCATTACTGCATTGACTATTTTGCAATGCTTCTTTTATGAGCGGGGTGAACAAAGAG
TTTCAGATATTGCTCGTGGAATTCTTGGAATTTTCACAACAATCATAATTGTAGTGACGA
TTCTCTCAGCAATTGGTCAAATTCATTGGTTAGATTTCCTCAACACTTGCAGTTACATTA
AACTTGCCATAACACTCATCAAATATGTGCCACAAGCGATTTTAAATTACAAAAGAAAAT
CAACAGTTGGATGGAGCATAGGAAATATTTTATTGGATTTTACTGGTGGAATTTTATCAA
TGCTTCAAATGATTCTTAACTCATACAACTACAATGATTGGCAATCAATTTTTGGTGATC
CAACAAAATTCGGTCTTGGTTTATTTTCAGTTCTATTTGATATTCTCTTTATTATTCAGC
ACTATGTCTTGTATAGGTTTAAAATCAGGCCTCCCGGAAGATAGCTCGCGTGCTGATCTT
ACAAAAGTGCCAACTGATAAAACCCAAAGATATTGAATTTCATAAGATTCTCTTCTTATC
TTAATCCCTTCATATTTTTATCCACTTATTTTGTTGACACTCTTATTTTTATTACAGTTG
ATAAGAAGAGTTTTAAAGTATTTTATATATTAATGAATATTGTATTTTACATAATCTCTC
ACATTTTGTACAGTAAATAAATTTAGAAAATATAAAATGAATTTTAATAAAAAGAATATT
TTATAAGCTCTCTTTTTATCTTCATTTAAAAA

>g3080.t9 Gene=g3080 Length=369
MFLSKFNLLLVALTTFFYVAKCQSLPKFAVSSSELTLIINETEQISLYLNEPLNQNVTIT
FSLNHYDLVTIVPMSMKIAANTSGNFNISVLAESPGHVDVTGVALPKVVDDFNLFFRIIV
ANSRIIIIVSAVVGWIYFVAWSISFYPQLVINYKRKSVVGLSFDFMALNFMGHTLYAIFN
TCLYFVPFFQEEYFNRFPRGLNPVELNDVFFSIHASAITALTILQCFFYERGEQRVSDIA
RGILGIFTTIIIVVTILSAIGQIHWLDFLNTCSYIKLAITLIKYVPQAILNYKRKSTVGW
SIGNILLDFTGGILSMLQMILNSYNYNDWQSIFGDPTKFGLGLFSVLFDILFIIQHYVLY
RFKIRPPGR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
3 g3080.t9 PANTHER PTHR13131 CYSTINOSIN 120 361 1.6E-110
4 g3080.t9 PANTHER PTHR13131:SF5 CYSTINOSIN 120 361 1.6E-110
1 g3080.t9 Pfam PF04193 PQ loop repeat 130 187 2.5E-19
2 g3080.t9 Pfam PF04193 PQ loop repeat 269 325 5.2E-21
24 g3080.t9 Phobius SIGNAL_PEPTIDE Signal peptide region 1 22 -
25 g3080.t9 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 7 -
26 g3080.t9 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 8 17 -
34 g3080.t9 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 18 22 -
22 g3080.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 23 124 -
33 g3080.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 125 146 -
16 g3080.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 147 166 -
30 g3080.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 167 189 -
23 g3080.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 190 208 -
31 g3080.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 209 230 -
19 g3080.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 231 241 -
29 g3080.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 242 262 -
20 g3080.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 263 267 -
28 g3080.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 268 286 -
17 g3080.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 287 297 -
32 g3080.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 298 321 -
21 g3080.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 322 340 -
27 g3080.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 341 360 -
18 g3080.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 361 369 -
12 g3080.t9 SMART SM00679 ctns 143 174 8.4E-8
13 g3080.t9 SMART SM00679 ctns 282 313 4.6E-10
14 g3080.t9 SignalP_EUK SignalP-noTM SignalP-noTM 1 22 -
15 g3080.t9 TIGRFAM TIGR00951 2A43: lysosomal Cystine Transporter 128 360 5.6E-86
7 g3080.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 125 147 -
8 g3080.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 168 190 -
9 g3080.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 210 229 -
11 g3080.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 242 264 -
10 g3080.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 274 292 -
6 g3080.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 299 321 -
5 g3080.t9 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

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