General information for g5534.t19
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5534 is located on chr_2: 10128055..10128867 (- 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_2 | g5534 | g5534.t19 | TTS | g5534.t19 | 10126405 | 10126405 |
| chr_2 | g5534 | g5534.t19 | isoform | g5534.t19 | 10127223 | 10128208 |
| chr_2 | g5534 | g5534.t19 | exon | g5534.t19.exon1 | 10127223 | 10127232 |
| chr_2 | g5534 | g5534.t19 | cds | g5534.t19.CDS1 | 10127224 | 10127232 |
| chr_2 | g5534 | g5534.t19 | exon | g5534.t19.exon2 | 10127297 | 10127334 |
| chr_2 | g5534 | g5534.t19 | cds | g5534.t19.CDS2 | 10127297 | 10127334 |
| chr_2 | g5534 | g5534.t19 | exon | g5534.t19.exon3 | 10127397 | 10127415 |
| chr_2 | g5534 | g5534.t19 | cds | g5534.t19.CDS3 | 10127397 | 10127415 |
| chr_2 | g5534 | g5534.t19 | exon | g5534.t19.exon4 | 10127478 | 10127569 |
| chr_2 | g5534 | g5534.t19 | cds | g5534.t19.CDS4 | 10127478 | 10127569 |
| chr_2 | g5534 | g5534.t19 | exon | g5534.t19.exon5 | 10127635 | 10127759 |
| chr_2 | g5534 | g5534.t19 | cds | g5534.t19.CDS5 | 10127635 | 10127759 |
| chr_2 | g5534 | g5534.t19 | exon | g5534.t19.exon6 | 10127837 | 10128062 |
| chr_2 | g5534 | g5534.t19 | cds | g5534.t19.CDS6 | 10127837 | 10128062 |
| chr_2 | g5534 | g5534.t19 | exon | g5534.t19.exon7 | 10128130 | 10128208 |
| chr_2 | g5534 | g5534.t19 | cds | g5534.t19.CDS7 | 10128130 | 10128208 |
| chr_2 | g5534 | g5534.t19 | TSS | g5534.t19 | 10128343 | 10128343 |
Sequences
>g5534.t19 Gene=g5534 Length=589
ATGAAATTTTTAACTTTTAATCTAAATATTTTAATCATCATTGTTCTGTCAAATTTAATA
TTGATTGAGTCACTCGAAGAGGGAAGTCCTTGTACGAGTTTTGATAATTCTCCAGGAGTT
TGTAAAGTTTTGTCACAATGCAACTGGGCAGTTGATAAGATTAAATCTAAAGAAATTGCA
ATTGGACAATTGATTAGATGTGGTTTTAAAAATCGAGATGTGATTATTTGTTGCAAACAT
AATGTTGCTCCGCCATTAGAATTAGTTGTGAACACTAAAAGTCCAGCATCTACAACAGTG
TATGGTGAAGACAGACCTCCAGTTTTCGTAACGTTTCAATCACAAAGAAAATCAATACAG
GCATGTGAACAAATTAAAAAAATTGTTCCAATTGGTGTTCAATTCAATATAATTGGCGGT
GAACAGGCTGGAGAATTTCCGCATCAAGTTGTGTTAGGATATCCCGATGAATTAGACCCA
AATAAAATTTCATACGATTGTGGTGGAAGTTTAATATCAAAGAATTTTATATTAACTGCC
GCTCATTGCGTCAATAACCGACAACGACAACCAAGTGTTATTTTACTTG
>g5534.t19 Gene=g5534 Length=196
MKFLTFNLNILIIIVLSNLILIESLEEGSPCTSFDNSPGVCKVLSQCNWAVDKIKSKEIA
IGQLIRCGFKNRDVIICCKHNVAPPLELVVNTKSPASTTVYGEDRPPVFVTFQSQRKSIQ
ACEQIKKIVPIGVQFNIIGGEQAGEFPHQVVLGYPDELDPNKISYDCGGSLISKNFILTA
AHCVNNRQRQPSVILL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g5534.t19 | Gene3D | G3DSA:2.40.10.10 | - | 117 | 196 | 6.4E-15 |
| 2 | g5534.t19 | PANTHER | PTHR24260:SF107 | EG:BACR7A4.3 PROTEIN-RELATED | 11 | 188 | 3.2E-20 |
| 3 | g5534.t19 | PANTHER | PTHR24260 | - | 11 | 188 | 3.2E-20 |
| 1 | g5534.t19 | Pfam | PF00089 | Trypsin | 142 | 193 | 3.2E-10 |
| 9 | g5534.t19 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 5 | - |
| 10 | g5534.t19 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 6 | 25 | - |
| 8 | g5534.t19 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 26 | 196 | - |
| 5 | g5534.t19 | ProSitePatterns | PS00134 | Serine proteases, trypsin family, histidine active site. | 178 | 183 | - |
| 4 | g5534.t19 | SUPERFAMILY | SSF50494 | Trypsin-like serine proteases | 119 | 189 | 4.12E-15 |
| 6 | g5534.t19 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 24 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5534/g5534.t19; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5534.t19.fa.iupred3.txt does not exist
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