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.t10 TTS g3080.t10 22588625 22588625
chr_3 g3080 g3080.t10 isoform g3080.t10 22589464 22590736
chr_3 g3080 g3080.t10 exon g3080.t10.exon1 22589464 22589747
chr_3 g3080 g3080.t10 cds g3080.t10.CDS1 22589466 22589747
chr_3 g3080 g3080.t10 exon g3080.t10.exon2 22589806 22590736
chr_3 g3080 g3080.t10 cds g3080.t10.CDS2 22589806 22590276
chr_3 g3080 g3080.t10 TSS g3080.t10 NA NA

Sequences

>g3080.t10 Gene=g3080 Length=1215
ATGTTTCTTAGTAAATTTAATTTGCTACTTGTAGCATTGACTACATTTTTTTGTAAGTAA
AAGAATTTCTAAAATAGAATATTTGTGTTGGATTGCGGAAAATTTCCTTAAATTAATTCA
GATCGTTGAACTTTCCACACAATTTCTATTTTTGGATTCTCATCCAATAAACGACTGCAA
AATTTTTTTAAATTGCGAATTTCGATTACAATTTTAATTTTAGATGTTGCAAAATGCCAA
AGTTTACCAAAATTTGCTGTGTCGTCAAGTGAATTGACTTTGATTATAAATGAAACTGAA
CAAATTTCACTTTATTTGAAGTAAGACATAAAAATTTATTTTGCTCTTGAAAATTAAAAT
TCTAAAACTAAAAAAACTCTTCTATAATAGTGAACCATTAAACCAAAATGTGACAATAAC
CTTCTCACTAAATCACTATGACTTGGTCACAATTGTTCCAATGTCAATGAAAATAGCGGC
AAATACTTCAGGAAACTTTAATATCTCAGTGCTTGCTGAATCACCAGGCCATGTCGATGT
CACTGGAGTAGCTCTTCCAAAAGTCGTTGACGATTTTAACTTATTCTTTCGAATAATCGT
TGCCAACTCTCGAATCATAATTATTGTCTCAGCTGTTGTTGGATGGATTTATTTTGTTGC
ATGGTCAATTTCATTTTATCCACAATTGGTCATCAATTACAAGCGTAAATCAGTTGTTGG
ATTGAGTTTTGATTTTATGGCATTGAACTTTATGGGACACACTCTCTATGCCATTTTCAA
CACTTGCCTCTATTTTGTGCCATTTTTTCAAGAAGAATATTTTAATCGATTCCCAAGAGG
ATTAAATCCTGTTGAATTGAATGACGTTTTCTTTTCAATTCATGCATCAGCCATTACTGC
ATTGACTATTTTGCAATGCTTCTTTTATGAGCGGGGTGAACAAAGAGTTTCAGATATTGC
TCGTGGAATTCTTGGAATTTTCACAACAATCATAATTGTAGTGACGATTCTCTCAGCAAT
TGGTCAAATTCATTGGTTAGATTTCCTCAACACTTGCAGTTACATTAAACTTGCCATAAC
ACTCATCAAATATGTGCCACAAGCGATTTTAAATTACAAAAGAAAATCAACAGTTGGATG
GAGCATAGGAAATATTTTATTGGATTTTACTGGTGGAATTTTATCAATGCTTCAAATGAT
TCTTAACTCATACAA

>g3080.t10 Gene=g3080 Length=251
MSMKIAANTSGNFNISVLAESPGHVDVTGVALPKVVDDFNLFFRIIVANSRIIIIVSAVV
GWIYFVAWSISFYPQLVINYKRKSVVGLSFDFMALNFMGHTLYAIFNTCLYFVPFFQEEY
FNRFPRGLNPVELNDVFFSIHASAITALTILQCFFYERGEQRVSDIARGILGIFTTIIIV
VTILSAIGQIHWLDFLNTCSYIKLAITLIKYVPQAILNYKRKSTVGWSIGNILLDFTGGI
LSMLQMILNSY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
3 g3080.t10 PANTHER PTHR13131 CYSTINOSIN 47 251 2.4E-88
1 g3080.t10 Pfam PF04193 PQ loop repeat 57 114 1.3E-19
2 g3080.t10 Pfam PF04193 PQ loop repeat 196 251 3.3E-20
18 g3080.t10 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 51 -
19 g3080.t10 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 52 73 -
14 g3080.t10 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 74 93 -
22 g3080.t10 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 94 116 -
15 g3080.t10 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 117 135 -
21 g3080.t10 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 136 157 -
13 g3080.t10 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 158 168 -
24 g3080.t10 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 169 189 -
16 g3080.t10 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 190 194 -
20 g3080.t10 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 195 213 -
12 g3080.t10 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 214 224 -
23 g3080.t10 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 225 248 -
17 g3080.t10 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 249 251 -
10 g3080.t10 SMART SM00679 ctns 70 101 8.4E-8
9 g3080.t10 SMART SM00679 ctns 209 240 4.6E-10
11 g3080.t10 TIGRFAM TIGR00951 2A43: lysosomal Cystine Transporter 55 251 1.3E-68
5 g3080.t10 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 52 74 -
6 g3080.t10 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 94 116 -
7 g3080.t10 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 137 156 -
8 g3080.t10 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 166 188 -
4 g3080.t10 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 225 247 -

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