Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Modulator of smoothened 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 g607 g607.t2 TTS g607.t2 4488735 4488735
chr_3 g607 g607.t2 isoform g607.t2 4489453 4491386
chr_3 g607 g607.t2 exon g607.t2.exon1 4489453 4489572
chr_3 g607 g607.t2 cds g607.t2.CDS1 4489455 4489572
chr_3 g607 g607.t2 exon g607.t2.exon2 4490848 4491152
chr_3 g607 g607.t2 cds g607.t2.CDS2 4490848 4491152
chr_3 g607 g607.t2 exon g607.t2.exon3 4491330 4491386
chr_3 g607 g607.t2 cds g607.t2.CDS3 4491330 4491386
chr_3 g607 g607.t2 TSS g607.t2 4491471 4491471

Sequences

>g607.t2 Gene=g607 Length=482
ATGGACAAATTTTCATTAATATCTGCTGGATTATTTTCAACTGCTGGCATTTGTGCTGTT
CTTTCTGTGGAATGGCTCATTACATTAATTTTAATTTTTCTCGGAATTATTTGCATTACG
ACAGTTGTCATATTATTATTTGCAAGTCGATGGGACAGAAATGTGATTTTCTATGCTCGT
TGGATTGGATTTACAGCAATGGTTGTTTTTTGTCTGGCAGCCGTTATTTTCCCTCTAGGA
TTTTACATTGAAGAAATTAACGGAGCTCAATTTCAACTACCAAACAGTCATCAAGTTGGT
ATTAGTTACATTTTCTTTATATTAGCACTTTGGATTACGGTCATATCAGAGCTTTTTGCT
GGACATAGGCAAGAAGCGAAGTGCAAAAGAGTGTACAATGCTCACAACACTGCTGCTGCT
GCTACAACCTGTTTGAAGTTTTTTTTTCTGCTCGACTCCAGCAAGTTGATCAGTCTTTTT
CA

>g607.t2 Gene=g607 Length=160
MDKFSLISAGLFSTAGICAVLSVEWLITLILIFLGIICITTVVILLFASRWDRNVIFYAR
WIGFTAMVVFCLAAVIFPLGFYIEEINGAQFQLPNSHQVGISYIFFILALWITVISELFA
GHRQEAKCKRVYNAHNTAAAATTCLKFFFLLDSSKLISLF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g607.t2 PANTHER PTHR31186 MODULATOR OF SMOOTHENED PROTEIN 21 121 8.2E-40
1 g607.t2 Pfam PF18800 Attenuator of Hedgehog 19 122 3.5E-46
11 g607.t2 Phobius SIGNAL_PEPTIDE Signal peptide region 1 15 -
12 g607.t2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 3 -
13 g607.t2 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 4 11 -
17 g607.t2 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 12 15 -
9 g607.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 16 24 -
16 g607.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 25 49 -
8 g607.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 50 60 -
15 g607.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 61 83 -
10 g607.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 84 102 -
14 g607.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 103 120 -
7 g607.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 121 160 -
4 g607.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 5 23 -
3 g607.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 27 49 -
6 g607.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 61 83 -
5 g607.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 98 120 -

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