General information for g17521.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Thyrostimulin alpha-2 subunit.
Parent gene
- The parent gene g17521 is located on chr_4: 13778856..13779514 (- strand)
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_4 | g17521 | g17521.t1 | TTS | g17521.t1 | 13778776 | 13778776 |
| chr_4 | g17521 | g17521.t1 | isoform | g17521.t1 | 13778856 | 13779514 |
| chr_4 | g17521 | g17521.t1 | exon | g17521.t1.exon1 | 13778856 | 13778993 |
| chr_4 | g17521 | g17521.t1 | cds | g17521.t1.CDS1 | 13778856 | 13778993 |
| chr_4 | g17521 | g17521.t1 | exon | g17521.t1.exon2 | 13779050 | 13779198 |
| chr_4 | g17521 | g17521.t1 | cds | g17521.t1.CDS2 | 13779050 | 13779198 |
| chr_4 | g17521 | g17521.t1 | exon | g17521.t1.exon3 | 13779427 | 13779514 |
| chr_4 | g17521 | g17521.t1 | cds | g17521.t1.CDS3 | 13779427 | 13779514 |
| chr_4 | g17521 | g17521.t1 | TSS | g17521.t1 | 13779575 | 13779575 |
Sequences
>g17521.t1 Gene=g17521 Length=375
ATGGTGATAATAAAAATTTTATTTTTTCTTTCTGTTACAAACGCAATTTTAGCCAATGAA
ACTGATGAAACTGGTGTTCAACCAAAACTAGGATGTCACCTTGTTGGCTACACAAGAAAA
GTTAATATTCCTGGCTGCATAGAATTTTCAGTGACAACAAATGCTTGTAGAGGTTTTTGT
GAAAGTTTTGCAGTTTCATCGAAATTTGCTGTTGGACCGCATAGACCAGAACAACCCATA
ATATCAGTTGGTCAGTGCTGCAACATCATGGAAAATGAAGAACTTAAAGTAAAAGTTCGC
TGTCTTGAAGGAATTCGTGAAGTGACATTTGGGTCAGCAACAAGTTGCAGCTGTTTCCAT
TGTAAAAAGTCTTAA
>g17521.t1 Gene=g17521 Length=124
MVIIKILFFLSVTNAILANETDETGVQPKLGCHLVGYTRKVNIPGCIEFSVTTNACRGFC
ESFAVSSKFAVGPHRPEQPIISVGQCCNIMENEELKVKVRCLEGIREVTFGSATSCSCFH
CKKS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g17521.t1 | Gene3D | G3DSA:2.10.90.10 | - | 11 | 124 | 6.2E-14 |
| 3 | g17521.t1 | PANTHER | PTHR31129 | GLYCOPROTEIN HORMONE ALPHA-2 | 18 | 123 | 7.1E-21 |
| 2 | g17521.t1 | Pfam | PF00007 | Cystine-knot domain | 31 | 123 | 1.2E-5 |
| 8 | g17521.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 18 | - |
| 9 | g17521.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 5 | - |
| 10 | g17521.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 6 | 13 | - |
| 11 | g17521.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 14 | 18 | - |
| 7 | g17521.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 19 | 124 | - |
| 5 | g17521.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
| 1 | g17521.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
| 4 | g17521.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 17 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
## Warning: Removed 1 row(s) containing missing values (geom_path).
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K25483 (glycoprotein hormone alpha-2)
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. There were no conditions that were differentially expressed