General information for g4013.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g4013 is located on chr_3: 29517114..29517775 (- 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_3 | g4013 | g4013.t1 | TTS | g4013.t1 | 29516270 | 29516270 |
| chr_3 | g4013 | g4013.t1 | isoform | g4013.t1 | 29517114 | 29517775 |
| chr_3 | g4013 | g4013.t1 | exon | g4013.t1.exon1 | 29517114 | 29517212 |
| chr_3 | g4013 | g4013.t1 | cds | g4013.t1.CDS1 | 29517114 | 29517212 |
| chr_3 | g4013 | g4013.t1 | exon | g4013.t1.exon2 | 29517281 | 29517351 |
| chr_3 | g4013 | g4013.t1 | cds | g4013.t1.CDS2 | 29517281 | 29517351 |
| chr_3 | g4013 | g4013.t1 | exon | g4013.t1.exon3 | 29517413 | 29517481 |
| chr_3 | g4013 | g4013.t1 | cds | g4013.t1.CDS3 | 29517413 | 29517481 |
| chr_3 | g4013 | g4013.t1 | exon | g4013.t1.exon4 | 29517544 | 29517675 |
| chr_3 | g4013 | g4013.t1 | cds | g4013.t1.CDS4 | 29517544 | 29517675 |
| chr_3 | g4013 | g4013.t1 | exon | g4013.t1.exon5 | 29517739 | 29517775 |
| chr_3 | g4013 | g4013.t1 | cds | g4013.t1.CDS5 | 29517739 | 29517775 |
| chr_3 | g4013 | g4013.t1 | TSS | g4013.t1 | 29517808 | 29517808 |
Sequences
>g4013.t1 Gene=g4013 Length=408
ATGAAAAAGTTTTTGATAGCATTAATTATAATTTCTGTGAAAGCAGACGAAGAAGAATTT
GATTGGAATTGGGAAGCAGGTATTCCACATTATCAAAAACCTCATTATAATGAACAAGGT
GAAGTTTTATTCTTTCCAAGAATCATAGGTGGACAAATTGCAGTACATGGTGAATTTCCT
GCAAAAATTTCACTTCAAAATCGTCGTGGTAATCATTTTTGCGGTGGTGCACTAATAGAT
CTACGTCATGTTTTGAGCGCAGCACATTGTTTAACTGATATTGACGGTCGAGTTTCAAAT
CCAAATGATATTCGATTAATGGGCGATGATCTTTCAATAGAAAGTCGAGCTTCACCTCAT
CGTCAGATATGTGACGCATATTTTCGCACATCCAAGTTACGATTTTGA
>g4013.t1 Gene=g4013 Length=135
MKKFLIALIIISVKADEEEFDWNWEAGIPHYQKPHYNEQGEVLFFPRIIGGQIAVHGEFP
AKISLQNRRGNHFCGGALIDLRHVLSAAHCLTDIDGRVSNPNDIRLMGDDLSIESRASPH
RQICDAYFRTSKLRF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g4013.t1 | Gene3D | G3DSA:2.40.10.10 | - | 48 | 59 | 3.8E-15 |
| 5 | g4013.t1 | Gene3D | G3DSA:2.40.10.10 | - | 60 | 124 | 3.8E-15 |
| 1 | g4013.t1 | Pfam | PF00089 | Trypsin | 48 | 105 | 6.9E-12 |
| 8 | g4013.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 15 | - |
| 9 | g4013.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 10 | g4013.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 11 | - |
| 11 | g4013.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 12 | 15 | - |
| 7 | g4013.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 16 | 135 | - |
| 3 | g4013.t1 | ProSitePatterns | PS00134 | Serine proteases, trypsin family, histidine active site. | 85 | 90 | - |
| 2 | g4013.t1 | SUPERFAMILY | SSF50494 | Trypsin-like serine proteases | 33 | 122 | 2.98E-18 |
| 4 | g4013.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 15 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0004252 | serine-type endopeptidase activity | MF |
| GO:0006508 | proteolysis | BP |
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. There were no conditions that were differentially expressed